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1557 variant records found

[show instead phene records]

By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.

WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.

Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.

OMIA Variant ID OMIA Phene-Species ID(s) Species Name Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Deleterious? Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Inferred EVA rsID Year Published PubMed ID(s) Acknowledgements
2 OMIA:000042-9031 chicken Wisconsin hypoalpha mutant (WHAM), United States of America (Chicken) Analphalipoproteinaemia ABCA1 missense Naturally occurring variant yes GRCg6a Z g.54877918C>T c.265G>A p.(E89K) 2002 12364545 Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
1126 OMIA:002238-9913 taurine cattle Shorthorn (Cattle) Ichthyosis, ABCA12-related ABCA12 missense Naturally occurring variant yes ARS-UCD1.2 2 g.103016791A>G c.6776T>C p.(L2259P) NM_001191294.2:c.6776T>C; NP_001178223.2:p.(Leu2259Pro) rs5334475100 2019 31568573
195 OMIA:002238-9913 taurine cattle Chianina (Cattle) Ichthyosis, ABCA12-related ABCA12 missense Naturally occurring variant yes ARS-UCD1.2 2 g.103025585T>C c.5804A>G p.(H1935R) rs5334474994 2008 18344998 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1220 OMIA:002238-9913 taurine cattle Polled Hereford (Cattle) Ichthyosis, ABCA12-related ABCA12 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 2 g.103043495_103043496insG c.5689_5690insC p.(S1784Ifs*33) BTA 2:103043495–103043496insG; ENSBTAT00000004518.6:c.5689‐5690insC; ENSBTAP00000004518.6:p.(Ser1784Ilefs*33) (Eager et al., 2020) rs3423092881 rs3423092881 2020 32567073
1379 OMIA:002238-9823 pig Bama Xiang Zhu, China (Pig) Ichthyosis ABCA12 splicing Chemical mutagenesis (ENU) unknown Sscrofa11.1 15 g.117250799T>C Intronic mutation IVS49-727 A>G results in splicing alteration resulting in a 132-nt insertion and a premature stop codon (Wang et al., 2019) 2019 30925591
1050 OMIA:002179-9615 dog Labrador Retriever (Dog) Stargardt disease 1 ABCA4 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 6 g.55146556dup c.4176dup p.(F1393Lfs*3) Mäkeläinen et al. (2019): "ENSCAFT00000005367 exon28 4170dupC* V1390fs" Importantly, the same authors also explain in Table S3 that "*The insertion is found in a cytosine mononucleotide-repeat region [55,146,550–55,146,556] and it is arbitrary at what position the actual insertion occurs. In the text we have denoted the insertion as c.4176insC, p.F1393Lfs*1395)." Variant information changed to reflect HGVS nomenclature 2019 30889179
607 OMIA:001402-9615 dog Border Collie (Dog) Adverse reaction to certain drugs ABCB1 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 14 CanFam3.1 published as c.73insAAT - allele is reflected by the reference sequence CanFam3.1 and NM_001003215.2 as reference: g.13737172_13737174; c.73_75, p.N25 2010 21113104
469 OMIA:001402-9615 dog Australian Shepherd (Dog) Border Collie (Dog) Collie (Dog) German Shepherd Dog (Dog) Long-Haired Whippet (Dog) Miniature Australian Shepherd Dog (Dog) Old English Sheepdog (Dog) Shetland Sheepdog (Dog) Silken Windhound (Dog) Waller (Dog) White Swiss Shepherd Dog (Dog) Adverse reaction to certain drugs ABCB1 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 14 g.13726596_13726599del c.228_231del p.(D77Afs*16) NM_001003215.2; NP_001003215.2 2001 11692082 Variant information gleaned from or confirmed by Donner et al. (2016) PLoS One 11:e0161005
442 OMIA:001402-9615 dog Border Collie (Dog) Adverse reaction to certain drugs ABCB1 regulatory Naturally occurring variant no CanFam3.1 14 g.13742402A>C published as Canfam2 chr14:16692274T>G, c.-6-180T>G, possible regulatory variant associated with resistance to phenobarbital treatment in epileptic Border Collies rs852787132 rs852787132 2011 21488961 Genomic coordinates in CanFam3.1 and EVA ID provided by Zoe Shmidt and Robert Kuhn.
1322 OMIA:001402-9685 domestic cat Domestic Longhair Domestic medium-haired Domestic Shorthair Ragdoll (Cat) Russian Blue (Cat) Siamese (Cat) Adverse reaction to certain drugs ABCB1 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 A2 g.93144355_93144356del c.1930_1931del NM_001171064.2; published as ABCB1:1930_1931delTC; resuling in a frameshift generating a series of stop codons immediately downstream from the deletion. The protein product is predicted to be severely truncated (~50%) and non functional (Mealey and Burke, 2015). The original paper does not identify breed but the variant was later reported in heterozyous form in several breeds: PMID:34125616. 2015 25660379 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1574 OMIA:002710-9615 dog Manchester Terrier (Dog) Cardiomyopathy, dilated, ABCC9-related ABCC9 SCDY/DCM missense Naturally occurring variant unknown Dog10K_Boxer_Tasha 27 g.21042635C>T c.3557G>A p.(R1186Q) XM_022410972.2; XP_022266680.2 2023 37239348
1499 OMIA:002589-8839 Mallard Blue eggshell ABCG2 regulatory Naturally occurring variant no BGI_duck1.0 NW_004676534.1 g.[3573054A>G;3573085A>G] The BGI_duck1.0 reference genome represents the blue eggshell genotype. 2020 33186356
1477 OMIA:002561-9913 taurine cattle Deutsche Holstein Schwarzbunt, Germany (Cattle) Infertility ABHD16B nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 13 g.53957903G>A c.652C>T p.(Q218*) ENSBTAT00000045249.4; ENSBTAP00000055253.1 rs468948776 rs468948776 2020 31963602
1388 OMIA:002368-9615 dog Golden Retriever (Dog) Ichthyosis, ABHD5-related ABHD5 ICH2 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 23 g.2587000_2587013del c.1006_1019del p.(D336Sfs*6) XM_542689.5; XP_542689.2 2022 34791225
1504 OMIA:002594-9823 pig N-acetyl-galactosamine intestinal concentration ABO deletion, gross (>20) Naturally occurring variant unknown 1 2.3kb deletion encompassing exon 8 2022 35477154
1177 OMIA:001089-9542 Japanese macaque Antigen B ABO haplotype Naturally occurring variant no Allele B reflects the peptide haplotype p.266Met + p.268Ala 2000 10984838
21 OMIA:001089-9544 Rhesus monkey Antigen A ABO haplotype Naturally occurring variant no p.266L + p.268G Allele A is reflected in the peptide haplotype p.266Leu + p.268Gly 1998 9583803
20 OMIA:001089-9541 crab-eating macaque A antigen ABO haplotype Naturally occurring variant no p.266L + p.268G Allele A is reflected in the peptide haplotype p.266Leu + p.268Gly 1998 9583803
1174 OMIA:001089-9544 Rhesus monkey Antigen B ABO haplotype Naturally occurring variant no p.266M + p.268A Allele B is a reflection of the peptide haplotype p.266Met + p.268Ala 1998 9583803
1175 OMIA:001089-9541 crab-eating macaque B antigen ABO haplotype Naturally occurring variant unknown p.266M + p.268A Allele B is a reflection of the peptide haplotype p.266Met + p.268Ala 1998 9583803
22 OMIA:001089-9579 agile gibbon Alleles A and B ABO missense Naturally occurring variant no c.2178C>A and c.2185G>C Haplotype c.2178C + c.2185G is allele A; haplotype c.2178A + c.2185C is allele B 2009 19298858
23 OMIA:001089-9580 common gibbon Blood group system ABO ABO missense Naturally occurring variant no c.2178C>A and c.2185G>C 2009 19298858
532 OMIA:001089-9598 chimpanzee O (lack of antigen) ABO O^del deletion, small (<=20) Naturally occurring variant no c.514_522delGTGCTGGAG p.(V172-E174del) 1999 10380696
24 OMIA:001089-9598 chimpanzee O (lack of antigen) ABO O^x missense Naturally occurring variant no c.791A>C p.(Y264C) 1999 10380696
1497 OMIA:002585-9615 dog Cavalier King Charles Spaniel (Dog) medium-chain acyl-CoA dehydrogenase ACADM delins, gross (>20) Naturally occurring variant yes UU_Cfam_GSD_1.0 6 g.71401388_71401389delinsCATAATTCTTAGACAATATTGAGAATTAAC c.444_445delinsGTTAATTCTCAATATTGTCTAAGAATTATG p.(T150Ifs*6) XM_038541645.1; XP_038397573.1 2022 36292732
972 OMIA:002140-9615 dog German Hunting Terrier (Dog) Exercise induced metabolic myopathy ACADVL nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 5 g.32193689C>A c.1728C>A p.(Y576*) XM_546581.5; XP_546581.3 2018 29491033
429 OMIA:001271-9913 taurine cattle Dexter (Cattle) Bulldog calf ACAN BD2 regulatory Naturally occurring variant yes ARS-UCD1.2 21 g.20377856C>T c.-198C>T rs3423095877 2007 17952705 Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
590 OMIA:001271-9913 taurine cattle Dexter (Cattle) Highland (Cattle) Bulldog calf ACAN BD1 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 21 g.20422104_20422105insGGCA c.2266_2267insGGCA Variant initially identified in Dexter cattle and later reported in additional breeds: PMID:26885599 2007 17952705 Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1060 OMIA:001271-9915 indicine cattle (zebu) Miniature Zebu, United Kingdom of Great Britain and Northern Ireland (Cattle) Bulldog calf ACAN insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 21 g.20428539_20428540insC c.5688_5689insC p.(V1897fs*9) cDNA position based on transcript NM_173981.2 2018 30305023
1001 OMIA:001271-9796 horse Miniature Horse (Horse) Dwarfism, ACAN-related ACAN D4 deletion, small (<=20) Naturally occurring variant yes EquCab3.0 1 g.95257480_95257500del c.7633_7653del p.(F2545_D2551del) 220110: corrected genomic position from g.95257458_95257500del to 95257480_95257500 and updated cDNA and published protein coordinates (p.(F2017_D2023del)) based on the following transcripts: ENSECAT00000040213.1:c.7633_7653del ENSECAP00000032890.1:p.Phe2545_Cys2551del rs1095048839 2018 30058072
788 OMIA:001271-9796 horse Miniature Horse (Horse) Shetland Pony (Horse) Dwarfism, ACAN-related ACAN D3* missense Naturally occurring variant yes EquCab3.0 1 g.95282140C>G c.1513G>C p.(A505P) ENSECAT00000040213.1:c.1513G>C ENSECAP00000032890.1:p.Ala505Pro This variant was named D3* by Eberth et al. (2018) rs1095048823 rs1095048823 2017 27942904 Variant coordinates obtained from Eberth et al. (2018) and EVA_ID link
1000 OMIA:001271-9796 horse Miniature Horse (Horse) Dwarfism, ACAN-related ACAN D2 missense Naturally occurring variant yes EquCab3.0 1 g.95284530C>T p.(V424M) rs3091781465 2018 30058072
999 OMIA:001271-9796 horse Miniature Horse (Horse) Dwarfism, ACAN-related ACAN D1 deletion, small (<=20) Naturally occurring variant yes EquCab3.0 1 g.95291271del c.245del p.(K82Rfs*54) 220110: changed g.95291270del to g.95291271del based on HGVS 3'rule. ENSECAT00000040213.1:c.245del ENSECAP00000032890.1:p.Lys82ArgfsTer54 rs1095048841 rs1095048841 2018 30058072
323 OMIA:000702-9031 chicken Nanomelia ACAN nonsense (stop-gain) Naturally occurring variant yes GRCg6a 10 g.13502829C>A c.4537G>T p.(E1513*) 1994 7827752 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1045 OMIA:002177-9615 dog Akita (Dog) American Akita (Dog) Amelogenesis imperfecta, ACP4-related ACPT insertion, small (<=20) Naturally occurring variant yes CanFam3.1 1 g.106051997dupC c.1189dupG p.(A397Gfs) XM_541473.2; XP_541473.2; ACPT is a synonym of ACP4 2019 30877375
1419 OMIA:002226-9913 taurine cattle Brown Swiss (Cattle) Haplotype with homozygous deficiency BH34 ACSL5 BH34 missense Naturally occurring variant yes ARS-UCD1.2 26 g.32940521C>G c.528C>G p.(N176K) NM_001075650.1 rs5357452907 2021 34915862
1259 OMIA:002226-9615 dog Australian Kelpie (Dog) Intestinal lipid malabsorption ACSL5 deletion, gross (>20) Naturally occurring variant yes CanFam3.1 28 g.23380074_23483377del NC_006610.3CFA28:g.23380074_23483377del (O/Brien et al., 2020) 2020 33106515
1073 OMIA:000388-9685 domestic cat Domestic Shorthair Fibrodysplasia ossificans progressiva ACVR1 missense Naturally occurring variant yes Felis_catus_9.0 C1 g.150014354C>T c.617G>A p.(R206H) XM_023259334.1; XP_023115102.1 2019 31007133 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
633 OMIA:001520-9615 dog Glen of Imaal Terrier (Dog) Cone-rod dystrophy 3 ADAM9 deletion, gross (>20) Naturally occurring variant yes 16 "a deletion of exons 15 and 16 which alters the reading frame leading to a premature stop codon" in the ADAM9 gene 2010 20691256
43 OMIA:001870-9615 dog Beagle (Dog) Glaucoma, primary open angle ADAMTS10 missense Naturally occurring variant yes CanFam3.1 20 g.53096339C>T c.1981G>A p.(G661R) XM_849227.3; XP_854320.1 2011 21379321
101 OMIA:001870-9615 dog Norwegian Elkhound (Dog) Glaucoma, primary open angle ADAMTS10 missense Naturally occurring variant yes CanFam3.1 20 g.53101896C>T c.1159G>A p.(A387T) XM_849227.3; XP_854320.1 2014 25372548 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
685 OMIA:001976-9615 dog Basset Hound (Dog) Glaucoma, primary open angle, ADAMTS17-related ADAMTS17 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 3 g.40614853_40614872del c.194_213del p.(L68Gfs*) XM_022416850.1; XP_022272558.1 2015 26474315
365 OMIA:000588-9615 dog American Toy Terrier (Dog) Chinese Crested (Dog) German Hunting Terrier (Dog) Jack Russell Terrier (Dog) Lancashire Heeler (Dog) Miniature Bull Terrier (Dog) Parson Russell Terrier (Dog) Patterdale Terrier (Dog) Rat Terrier (Dog) Sealyham Terrier (Dog) Tenterfield Terrier (Dog) Tibetan Terrier (Dog) Toy Fox Terrier (Dog) Volpino Italiano (Dog) Welsh Terrier (Dog) Wire Fox Terrier (Dog) Yorkshire Terrier (Dog) Lens luxation ADAMTS17 splicing Naturally occurring variant yes CanFam3.1 3 g.40782144G>A c.1473+1G>A XM_022416850.1; additional breeds reported by PMID:22050825 and PMID:37582787 rs1152388408 rs1152388408 2010 20375329 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
96 OMIA:001976-9615 dog Basset Fauve de Bretagne (Dog) Glaucoma, primary open angle, ADAMTS17-related ADAMTS17 missense Naturally occurring variant yes CanFam3.1 3 g.40808345G>A c.1552G>A p.(G518S) XM_022416851.1; XP_022272559.1 2015 26474315 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1086 OMIA:001976-9615 dog Petit Basset Griffon Vendeen (Dog) Glaucoma, primary open angle, ADAMTS17-related ADAMTS17 inversion Naturally occurring variant yes CanFam3.1 3 g.40812274_45768123inv c.1721+2668_*4831255inv XM_545825.4; Forman et al. (2015): "a 4.96 Mb inversion . . . with breakpoints in intron 12 of ADAMTS17 (chr3:40,812,274) and a downstream intergenic region (chr3:45,768,123) [Canfam3.1]… Analysis of RNAseq data revealed novel exon expression for ADAMTS17 due to cryptic splicing occurring 3’ of the exons located immediately upstream of the inversion event." 2015 26683476
942 OMIA:000588-9615 OMIA:001976-9615 dog Chinese Shar-Pei (Dog) Primary open-angle glaucoma (POAG), primary lens luxation (PLL), or both ADAMTS17 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 3 g.40935387_40935392del c.3069_3074del p.(V1024_V1025del) XM_014112382.2; XP_013967857.1; published as c.3070_3075delCGTGGT; p.(V1025_V1026del) 2018 29287154
486 OMIA:000328-9913 taurine cattle Belgian Blue (Cattle) Ehlers-Danlos syndrome, type VII (Dermatosparaxis) ADAMTS2 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 7 g.2017035_2017051delinsAGC c.464_480delinsAGC 1999 10417273 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
1513 OMIA:000328-9615 dog Alapaha Blue Blood Bulldog (Dog) obsolete Pit Bull Terrier (Dog) Ehlers-Danlos syndrome, type VII (Dermatosparaxis) ADAMTS2 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 11 g.2280117delC c.10delC p.(P4Rfs*175) 2022 36421833
1117 OMIA:000328-9615 dog Doberman Pinscher (Dog) Ehlers-Danlos syndrome, type VII (Dermatosparaxis) ADAMTS2 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 11 g.2408978C>T c.769C>T p.(R257*) 2019 31294848
1514 OMIA:000328-9615 dog Catahoula Leopard Dog (Dog) Ehlers-Danlos syndrome, type VII (Dermatosparaxis) ADAMTS2 missense Genome-editing (CRISPR-Cas9) yes CanFam3.1 11 g.2491238G>A c.2897G>A p.(R966H) 2022 36421833
1589 OMIA:000328-9685 domestic cat Domestic Shorthair Ehlers-Danlos syndrome ADAMTS2 delins, small (<=20) Naturally occurring variant yes F.catus_Fca126_mat1.0 A1 g.90995621dup c.698dup p.(Ser235fs*3) XM_023254116.2; XP_023109884.2 2023 37462293
318 OMIA:000328-9940 sheep Dorper (Sheep) Ehlers-Danlos syndrome, type VII (Dermatosparaxis) ADAMTS2 nonsense (stop-gain) Naturally occurring variant yes Oar_rambouillet_v1.0 5 g.1938399G>T c.424G>T p.(E142*) XM_012156230:c.424G>T, XP_012011620:p.Glu142* (Joller et al., 2017) 2012 22497338 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
857 OMIA:000328-9940 sheep Dorper (Sheep) Ehlers-Danlos syndrome, type VII (Dermatosparaxis) ADAMTS2 nonsense (stop-gain) Naturally occurring variant yes Oar_rambouillet_v1.0 5 g.2088231G>A c.805G>A p.(V269M) XM_012156230:c.805G>A, XP_012011620:p.Val269Met (Joller et al., 2017) 2015 25354687 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
537 OMIA:001140-9615 dog Nova Scotia Duck Tolling Retriever (Dog) Cleft lip with or without cleft palate ADAMTS20 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 27 g.10553479_10553480del c.1358_1359del p.(K453Ifs*4) XM_022410988.1; XP_022266696.1; published as c.1360_1361delAA and p.(K453Ifs*3); coordinates in the table have been updated to a recent reference genome and / or transcript and HGVS nomenclature 2015 25798845 Genomic position in CanFam3.1 provided by Mateo Etcheveste and Robert Kuhn.
1163 OMIA:001562-9913 taurine cattle Cikasto govedo, Slovenia (Cattle) Pulmonary hypoplasia and anasarca syndrome ADAMTS3 missense Naturally occurring variant yes ARS-UCD1.2 6 g.87462016G>A c.1222C>T p.(H408T) NM_001192797.1: c.1222C>T; NP_001179726.1: p.(His408Tyr) (Häfliger et al., 2020) rs5334475098 2020 32069517
60 OMIA:001509-9615 dog Beagle (Dog) Musladin-Lueke syndrome ADAMTSL2 missense Naturally occurring variant yes CanFam3.1 9 g.49931561C>T c.661C>T p.(R221C) 2010 20862248 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
935 OMIA:001511-9913 taurine cattle Angus (Cattle) Contractual arachnodactyly (Fawn calf syndrome) ADAMTSL3 deletion, gross (>20) Naturally occurring variant yes 21 "a large (~58 kilobase pair) deletion affecting the ADAMTSL3 gene" 2014 Reference not in PubMed; see OMIA 001511-9913 for reference details
1435 OMIA:002535-9913 taurine cattle Original Schweizer Braunvieh, Switzerland (Cattle) Congenital cataract ADAMTSL4 missense Naturally occurring variant yes ARS-UCD1.2 3 g.20146737C>T c.2327G>A p.(R776H) NM_001101061.1; NP_001094531.1 rs5353205567 2022 35233794
466 OMIA:001577-9615 dog Curly Coated Retriever (Dog) Glycogen storage disease IIIa AGL deletion, small (<=20) Naturally occurring variant yes CanFam3.1 6 g.50050457del c.4223del p.(K1408Sfs*6) NM_001048096.1; NP_001041561.1; published as c.4223delA; genomic position adjusted to HGVS 3' rule 2007 17338148 Genomic and protein coordinates in CanFam3.1 provided by Robert Kuhn
934 OMIA:002135-9913 taurine cattle Angus (Cattle) Arthrogryposis multiplex congenita, AGRN-related AGRN deletion, gross (>20) Naturally occurring variant yes 16 A 23,363 bp deletion "encompasses the entirety of the ISG15 ubiquitin-like modifier (ISG15) gene . . . one or both of the 5' regulatory region of the hairy and enhancer split 4 (HES4) and of the agrin (AGRN) gene and of the first two exons of the AGRN gene" (Beever and Marron, 2011) 2011 Reference not in PubMed; see OMIA 002135-9913 for reference details
233 OMIA:000662-9940 sheep Romney Marsh (Sheep) Motor neuron disease, lower AGTPBP1 missense Naturally occurring variant yes Oar_rambouillet_v1.0 2 g.35795594G>C c.2909G>C p.(R970P) protein and cDNA positions are based on XP_014948529.2 and XM_015093043.2, respectively 2012 22588130 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
75 OMIA:001672-9615 dog Coton de Tulear (Dog) Primary hyperoxaluria type I (Oxalosis I) AGXT missense Naturally occurring variant yes CanFam3.1 25 g.50968854G>A c.304G>A p.(G102S) XP_003639939.1:p.Gly102Ser rs397510072 rs397510072 2012 22486513 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1252 OMIA:001672-9940 sheep Zwartbles (Sheep) Type 1 Primary Hyperoxaluria AGXT missense Naturally occurring variant yes Oar_rambouillet_v1.0 1 g.801189C>T c.584G>A p.(C195Y) NC_040252.1: g.801189C>T; XM_027966918.1: c.584G>A; XP_027822719.1: p.Cys195Tyr (Letko et al., 2020) 2020 33003365
1214 OMIA:001222-9685 domestic cat Persian (Cat) Leber congenital amaurosis AIPL1 nonsense (stop-gain) Naturally occurring variant yes Felis_catus_9.0 E1 g.940445C>T c.577C>T p.(R193*) XM_023243858.1:c.577C>T 2016 27030474 The genomic location on Felis_catus_9.0 and transcript information is based on Rodney et al. 2021 (PMID: 33785770)
1629 OMIA:002788-9913 taurine cattle Holstein Friesian (Cattle) Subfertility, AK9-related AK9 splicing Naturally occurring variant yes ARS-UCD1.2 9 g.40620329A>G rs457222030 rs457222030 2021 34028060
1094 OMIA:002205-9615 dog Collie Rough (Dog) Recurrent inflammatory pulmonary disease AKNA deletion, small (<=20) Naturally occurring variant yes CanFam3.1 11 g.68576241_68576244del c.2717_2720delACAG p.(D906Afs*173) XM_014117950.2: c.2717_2720delACAG; XP_013973425.1:p.(Asp906Alafs*173) 2019 31357536
1240 OMIA:002250-9615 dog Saluki (Dog) Succinic Semialdehyde Dehydrogenase Deficiency ALDH5A1 missense Naturally occurring variant yes CanFam3.1 35 g.22572768G>A c.866G>A p.(G288D) XM_014110599.2: c.866G>A; XP_013966074.2: p.(Gly288Asp) (Vernau et al., 2020) 2020 32887425
1292 OMIA:002316-9685 domestic cat American Shorthair (Cat) Exotic Shorthair (Cat) Munchkin (Cat) Scottish Fold (Cat) Sphynx (Cat) Cardiomyopathy, hypertrophic ALMS1 missense Naturally occurring variant unknown Felis_catus_9.0 A3 g.92439157G>C c.7384G>C p.(G2462R) cDNA and protein positions have been predicted using Ensemble VEP based on transcript ENSFCAT00000077013.1; variant initially reported in Sphynx cats and in a later study (Akiyama et al., 2023) identified in other breeds. Turba et al., 2023 report additional variants in the vicinity that can result in allele dropout in DNA tests and indicate "the need to verify the correspondence between the g.92439157 C variant frequency and the prevalence of HCM" due to high allele frequency of the variant in Sphynx cats in their study. rs5334475133 2021 33639992
1021 OMIA:002162-9615 dog Karelian Bear Dog (Dog) Hypophosphatasia ALPL missense Naturally occurring variant yes CanFam3.1 2 g.77561953A>C c.1301T>G p.(V434G) XM_005617214.3; XP_005617271.1 2019 30700765
1486 OMIA:002162-9940 sheep Hypophosphatasia ALPL missense Genome-editing (CRISPR-Cas9) yes Oar_rambouillet_v1.0 2 g.260716094G>C c.1077C>G p.(I359M) XM_027965561.1; XP_027821362.1 2018 30446691
550 OMIA:002717-9685 domestic cat Burmese (Cat) Brachycephaly ALX1 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 B4 g.110088245_110088256del c.497_508del p.(A166_T169del) XM_003989090.4; XP_003989139.1; published as c.496delCTCTCAGGACTG 2016 26610632 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
764 OMIA:001009-9913 taurine cattle Shorthorn (Cattle) Tibial hemimelia ALX4 deletion, gross (>20) Naturally occurring variant yes 15 Deletion of 45,694 bp including exon 1 of ALX4 2012 Reference not in PubMed; see OMIA 001009-9913 for reference details
763 OMIA:001009-9913 taurine cattle Galloway (Cattle) Tibial hemimelia ALX4 ALX4dup-GAU duplication Naturally occurring variant yes ARS-UCD1.2 15 g.74384916_74384935dup UMD3.1 position is g.75154399_75154418dup. Duplication of 20bp in exon 2 is predicted to result in a frameshift leading to a premature stop codon and truncated protein. 2015 26076463 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. The same ARS-UCD1.2 location in the reverse order was included in the paper by Buitkamp et al. (2022). The allele name ALX4dup-GAU was also given by Buitkamp et al. (2022).
1516 OMIA:001009-9913 taurine cattle Galloway (Cattle) Tibial hemimelia ALX4 ALX4dup-LfL duplication Naturally occurring variant yes ARS-UCD1.2 15 g.74384938_74384919dup Buitkamp et al. (2022): "The ALX4dup-LfL duplication results in a frameshift (amino acid position 151) leading to a truncated protein of 248 nt in length, compared with 303 nt of the wild-type protein (XP_027418402.1)". 2023 36585373
280 OMIA:002775-9615 dog Miniature Schnauzer (Dog) Persistent Mullerian duct syndrome AMHR2 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 27 g.1794738G>A c.262C>T p.(R88*) XM_543632.6; XP_543632.4; published as c.241C>T; coordinates in the table have been updated to a recent reference genome and / or transcript 2009 18723470
639 OMIA:000565-9615 dog Giant Schnauzer (Dog) Intestinal cobalamin malabsorption, AMN-related AMN deletion, gross (>20) Naturally occurring variant yes CanFam3.1 8 g.70807271_70807303del c.1113_1145del p.(G372_A382del) NM_001002960.1; NP_001002960.1 2005 15845892 Genomic position in CanFam3.1 provided by Robert Kuhn and Mateo Etcheveste.
426 OMIA:000565-9615 dog Australian Shepherd (Dog) Intestinal cobalamin malabsorption, AMN-related AMN start-lost Naturally occurring variant yes ROS_Cfam_1.0 8 g.71077084G>A c.3G>A p.(M1?) NM_001002960.1; NP_001002960.1 2005 15845892
353 OMIA:002539-9615 dog Dalmatian (Dog) Respiratory distress syndrome ANLN nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 14 g.47812143C>T c.31C>T p.(R11*) 2017 28222102 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
422 OMIA:001353-9615 dog German Shepherd Dog (Dog) Platelet receptor for factor X, deficiency of ANO6 splicing Naturally occurring variant yes CanFam3.1 27 g.8912219C>T c.1934+1G>A XM_005636953.1 2015 26414452 Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
927 OMIA:002083-9913 taurine cattle Japanese Black, Japan (Cattle) Abortion (embryonic lethality), ANXA10-related ANXA10 repeat variation Naturally occurring variant yes 8 "a "34-kb deleted-type" CNV "associated with embryonic mortality at 30-60 days after artificial insemination. The CNV harbors exon 2 to 6 of ANNEXIN A10 (ANXA10). . . . Western blot analysis showed that the CNV results in a null allele of ANXA10." 2016 27881083
580 OMIA:000248-9615 dog Collie (Dog) Neutropenia, cyclic AP3B1 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 3 g.28663129_28663130insA c.2407_2408insA p.(T803Nfs*5) NM_001002974.2; NP_001002974.1; a single base pair (A) insertion in exon 20 of the AP3 beta gene (AP3B1) rs1152388405 2003 12897784
286 OMIA:000001-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Holstein (black and white) (Cattle) Abortion due to a nonsense mutation in APAF1 on haplotype HH1 APAF1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 5 g.62810245C>T c.1741C>T p.(Q581*) Variant initially reported in Holstein Friesian cattle and later reported in additional breeds: PMID:34779908. rs448942533 rs448942533 2016 27289157 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1206 OMIA:001916-9615 dog Jack Russell Terrier (Dog) Familial Adenomatous Polyposis APC delins, small (<=20) Naturally occurring variant yes CanFam3.1 3 g.312131_312132delinsAA c.[462_463delinsTT] p.(K155X) XM_014111995.2; XP_013967470.1 2020 32445578 Reference assembly and genomic location kindly provided by Kyoko Yoshizaki, 17 Dec 2020
731 OMIA:001965-9913 taurine cattle Holstein (black and white) (Cattle) Holstein cholesterol deficiency APOB insertion, gross (>20) Naturally occurring variant yes 11 "1.3kb insertion of a transposable LTR element (ERV2-1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing [p.Gly135ValfsX10)]" 2016 26763170
436 OMIA:000991-9796 horse Quarter Horse (Horse) Androgen insensitivity syndrome (AIS) AR regulatory Naturally occurring variant yes EquCab3.0 X g.52728703A>G c.1A>G NM_001163891.1; NP_001157363.1; mutation in start codon 2012 22095250 The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022
1143 OMIA:000991-9796 horse Tennessee Walking Horse (Horse) Androgen insensitivity syndrome (AIS) AR deletion, small (<=20) Naturally occurring variant yes EquCab3.0 X g.52728885del c.183del p.(R63Gfs) NM_001163891.1; NP_001157363.1; published as c.183delT and p.(Ser61fs); c. and p. information in the table has been updated to HGVS nomenclature 2020 31936796 The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022
783 OMIA:000991-9796 horse Androgen insensitivity syndrome AR deletion, gross (>20) Naturally occurring variant yes EquCab3.0 X g.52808634_52808658del c.1630_1654del NM_001163891.1; NP_001157363.1; the deletion is predicted to create a frameshift: "resulting in altered amino acid composition from p.543Lys and a premature stop codon 44 amino acid residues downstream in exon 3" 2017 28192783
786 OMIA:000991-9796 horse Thoroughbred (Horse) Androgen insensitivity syndrome AR missense Naturally occurring variant yes EquCab3.0 X g.52872393G>C c.2042G>C p.(W681S) NM_001163891.1; NP_001157363.1 2016 27073903 The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022; p. coordinates obtained from Villagomez et al. (2019)
1144 OMIA:000991-9796 horse Thoroughbred (Horse) Androgen insensitivity syndrome (AIS) AR missense Naturally occurring variant yes EquCab3.0 X g.52878093C>T c.2132C>T p.(A711V) NM_001163891.1; NP_001157363.1 2020 31936796
960 OMIA:001917-9615 dog Leonberger (Dog) Saint Bernard (Dog) Polyneuropathy, ARHGEF10-related ARHGEF10 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 16 g.54349199_54349208del c.1955_1958+6del XM_005630036.3; XP_005630093.1; published as c.1955_1958+6delCACGGTGAGC - eliminating the 3'-splice junction of exon 17 and creating an alternate splice site leading to a truncated protein 2014 25275565 Genomic coordinates in CanFam3.1 provided by Robert Kuhn
780 OMIA:001334-9913 taurine cattle Swedish Red (Cattle) Sperm, short tail ARMC3 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 13 g.24024660del c.1442del p.(A451fs*26) rs797454424 2016 26923438 Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
56 OMIA:000666-9615 dog Miniature Schnauzer (Dog) Mucopolysaccharidosis VI ARSB deletion, gross (>20) Naturally occurring variant yes CanFam3.1 3 g.27870127_27870182del c.-24_32del NM_001048133.1 2020 32985704 g. coordinate kindly provided by Karthik Raj 29 Oct 2020
640 OMIA:000666-9615 dog Poodle, Miniature (Dog) Mucopolysaccharidosis VI ARSB deletion, gross (>20) Naturally occurring variant yes CanFam3.1 3 g.27870253_27870274del c.103_124del p.(A35Gfs*108) NM_001048133.1; NP_001041598.1 2012 22329490 Variant information initially provided by Karthik Raj and Urs Giger
859 OMIA:000666-9615 dog Great Dane (Dog) Mucopolysaccharidosis VI ARSB nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 3 g.27870445C>T c.295C>T p.(Q99*) NM_001048133.1; NP_001041598.1 2018 29157190 Variant information initially provided by Karthik Raj and Urs Giger, and confirmed by Ensembl's VEP
1258 OMIA:000666-9615 dog Miniature Pinscher (Dog) Mucopolysaccharidosis VI ARSB missense Naturally occurring variant yes CanFam3.1 3 g.27950471G>A c.910G>A p.(G304R) NM_001048133.1; NP_001041598.1 2020 32985704 g. coordinate kindly provided by Karthik Raj 29 Oct 2020
1320 OMIA:000666-9685 domestic cat Siamese (Cat) Mucopolysaccharidosis VI, mild, in L476P/D520N cats ARSB missense Naturally occurring variant yes Felis_catus_9.0 A1 g.145138738C>T c.1558G>A p.(D520N) NM_001142259.1; NP_001135731.1; D520N/D520N and L476P/D520N cats have normal growth and appearance. L476P/D520N cats have a very mild MPS VI phenotype (increased incidence of degenerative joint disease). 1998 9421472 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
132 OMIA:000666-9685 domestic cat Domestic Shorthair Siamese (Cat) Mucopolysaccharidosis VI ARSB missense Naturally occurring variant yes Felis_catus_9.0 A1 g.145138869A>G c.1427T>C p.(L476P) NM_001142259.1; NP_001135731.1 rs5334475159 1996 8910299 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
67 OMIA:001503-9615 dog American Staffordshire Terrier (Dog) Neuronal ceroid lipofuscinosis, 4A ARSG missense Naturally occurring variant yes CanFam3.1 9 g.15071276G>A c.296G>A p.(R99H) 2010 20679209 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1321 OMIA:002200-9915 indicine cattle (zebu) Brahman (Cattle) Nellore, India (Sheep) Darkness of hair coat ASIP delins, gross (>20) Naturally occurring variant unknown 13 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons (Trigo et al.2021) 2021 33910501
712 OMIA:000201-9913 taurine cattle Normande (Cattle) Brindle ASIP Abr insertion, gross (>20) Naturally occurring variant no 13 "insertion of a full-length Bos taurus LINE element" 2006 16827753
1199 OMIA:000201-9925 goat Peacock Goat (Goat) Valais Grüenochte Peacock ASIP A^pc repeat variation Naturally occurring variant no 13 "The ASIP allele in Peacock goats, which we propose to term “peacock” (A^pc), has a quadruplication of the same ~45 kb region having five copies in the A^b allele. It is additionally flanked by triplicated segments of 27,996 bp and 41,807 bp on the left and right side of the quadruplicated sequence (Fig 3, S4 Fig, S5 Table). The central part of the A^pc allele has exactly the same breakpoints as the A^b allele suggesting a common origin of A^b and A^pc." (Henkel et al., 2019) "63'158'171-63'203'851: 4 copies (corresponds to the CNV in the Ab allele)" (Table S5; Henkel et al., 2019) 200922: Marius picked this g. entry up as requiring attention: "g.63130175_63245658 (3 copies)". Because this will take time to sort out, I have removed it from the g. field for the time being. 2019 31841508
1200 OMIA:000201-9925 goat Bezoar (Goat) Valais Blackneck (Goat) Valais Copperneck Wild type or Bezaur ASIP A^bz reference sequence allele Naturally occurring variant no 13 "The goat genome reference sequence is derived from a San Clemente goat, which has a similar coat color pattern as bezoars. The genome reference therefore supposedly represents the wildtype allele at the ASIP locus, termed “bezoar” (Abz) [8]. Bezoars and all other Swiss goat breeds did not show any CNVs at the ASIP locus." (Henkel et al., 2019) 2019 31841508
1075 OMIA:001602-93934 Japanese quail Feather colour, fawn-2/beige ASIP Y^f2 duplication Naturally occurring variant no 20 Robic et al. (2019) concluded "that fawn-2 and beige are the same allele, and that it is caused by a 70,895-bp tandem duplication . . . [with breakpoints] (NC-029535 [1,371,395(or 98)–1,442,295 (or 98)]) . . . located downstream of the ITCH exon 1 and upstream of the ASIP exon e4 (5′ UTR). . . . The 70,895 bp of the duplicated region include the entire AHCY gene on one strand, and parts of the ASIP and ITCH genes on the other strand." 2019 30987584
665 OMIA:000201-10042 North American deer mouse New Hampshire (Chicken) Melanic (non-agouti) ASIP deletion, gross (>20) Naturally occurring variant no "a 125-kb deletion, which includes the upstream regulatory region and exons 1 and 2 of Agouti, results in a loss of Agouti expression" 2009 19649329
251 OMIA:000201-61386 Kodkod Melanism (black coat) ASIP missense Naturally occurring variant no p.(C126Y) 2015 25695801
252 OMIA:000201-61406 Colocolo Melanism (black coat) ASIP missense Naturally occurring variant no p.(R120C) 2015 25695801
1119 OMIA:000201-10141 domestic guinea pig Recessive black Asip deletion, small (<=20) Naturally occurring variant no c.181_184delTTCA MH026115: c.181_184delTTCA; the deletion leads to a truncated protein of 77 amino acids due to the premature stop codon. 2019 30746725
330 OMIA:000201-10042 North American deer mouse Alaska, United States of America (North American deer mouse) Melanic (non-agouti) ASIP nonsense (stop-gain) Naturally occurring variant no c.193?>? p.(Q65*) 2009 19649329
333 OMIA:000201-9691 leopard Coat colour, black (black panther) ASIP nonsense (stop-gain) Naturally occurring variant no c.333C>A p.(C111*) 2012 23251368
1219 OMIA:000201-9858 Western roe deer Melanistic (black) ASIP missense Naturally occurring variant no c.33G>T p.(L11F) 2020 32545389
149 OMIA:000201-9793 ass (donkey) Âne de Provence, France (Ass) Âne normand, France (Ass) Dezhou, China (Ass) Miniature, United States of America (Ass) No light points ASIP NLP missense Naturally occurring variant no c.349T>C p.(C117R) 2015 25887951
1587 OMIA:000201-9691 leopard Coat colour, black (black panther) ASIP missense Naturally occurring variant no c.353C>A p.(C113F) 2023 37440497
1666 OMIA:000201-10007 tassel-eared squirrel Coat colour, black ASIP missense Naturally occurring variant no c.370T>C p.(C124R) 2024 38396615
504 OMIA:001602-93934 Japanese quail Feather colour, recessive black ASIP rb deletion, small (<=20) Naturally occurring variant no 20 c.373_380del "A deletion of 8 bases was found in the ASIP gene" 2008 18287406
253 OMIA:000201-61455 Asiatic golden cat Black ASIP missense Naturally occurring variant no c.384C>G p.(C128W) 2012 23251368
567 OMIA:000201-9986 rabbit New Zealand White (Rabbit) Black (non-agouti) ASIP a insertion, small (<=20) Naturally occurring variant no 4 c.5_6insA Letko et al. (2020): NM_001122939.1:c.5_6insA 2010 20004240
1010 OMIA:000201-9838 Arabian camel Black and dark-brown coat colour ASIP haplotype Naturally occurring variant no c.[23delT;c.25G>A] KU179868; c.[23delT;c.25G>A]. As described by Almathen et al. (2018), this haplotype comprises "a 1-bp deletion (23delT/T) and a SNP (25G/A) in exon 2 of ASIP". 2018 29893870
654 OMIA:001602-93934 Japanese quail Feather colour, lethal yellow ASIP Y deletion, gross (>20) Naturally occurring variant yes 20 g.1463709_1604872del Nadeau et al. (2008): "a >90-kb [141162bp] deletion upstream of ASIP" 2008 18287407 The g. coordinates were provided by Robic et al. (2019)
509 OMIA:000201-9796 horse Coat colour, recessive black ASIP a deletion, small (<=20) Naturally occurring variant no 22 g.2174_2184del c.191_201del 2001 11353392
1196 OMIA:000201-9925 goat Appenzell (Goat) Girgentana, Italy (Goat) Saanen (Goat) White or tan ASIP A^Wt repeat variation Naturally occurring variant no ARS1 13 "CNV [copy number variation] affecting a region of less that 100 kb including the ASIP and AHCY genes" (Fontanesi et al., 2009)."spans 154,677 bp ofthe reference genome sequence and comprises the entire coding sequence ofthe ASIP, AHCYand ITCH genes. The individual copies are arranged in tandem in a head to tail orientation." (Henkel et al., 2019) 200922: moved the g. entry to here (g.63,226,824-63,381,501 (3 copies)) until it can be standardised 2009 20016133
1197 OMIA:000201-9925 goat Grisons Striped (Goat) Toggenburg (Goat) Swiss markings ASIP A^sm repeat variation Naturally occurring variant no ARS1 13 "8 tandem copies of a 13,433 bp sequence from the 5’-flanking region of ASIP" (Henkel et al., 2019) 200922: moved g. entry to here (g.63,129,198-63,142,631 (8 copies)) until it can be fixed 2019 31841508
1198 OMIA:000201-9925 goat Chamois Coloured (Goat) St Gallen Booted Goat (Goat) Badgerface ASIP A^b repeat variation Naturally occurring variant no ARS1 13 "a five-fold amplification of45,680 bp located ~61 kb downstream ofthe Asm amplification" (Henkel et al., 2019) 200922: move the g. entry to here (g.63,158,171-63,203,851 (5 copies)), until it can be fixed 2019 31841508
1382 OMIA:000201-9615 dog Dominant yellow ASIP DY reference sequence allele Naturally occurring variant no CanFam3.1 24 CanFam3.1 The reference sequence CanFam3.1 represents the dominant yellow phenotype. 2021 34385618
1386 OMIA:000201-9615 dog Black saddle ASIP BS delins, gross (>20) Naturally occurring variant no CanFam3.1 24 g.23378062_23379640delins[MT319116.1:424_663] Likely causal regulatory promoter variant 2021 34385618
30 OMIA:000201-9615 dog German Shepherd Dog (Dog) Recessive black ASIP missense Naturally occurring variant no CanFam3.1 24 g.23393552C>T c.286C>T p.(R96C) rs851336386 rs851336386 2004 15520882 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1385 OMIA:000201-9615 dog Black back 3 ASIP BB3 haplotype Naturally occurring variant no CanFam3.1 24 g.[23353288_23353472del;23354716_23354751A[4];23377890_23378086del;23378320_23378343del;g.23378858_2 Haplotype containing a likely causal regulatory promoter variant 2021 34385618
1380 OMIA:000201-9615 dog Agouti ASIP AG haplotype Naturally occurring variant no CanFam3.1 24 g.[23353288_23353472del;23354716_23354751A[4];23377890_23378086del;23378320_23378343del] Haplotype containing a likely causal regulatory promoter variant 2021 34385618
1383 OMIA:000201-9615 dog Black back 1 ASIP BB1 haplotype Naturally occurring variant no CanFam3.1 24 g.[23353288_23353472del;23354716_23354751A[4];23378062_23378231delins[MT319115.1:424_674] Haplotype containing a likely causal regulatory promoter variant 2021 34385618
1384 OMIA:000201-9615 dog Black back 2 ASIP BB2 haplotype Naturally occurring variant no CanFam3.1 24 g.[23353288_23353472del;23354716_23354751A[4];23378062_23379640delins[MT319116.1:424_663]] Haplotype containing a likely causal regulatory promoter variant 2021 34385618
1381 OMIA:000201-9615 dog Shaded yellow ASIP SY haplotype Naturally occurring variant no CanFam3.1 24 g.[23353288_23353472del;23354716_23354751A[4]] Haplotype containing a likely causal regulatory promoter variant 2021 34385618
1452 OMIA:002549-9685 domestic cat Bengal (Cat) Coat colour and pattern, charcoal ASIP A^Pben missense Naturally occurring variant no Felis_catus_9.0 A3 c.251A>G p.(Q84R) variant contributes to A^Pbe haplotype associated with charcoal colour/pattern (in exon 4, not present in Felis_catus_9.0) 2014 25143047
1453 OMIA:002549-9685 domestic cat Bengal (Cat) Coat colour and pattern, charcoal ASIP A^Pben missense Naturally occurring variant no Felis_catus_9.0 A3 c.302A>G p.(D101G) variant contributes to A^Pbe haplotype associated with charcoal colour/pattern (in exon 4, not present in Felis_catus_9.0) 2014 25143047
1450 OMIA:002549-9685 domestic cat Bengal (Cat) Coat colour and pattern, charcoal ASIP A^Pben missense Naturally occurring variant no Felis_catus_9.0 A3 g.25086548A>G c.142T>C p.(S48P) NM_001009190.1; NP_001009190.1; variant contributes to A^Pbe haplotype associated with charcoal colour/pattern 2014 25143047
493 OMIA:000201-9685 domestic cat Coat colour, non-agouti (black) ASIP a deletion, small (<=20) Naturally occurring variant no Felis_catus_9.0 A3 g.25086566_25086567del c.123_124del p.(M42Efs*59) NM_001009190.1; NP_001009190.1; "a 2 bp deletion in the ASIP gene [at nucleotide positions 123-124]" rs5334475125 2003 12620197 The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770
1451 OMIA:002549-9685 domestic cat Bengal (Cat) Coat colour and pattern, charcoal ASIP A^Pben missense Naturally occurring variant no Felis_catus_9.0 A3 g.25086649C>G c.41G>C p.(C14S) NM_001009190.1; NP_001009190.1; variant contributes to A^Pbe haplotype associated with charcoal colour/pattern 2014 25143047
714 OMIA:000201-9940 sheep Merino (Sheep) White fleece ASIP Wt insertion, gross (>20) Naturally occurring variant no Oar_rambouillet_v1.0 13 a 190kb tandem duplication encompassing the ASIP gene, the neighbouring AHCY gene and the promoter for a third gene ITCH 2008 18493018
1112 OMIA:000201-9940 sheep Recessive black ASIP a missense Naturally occurring variant no Oar_rambouillet_v1.0 13 g.66474980T>A c.376T>A p.(C126S) Published as g.5172T>A (Norris et al. 2008). cDNA and protein positions based on NM_001134303.1 and NP_001127775.1 2008 18493018 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1111 OMIA:000201-9940 sheep Recessive black ASIP a deletion, small (<=20) Naturally occurring variant no Oar_rambouillet_v1.0 13 g.66475132_66475136del published as g.100_105del / D5 and predicted to result in a frame shift followed by a premature stop codon 63 amino acids downstream of the start site 2002 12354151 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1134 OMIA:000201-9986 rabbit Black and tan ASIP a^t deletion, gross (>20) Naturally occurring variant no OryCun2.0 4 g.5455408_5466123del Letko et al. (2020): NC_013672.1:g.5,455,408_5,466,123del 2020 31729778
667 OMIA:000201-9627 red fox Dark Standard Silver ASIP deletion, gross (>20) Naturally occurring variant no VulVul2.2 NW_020356514.1 A 16.5-kb deletion resulting in "a 166-nt deletion in the Standard Silver fox cDNA, spanning the second exon ... .This deletion removes the start codon and entire signal peptide" 1997 9054949
1309 OMIA:002325-9685 domestic cat Encephalopathy, spongy ASPA missense Naturally occurring variant yes Felis_catus_9.0 E1 g.13585610C>G c.859G>C p.(A287P) XM_006939957.4; XP_006940019.1 2021 33779415
111 OMIA:002099-9615 dog German Shepherd Dog (Dog) Ichthyosis, ASPRV1-related ASPRV1 missense Naturally occurring variant yes CanFam3.1 10 g.68587027A>G c.1052T>C p.(L351P) XM_014117456.1; XP_013972931.1 2017 28249031 Genomic position in CanFam3.1 provided by Robert Kuhn and Mateo Etcheveste.
289 OMIA:000194-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Brown Swiss (Cattle) Holstein Friesian (Cattle) Citrullinaemia ASS1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 11 g.100781668C>T c.256C>T p.(R86*) Variant initially identified in Holstein Friesian and later reported in additional breeds: PMID:30014197, PMID:34779908. rs5334475062 1989 2813370 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
65 OMIA:001471-9615 dog Poodle, Standard (Dog) Neonatal encephalopathy with seizures ATF2 missense Naturally occurring variant yes CanFam3.1 36 g.19078954A>C c.152T>G p.(M51R) 2008 18074159 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
94 OMIA:001954-9615 dog Lagotto Romagnolo (Dog) Neurodegenerative vacuolar storage disease ATG4D missense Naturally occurring variant yes CanFam3.1 20 g.50618958C>T c.1288G>A p.(A430T) 2015 25875846 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1067 OMIA:001552-9615 dog Australian Cattle Dog (Dog) Neuronal ceroid lipofuscinosis, 12 ATP13A2 missense Naturally occurring variant yes CanFam3.1 2 g.81208162C>T c.1118C>T p.(T373I) XM_005617949.3; XP_005618006.1 2019 30956123
400 OMIA:001552-9615 dog Tibetan Terrier (Dog) Neuronal ceroid lipofuscinosis, 12 ATP13A2 splicing Naturally occurring variant yes CanFam3.1 2 g.81210367del c.1623del XM_005617949.3; XP_005618006.1; variant was published as c.1623delG p.P541fs*597 by Farias et al. (2011); Wöhlke et al. (2011) provided an alternate transcript position c.1620delG and proposed that the variant causes exon 16 skipping in NCL-affected Tibetan terriers. The sequence information provided by Wöhlke et al. (2011) corresponds to XM_005617949.3:c.1623del 2011 21362476 22022275
734 OMIA:002110-9615 dog Belgian Shepherd Dog (Dog) Ataxia, cerebellar, ATP1B2-related ATP1B2 insertion, gross (>20) Naturally occurring variant yes CanFam3.1 5 g.32551064_32551065ins[LT796559.1:g.50_276] c.130_131ins[LT796559.1:g.50_276] XM_546597.5; "a 227 bp SINE insertion into exon 2 of the ATP1B2 gene" 2017 28620085
188 OMIA:001450-9913 taurine cattle Belgian Blue (Cattle) Maas-Rijn-Ijssel (Cattle) Congenital muscular dystonia 1 ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25933247G>A c.1675C>T p.(R559C) rs5334475104 2008 18344998 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
219 OMIA:001464-9913 taurine cattle Romagnola (Cattle) Pseudomyotonia, congenital ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25939141C>A c.857G>T p.(G286V) This variant was identified as part of a haplotype with the G211V variant in Romagnola cattle. Akyürek et al. (2022; PMID: 36293223) suggest that the G286V variant is likely to be benign and that the G211V is likely to be causal. rs3423529256 2012 23046865 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
218 OMIA:001464-9913 taurine cattle Romagnola (Cattle) Pseudomyotonia, congenital ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25939366C>A c.632G>T p.(G211V) rs5334474971 2012 23046865 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
205 OMIA:001464-9913 taurine cattle Chianina (Cattle) Marchigiana (Cattle) Romagnola (Cattle) Pseudomyotonia, congenital ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25940510C>T c.491G>A p.(R164H) Variant initially identified in Chianina cattle and later reported in additional breeds: PMID: 35717834 rs3423529241 2008 18786632 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1192 OMIA:002265-9615 dog Irish Terrier (Dog) Darier disease ATP2A2 insertion, gross (>20) Naturally occurring variant yes CanFam3.1 26 g.8200944_8200945insN[(205)] c.2098-3_2098-2insN[(205)] p.(T700Vfs*6) NM_001003214.1; NP_001003214.1; Linek et al. (2020): "a heterozygous SINE insertion [~205bp] into the ATP2A2 gene, at the end of intron 14, close to the boundary of exon 15", giving rise to NP_001003214.1:p.(Thr700Valfs*6) 2020 32354065
1533 OMIA:002265-9615 dog Shih Tzu (Dog) Darier disease ATP2A2 missense Naturally occurring variant yes UU_Cfam_GSD_1.0 26 g.8434781A>C c.2425A>C p.(N809H) NM_001003214.1; NP_001003214.1 2023 36883421
107 OMIA:002608-9615 dog Labrador Retriever (Dog) Modifier of copper toxicosis ATP7A missense Naturally occurring variant yes CanFam3.1 X g.60279238C>T c.980C>T p.(T327I) rs852523339 rs852523339 2016 26747866 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The phenotype was renamed from 'Menkes disease' to 'Modifier of copper toxicosis' based on feedback from Tom Nagels [10/01/2023].
1347 OMIA:001071-9685 domestic cat Wilson disease ATP7B missense Naturally occurring variant yes A1 p.(P550L) 2020 31687873
106 OMIA:001071-9615 dog Labrador Retriever (Dog) Wilson disease ATP7B missense Naturally occurring variant yes CanFam3.1 22 g.225112G>A c.4151G>A p.(R1384Q) XM_005633831.3; XP_005633888.1; variant published as c.4358G>A / p.(R1453Q) and the variant coordinates in this table have been changed to reflect recent transcript IDs; conflicting evidence in regard to causality of this variant are reported in the literature - see https://omia.org/OMIA001071/9615/ for details rs851958524 rs851958524 2016 26747866 30 Dec 2020: correct genomic location provided by Angelica K Kallenberg
1590 OMIA:001071-9685 domestic cat Domestic Longhair Wilson disease ATP7B missense Naturally occurring variant yes Felis_catus_9.0 A1 g.19609511T>A c.3670T>A p.(W1224R) XM_023251165.1; XP_023106933.1; variant heterozygous in a single affected cat 2023 37427085
1136 OMIA:001071-9685 domestic cat Wilson disease ATP7B missense Naturally occurring variant yes Felis_catus_9.0 A1 g.19611002C>G c.3890C>G p.(T1297R) XM_023251176.1; XM_023251176.1 2019 30561139 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1076 OMIA:001645-10036 golden hamster Black tremor Atrn insertion, gross (>20) Naturally occurring variant yes Kuramoto et al. (2002): "an approximately 10-kb DNA fragment, which had 557-bp direct repeats in both ends and was flanked by the identical 6-bp target duplication sequences, [that] was inserted into exon 24" 2002 11773967
348 OMIA:000487-9796 horse Belgian Draft (Horse) Friesian (Horse) Hydrocephalus B3GALNT2 nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 1 g.76887901C>T c.1423C>T p.(Q475*) XM_001491545; XP_001491595; Ducro et al. (2015): "The nomenclature for the mutation is c.1423C>T [GenBank:XM_001491545] corresponding to p.Gln475* [GenBank:XP_001491595]". As at 25 April 2019, Ensembl's Variant Effect Predictor (VEP) gives the EquCab3 c. and p. coordinates as having not changed from the EquCab2 coordinates reported by Ducro et al. (2015). The Ensembl ref is ENSECAT00000049072 rs3429464524 rs3429464524 2015 26452345 c. and p. variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. EquCab3 g. coordinate provided by Meredith O’Connell, working under the supervision of Professor Ernie Bailey, 24 April 2019
439 OMIA:001885-9940 sheep Lacaune (Sheep) Fecundity, Lacaune, FecL B4GALNT2 regulatory Naturally occurring variant no Oar_v3.1 11 g.36938224T>A c.766+2831A>T ENSOART00000006875.1:c.766+2831A>T ENSOART00000006877.1:c.781+2831A>T rs588626728 2013 24086150
440 OMIA:001885-9940 sheep Lacaune (Sheep) Fecundity, Lacaune, FecL B4GALNT2 regulatory Naturally occurring variant no Oar_v3.1 11 g.37034573A>G 2013 24086150
421 OMIA:002068-9796 horse Friesian (Horse) Dwarfism, Friesian B4GALT7 splicing Naturally occurring variant yes EquCab3.0 14 g.3772591C>T c.50G>A p.(R17K) rs3447120064 2016 27793082 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. FN thanks Elizabeth Huffman, who updated the g. coordinates to EquCab3, working under the supervision of Professor Ernie Bailey; 23 April 2020.
1391 OMIA:002484-9615 dog Shetland Sheepdog (Dog) Bardet-Biedl syndrome 2 BBS2 missense Naturally occurring variant yes CanFam3.1 2 g.59693737G>C c.1222G>C p.(A408P) ENSCAFT00000014523.5; ENSCAFP00000013435.4 2021 34828377
356 OMIA:002045-9615 dog Puli (Dog) Bardet-Biedl syndrome 4 BBS4 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 30 g.36063748A>T c.58A>T p.(K20*) 2017 28533336
1131 OMIA:002216-9544 Rhesus monkey Bardet-Biedl syndrome 7 BBS7 deletion, small (<=20) Naturally occurring variant yes Mmul_8.0.1 c.160delG p.(A54fs) 2019 31589838
1049 OMIA:002178-9823 pig Large White (Pig) Abortion, BBS9 and BMPER-related BBS9 deletion, gross (>20) Naturally occurring variant yes Sscrofa11.1 18 g.39817373_40029300del Derks et al. (2018): "a large deletion in complete LD with the SSC18 haplotype of approximately 212kb (position 39,817,373 to 40,029,300), spanning a part of the BBS9 gene ... [and reducing] expression of the downstream BMPER gene" 2018 30231021
635 OMIA:001592-9615 dog Cavalier King Charles Spaniel (Dog) Episodic falling BCAN deletion, gross (>20) Naturally occurring variant yes CanFam3.1 7 g.41325010_41340731delinsAAGGCC c.-13991_466+85delinsGGCCTT XM_005622698.1; a 15.7kb deletion in the BCAN gene removing the first 3 exons 2012 21821125
298 OMIA:000627-9913 taurine cattle Polled Hereford (Cattle) Maple syrup urine disease BCKDHA nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 18 g.50551011C>T c.148C>T p.(Q50*) cDNA position based on ENSBTAT00000021342.6 rs5334475064 1990 2303405
200 OMIA:000627-9913 taurine cattle Shorthorn (Cattle) Maple syrup urine disease BCKDHA missense Naturally occurring variant yes ARS-UCD1.2 18 g.50560242C>T c.1380C>T p.(P372L) rs3423447991 1999 10425233 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1333 OMIA:001079-9940 sheep spælsau (Sheep) yellow fat BCO2 insertion, gross (>20) Naturally occurring variant yes 15 "insertion of a 7.9 kb endogenous Jaagsiekte Sheep Retrovirus (enJSRV) sequence in the first intron of the BCO2 gene" (Kent et al. 2021) 2021 34193038
549 OMIA:001079-9986 rabbit Flemish Giant (Rabbit) New Zealand White (Rabbit) Yellow fat BCO2 deletion, small (<=20) Naturally occurring variant yes 1 delAAT 2015 26002694
1375 OMIA:002466-48883 OMIA:002466-48882 OMIA:002466-87173 OMIA:002466-48884 OMIA:002466-48885 OMIA:002466-48886 OMIA:002466-1553461 medium ground-finch Beak colour, yellow BCO2 synonymous Naturally occurring variant no 24 g.6166878G>A p.(V?V) synonymous change 32 bp into exon 4 2021 34687609
305 OMIA:001079-9913 taurine cattle Holstein (black and white) (Cattle) Yellow fat BCO2 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 15 g.22552375G>A c.306G>A p.(W102*) UMD3.1 position is g.22877552G>A; cDNA position is based on XM_024975217.1 rs109226280 rs109226280 2009 19398771 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1559 OMIA:002466-9135 common canary Beak and leg colour, red BCO2 missense Naturally occurring variant no NW_022042652.1 g.75258192G>A p.R413H 2020 31930402 XP_009096268.1, genomic position as reported by Bovo et al. (2023) PMID:37194440
320 OMIA:001079-9940 sheep spælsau (Sheep) Yellow fat BCO2 nonsense (stop-gain) Naturally occurring variant yes Oar_rambouillet_v1.0 15 g.25024133C>T c.196C>T p.(Q66*) Oar_v3.1 position is g.21947481C>T rs1090867485 2010 20122251 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
737 OMIA:001554-9615 dog Finnish Lapphund (Dog) Lapponian Herder (Dog) Multifocal retinopathy 3 BEST1 cmr3 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 18 g.54470590del c.1388del p.(P463Hfs) NM_001097545.1; NP_001091014.1; published as c.1388delC; variant initially identified in Lapponian Herder and later reported in additional breeds: PMID:27525650 rs397509969 2010 21197113 Variant information and allele abbreviation gleaned from or confirmed by Donner et al. (2016) PLoS One 11:e0161005 and genomic position in CanFam3.1 and EVA ID provided by Mateo Etcheveste and Robert Kuhn.
59 OMIA:001553-9615 dog Coton de Tulear (Dog) Multifocal retinopathy 2 BEST1 cmr2 missense Naturally occurring variant yes CanFam3.1 18 g.54476143C>T c.482G>A p.(G161D) NM_001097545.1; NP_001091014.1 2007 17460247 Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
275 OMIA:001444-9615 dog Boerboel (Dog) Bull Mastiff (Dog) English Mastiff (Dog) Great Pyrenees (Dog) Multifocal retinopathy 1 BEST1 cmr1 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 18 g.54478586G>A c.73C>T p.(R25*) NM_001097545.1; NP_001091014.1 2007 17460247 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
398 OMIA:001660-9615 dog Great Dane (Dog) Inherited myopathy of Great Danes BIN1 splicing Naturally occurring variant yes CanFam3.1 19 g.23522400A>G c.786-2A>G p.(R262_K263insASASRPFPQ) XM_014121413.2; XP_013976888.1; published as IVS10-2A>G, updated in this table to HGVS nomenclature 2013 23754947
244 OMIA:002306-9940 sheep Belclare (Sheep) Cambridge (Sheep) Fecundity, Belclare BMP15 FecX(B) missense Naturally occurring variant no Oar_rambouillet_v1.0 X g.56594843C>A c.1100G>T p.(S367I) 2004 14627550 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
238 OMIA:002306-9940 sheep Olkuska (Sheep) Fecundity, Olkuska BMP15 FecX(O) missense Naturally occurring variant no Oar_rambouillet_v1.0 X g.56594934T>G c.1009A>C p.(N337H) Protein and cDNA positions based on NP_001108239.1 and NM_001114767.1, respectively. 2013 23637641 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
236 OMIA:002306-9940 sheep Lacaune (Sheep) Fecundity, Lacaune BMP15 FecX(L) missense Naturally occurring variant no Oar_rambouillet_v1.0 X g.56594981C>T c.962G>A p.(C321Y) cDNA position based on NP_001108239.1 2007 17038554 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
237 OMIA:002306-9940 sheep Grivette (Sheep) Fecundity, Grivette BMP15 FecX(Gr) missense Naturally occurring variant no Oar_rambouillet_v1.0 X g.56594993G>A c.950C>T p.(T317I) protein and cDNA positions based on NP_001108239.1 and NM_001114767.1, respectively 2013 23637641 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
235 OMIA:002306-9940 sheep Romney Marsh (Sheep) Fecundity, Inverdale BMP15 FecX(I) missense Naturally occurring variant no Oar_rambouillet_v1.0 X g.56595047A>T c.896T>A p.(V299D) protein and cDNA positions based on NP_001108239.1 and NM_001114767.1, respectively rs398521635 2000 10888873 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
335 OMIA:002306-9940 sheep Romney Marsh (Sheep) Fecundity, Hanna BMP15 FecX(H) nonsense (stop-gain) Naturally occurring variant no Oar_rambouillet_v1.0 X g.56595072G>A c.871C>T p.(Q291*) previously listed as c.1184C>T; protein and cDNA position based on NP_001108239.1 and NM_001114767.1, respectively rs413916687 2000 10888873
334 OMIA:002306-9940 sheep Cambridge (Sheep) Fecundity, Galway BMP15 FecX(G) nonsense (stop-gain) Naturally occurring variant no Oar_rambouillet_v1.0 X g.56595225G>A c.718C>T p.(Q239*) rs425019156 2004 14627550
521 OMIA:002306-9940 sheep Rasa Aragonesa, Spain (Sheep) Fecundity, Rasa Aragonesa BMP15 FecX(R) deletion, small (<=20) Naturally occurring variant no Oar_rambouillet_v1.0 X g.56595467_56595483del c.460_476del p.(W154Nfs*55) published as c.525_541delTGGGTCCAGAAAAGCCC based on AF236079, protein and cDNA position in table based on NP_001108239.1 and NM_001114767.1, respectively 2008 18355397 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
755 OMIA:002306-9940 sheep Tunisian Barbary (Sheep) Fecundity, Barbarine BMP15 FecX(Bar) complex rearrangement Naturally occurring variant no Oar_rambouillet_v1.0 X g.[56600937insG;56600945_56600947del;56600948C>A] c.[301G>T;302_304delCTA;310insC] p.(A101Cfs*113) "a composite polymorphism associating a single nucleotide substitution (c.301G > T), a 3 bp deletion (c.302_304delCTA) and a C insertion (c.310insC) in the ovine BMP15 cDNA leading to a frame shift at protein position 101" - cDNA positions based on NM_001114767 2017 28506298
1341 OMIA:002306-9940 sheep Rasa Aragonesa, Spain (Sheep) Fecundity BMP15 FecX(RA) missense Naturally occurring variant unknown Oar_v3.1 X g.50970948C>T c.1172C>T p.(T400I) protein position based on ENSOART00000010201 2020 31927415
1345 OMIA:002306-9940 sheep Blanc Du Massif Central (Sheep) Noir du Velay, France (Sheep) Fecundity BMP15 FecX(N) regulatory Naturally occurring variant unknown Oar_v3.1 X g.50977717T>A 2020 32636872
1281 OMIA:002306-9823 pig German Landrace (Pig) Infertility and increased litter size BMP15 nonsense (stop-gain) Naturally occurring variant yes Sscrofa11.1 X g.44618787C>T p.(R212*) "NP_001005155.2:p.R212X" (Flossmann et al., 2021) 2021 33413103
241 OMIA:000383-9940 sheep Booroola (Sheep) Small Tailed Han, China (Sheep) Fecundity, Booroola BMPR1B FecB(B) missense Naturally occurring variant no Oar_rambouillet_v1.0 6 g.34010859T>C c.914A>G p.(Q305R) Position on Oar_v3.1: g.29382188T>C rs418841713 2001 11259271 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool, the genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1254 OMIA:000576-9823 pig Yorkshire (Pig) Knobbed acrosome defect BOLL deletion, gross (>20) Naturally occurring variant yes Sscrofa11.1 15 g.101549770_101604750del 2020 32975846
851 OMIA:002132-9615 dog German Shorthaired Pointer (Dog) Abortion (embryonic lethality), BTBD17-related BTBD17 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 9 g.6048201_6048202insG c.85+206_85+207insG ROS_Cfam_1.0:g.6720627_6720628insG ENSCAFT00845033049.1:c.85+206_85+207insG; the homozygous variant genotype is associated with embryonic lethality in German Shorthaired Pointer, but may not be causal as the variant was observed at a high frequency in both heterozygous and homozygous form across normal dogs from multiple breeds (PMID:37582787) rs852549625 2017 29053721
981 OMIA:001991-9913 taurine cattle Nordic Red (Cattle) Stillbirth BTBD9 deletion, gross (>20) Naturally occurring variant yes 23 "∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8)" 2016 27091210
325 OMIA:001622-9031 chicken Resistance to avian sarcoma and leukosis viruses, subgroup C BTN1A1 nonsense (stop-gain) Naturally occurring variant no GRCg6a 28 g.903289G>T c.165C>A p.(C55*) rs735807319 rs735807319 2005 16051833 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
455 OMIA:000155-9615 dog Brittany Spaniel (Dog) C3 deficiency C3 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 20 g.53573746del c.2136del p.(F712Lfs*11) XM_038428862.1; XP_038284790.1 "a deletion of a cytosine at position 2136 (codon 712), leading to a frameshift that generates a stop codon 11 amino acids downstream" 1998 9510185
1660 OMIA:002819-9913 taurine cattle Holstein Friesian (Cattle) Muscle weakness CACNA1S missense Naturally occurring variant yes ARS-UCD1.2 16 g.79613592C>T c.3853G>A p.G1285S ENSBTAT00000065901.3; ENSBTAP00000054797.3 rs3423414874 rs3423414874 2024 38246543
1087 OMIA:002201-9913 taurine cattle Normande (Cattle) Abortion due to haplotype NH7 CAD missense Naturally occurring variant yes ARS-UCD1.2 11 g.72409143T>C p.(Y452C) published as CAD g.72399397T>C; p.Tyr452Cys rs5334475092 2019 31056337 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1490 OMIA:002573-151761 yellow-crowned parrot Lewy body-like disease CADPS2 missense Naturally occurring variant yes c.1675G>C p.(V559L) 2022 36086934
105 OMIA:001820-9615 dog Parson Russell Terrier (Dog) Ataxia, spinocerebellar CAPN1 missense Naturally occurring variant yes CanFam3.1 18 g.52009339C>T c.344G>A p.(C115Y) XM_540866.5; XP_540866.2 2013 23741357 Genomic coordinates in CanFam3.1 provided by Robert Kuhn
49 OMIA:001138-9615 dog American Foxhound (Dog) Beagle (Dog) English Foxhound (Dog) Harrier (Dog) Poodle, Miniature (Dog) Treeing Walker Coonhound (Dog) Hypocatalasia CAT missense Naturally occurring variant yes CanFam3.1 18 g.33397548C>T c.979G>A p.(A327T) Variant initially identified in Beagle and later reported in additional breeds: PMID:29708978, PMID27525650 2000 11137458 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
516 OMIA:001416-9612 gray wolf Coat colour, dominant black CBD103 K^B deletion, small (<=20) Naturally occurring variant no 3bp deletion of the CBD103 gene 2009 19197024
520 OMIA:001416-9614 coyote Coat colour, dominant black CBD103 deletion, small (<=20) Naturally occurring variant no 3bp deletion of the CBD103 gene 2009 19197024
458 OMIA:001416-9615 dog Coat colour, dominant black CBD103 ΔG23 = K^B deletion, small (<=20) Naturally occurring variant no CanFam3.1 16 g.58965449_58965451del c.231_233del p.(G78del) "a 3-base pair (bp) deletion in the second exon of CBD103, the ortholog of human DEFB103, that predicts an in-frame glycine deletion (ΔG23)" rs851502010 rs851502010 2007 17947548 Genomic location provided by Professor Claire Wade August 2018. Allele designations taken from Ollivier et al. (2013)
1032 OMIA:002167-9913 taurine cattle Nordic Red (Cattle) Asthenospermia CCDC189 splicing Naturally occurring variant yes ARS-UCD1.2 25 g.26880841C>T Touru et al. (2019): "a variant disrupting a canonical 5’ splice donor site (GCA_000003055.3:Chr25:g.27138357C>T) in CCDC189 (transcript - ID:ENSBTAT00000045037) encoding the coiled-coil domain containing protein 189." rs5334474909 2019 30975085
266 OMIA:001540-9615 dog Old English Sheepdog (Dog) Ciliary dyskinesia, primary CCDC39 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 34 g.13952270G>A c.286C>T p.(R96*) 2011 21131972 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1403 OMIA:002342-9940 sheep Blanc Du Massif Central (Sheep) Lacaune (Sheep) Ciliary dyskinesia, primary (respiratory failure) CCDC65 LDHH6 nonsense (stop-gain) Naturally occurring variant yes Oar_rambouillet_v1.0 3 g.147207999C>A c.521G>T p.(E111*) XM_004006389.4; XP_004006438.1; published as NC_040254.1:g.147,207,999C>A rs1085624756 2021 35052387
1274 OMIA:001521-9615 dog Portuguese Water Dog (Dog) Progressive retinal atrophy, early onset CCDC66 EOPRA insertion, small (<=20) Naturally occurring variant yes CanFam3.1 20 g.33717704_33717705insT c.2262_c.2263insA p.(V747Sfs*8) 2020 33273526
574 OMIA:001521-9615 dog Schapendoes (Dog) Generalized PRA CCDC66 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 20 g.33745452_33745453insT c.521_522insA p.(N174Kfs*2) NM_001168012.1; NP_001161484.1; genomic coordinates in accordance with HGVS 3'-rule 2010 19777273 Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
538 OMIA:001299-9031 chicken Resistance to avian sarcoma and leukosis viruses, subgroup A CD320 deletion, small (<=20) Naturally occurring variant no 28 c.502_511delCGCTCACCCC 2015 25873518
539 OMIA:001299-9031 chicken Resistance to avian sarcoma and leukosis viruses, subgroup A CD320 deletion, small (<=20) Naturally occurring variant no 28 c.502_516delCGCTCACCCCGCCCC 2015 25873518
395 OMIA:001299-9031 chicken Resistance to avian sarcoma and leukosis viruses, subgroup A CD320 splicing Naturally occurring variant no 28 c.506-515del10 2012 22171251
396 OMIA:001299-9031 chicken Resistance to avian sarcoma and leukosis viruses, subgroup A CD320 splicing Naturally occurring variant no 28 c.507-511del5 2012 22171251
603 OMIA:001299-9031 chicken Resistance to avian sarcoma and leukosis viruses, subgroup A CD320 tva^r2 insertion, small (<=20) Naturally occurring variant no GRCg6a 28 g.985659_985660insCTCG c.48_49insCTCG p.(P18Afs) NM_001044645.1; NP_001038110.1 2004 15564460 Genomic position in GRCg6a provided by Joshua Khamis.
12 OMIA:001299-9031 chicken Resistance to avian sarcoma and leukosis viruses, subgroup A CD320 tva^r missense Naturally occurring variant no GRCg6a 28 g.985980C>G c.185C>G p.(C62W) NM_001044645.1; NP_001038110.1; published as c.120C>G and p.(C40W); coordinates in the table have been updated to a recent reference genome and / or transcript 2004 15564460 Genomic position in GRCg6a provided by Joshua Khamis.
1340 OMIA:002386-9544 Rhesus monkey OKT4 epitope deficiency CD4 missense Naturally occurring variant unknown 11 c.C793T p.(A265W) 2021 33893743
1528 OMIA:002626-9913 taurine cattle Japanese Black, Japan (Cattle) Haplotype with homozygous deficiency JBH17, CDC45-related CDC45 splicing Naturally occurring variant yes UMD_3.1.1 17 g.74743512G>T located in a splicing donor site at a distance of 5 bp, affecting pre-mRNA splicing 2021 33758295
1496 OMIA:002584-9615 dog Beauceron (Dog) Deafness, CDH23-related CDH23 missense Naturally occurring variant yes CanFam 3.1 4 g:22340631C>T c.700C>T p.(P234S) ON462053; XM_022417544.1; XP_022273252.1 2022 36308003 The UU_Cfam_GSD_1.0 genomic variant coordinate is: g.Chr4:23074925C>T
3 OMIA:000102-9031 chicken Sex-linked extreme dilution CDKN2A B0 complex rearrangement Naturally occurring variant no Z The B0 allele is characterised by two non-coding variants: "The first, SNP1, is within the CDKN2A (ARF) promoter region, 265 bp upstream of the transcription start site (according to GenBank AY138245), and the second, SNP2, is located at nucleotide position 385 bp in CDKN2A intron 1" 2010 20374521
5 OMIA:000102-9031 chicken Sex-linked dilution CDKN2A B2 missense Naturally occurring variant no GRCg6a Z g.78856557G>A c.28C>T p.(R10C) rs1059941965 2010 20374521 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
4 OMIA:000102-9031 chicken Sex-linked barring CDKN2A B1 missense Naturally occurring variant no GRCg6a Z g.78856559A>T c.26T>A p.(V9D) rs3388417177 2010 20374521 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
863 OMIA:001890-198806 ruff Male body size/courtship behaviour CENPN inversion Naturally occurring variant unknown "a 4.5Mb inversion on the ruff orthologue of chicken chromosomr GGA11 which, due to the well-known lethality of recombinants within an inversion, has created a supergene determining male breeding behaviour, body size and plumage colour" 2016 26569123
991 OMIA:001830-9913 taurine cattle Holstein (black and white) (Cattle) Abortion due to haplotype HH7 CENPU deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 27 g.15123637_15123640del Hozé et al. (2019): "Considering that CENPU is transcribed in the antisense orientation, this mutation is predicted to result in deletion of the nucleotides located at position +3 to + 6 bp after the splicing donor site of exon 11. Using cross-species nucleotide alignment, we observed that the nucleotide at position +3 is entirely conserved among vertebrates . . . , which suggests that it plays an important role in regulation of CENPU splicing. If modified after exon 11, the abnormal splicing of CENPU could cause mRNA decay or the production of a protein modified after residue 319 out of 409 AA. Based on these factors, we assumed that mutation g.14168130_14168133delTACT on chromosome 27 alters the splicing of CENPU and is embryonic lethal." 2020 31733857
964 OMIA:001502-9913 taurine cattle Montbéliarde (Cattle) Caprine-like Generalized Hypoplasia Syndrome CEP250 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 13 g.64710424C>T c.493C>T p.(Q165*) rs5334474991 2015 25902731 Coordinates obtained from and/or confirmed by EBI's VEP
384 OMIA:001244-9685 domestic cat Abyssinian (Cat) American Curl (Cat) American Wirehair (Cat) Balinese (Cat) Bengal (Cat) Colorpoint Shorthair (Cat) Cornish Rex (Cat) Munchkin (Cat) Ocicat (Cat) Oriental Shorthair (Cat) Peterbald (Cat) Siamese (Cat) Singapura (Cat) Somali (Cat) Tonkinese (Cat) Retinal degeneration II CEP290 splicing Naturally occurring variant yes Felis_catus_9.0 B4 g.112522818A>C c.7584+9T>G XM_023256243.1; published as IVS50 + 9T>G. The cat sequenced to generate the Felis_catus_9.0 reference genome is homozygous for the likely causal variant. The genomic and cDNA coordinates had therefore been previously listed in this table as g.112522818TC>A and c.7584+9G>T. The information has been updated based on feedback from 潘旭 to reflect that the likely causal variant is c.7584+9G and that the normal allele is c.7584+9T[6/4/2023]. 2007 17507457 The genomic location on Felis_catus_9.0 and transcript information is based on Rodney et al. 2021 (PMID: 33785770). Variant was initially identified in the Abyssinian and Somali breeds but identified to be present in several other breeds (Menotti-Raymond et al., 2020; Pubmed:19747862)
177 OMIA:000636-9823 pig Membranoproliferative glomerulonephritis type II CFH missense Naturally occurring variant yes Sscrofa11.1 10 c.3610T>G p.(I1166R) CFH is located on Chr10 in Sscrofa10.2 g.2553907T>G, but recorded as 'unplaced/NW_018085100.1' in Sscrofa11.1. 2002 12466119 The genomic location on Sscrofa11.1 was determined by Stephanie Shields (27/05/2020)
1479 OMIA:001794-9940 sheep Romney (Sheep) Cystic fibrosis CFTR nonsense (stop-gain) Genome-editing (CRISPR-Cas9) yes Oar_rambouillet_v1.0 4 g.57192317C>A c.1621G>T p.(G541*) NM_001009781.1; NP_001009781.1; published as p.(G542X), coordinates in this table are updated to recent reference sequence 2021 34632318
1478 OMIA:001794-9940 sheep Romney (Sheep) Cystic fibrosis CFTR deletion, small (<=20) Genome-editing (CRISPR-Cas9) yes Oar_rambouillet_v1.0 4 g.57218683_57218685del c.1518_1520del p.(F507del) NM_001009781.1; NP_001009781.1; published as p.(F508del), coordinates are updated in this table to recent reference sequence 2021 34632318
61 OMIA:002072-9615 dog Old Danish Pointing Dog (Dog) Myasthenic syndrome, congenital CHAT missense Naturally occurring variant yes CanFam3.1 28 g.1484906G>A c.85G>A p.(V29M) XM_005637485.3; XP_005637542.1 2007 17586598 20181218 Thanks to Maarten de Groot for advising FN of the genomic location of this variant.
838 OMIA:002125-9913 taurine cattle Montbéliarde (Cattle) Neurocristopathy CHD7 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 14 g.26402250_26402254del p.(K594Afs*29) 2017 28904385
554 OMIA:002022-9913 taurine cattle Red Dane (Cattle) Arthrogryposis multiplex congenita, CHRNB1-related CHRNB1 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.27122027del c.55del p.(A19Pfs47*) Published as Chr19:27757270CG > C; CHRNB1 c.55delG; (p.Ala19Profs47*) rs5334474854 2016 27364156 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
490 OMIA:000685-9915 indicine cattle (zebu) Brahman (Cattle) Myasthenic syndrome, congenital, CHRNE-related CHRNE 470del20 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.26485848_26485867del c.470_489del Kraner et al. (2002): "a loss of 20 bp within the coding sequence of exon 5 (Fig. 2), between nucleotide 469 and 490 (nucleotide numbering referring to the cDNA sequence published under accession number X02597". These authors (and subsequent authors) call this variant "470del20". The current (2020) HGVS nomenclature is c.470_489del 200922: g. information move here (g.27119615) until standardised rs5334475050 2002 12481987 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
614 OMIA:000685-9615 dog Jack Russell Terrier (Dog) Myasthenic syndrome, congenital, due to CHRNE CHRNE insertion, small (<=20) Naturally occurring variant yes CanFam3.1 5 g.31705136_31705137insC c.636_637insC p.(G212Rfs*274) ENSCAFT00000083466.1; ENSCAFP00000057633.1; published as c.633_634insC, coordinates in the table updated in accordance to HGVS 3'-rule 2015 26429099
804 OMIA:000685-9615 dog Heideterrier (Dog) Myasthenic syndrome, congenital, due to CHRNE CHRNE insertion, small (<=20) Naturally occurring variant yes CanFam3.1 5 g.31707450_31707451insG c.1436_1437insG p.(S479Rfs*14) XM_014113502.1; XP_013968977.1 2017 28508416
1664 OMIA:000698-9940 sheep Myotonia CLCN1 unpublished unknown Entry has been created to generate an OMIAvariantID for a variant that is currently in the process of being published. Information will be updated once manuscript has been published. 2024 Reference not in PubMed; see OMIA 000698-9940 for reference details
399 OMIA:000698-89462 water buffalo Murrah (Buffalo) Myotonia CLCN1 splicing Naturally occurring variant yes c.396C>T 2013 23339992
224 OMIA:000698-9925 goat Myotonia CLCN1 missense Naturally occurring variant yes ARS1 4 g.13857007C>G c.2590G>C p.(P864A) ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000031898.1 rs5334475115 1996 8855341
609 OMIA:000698-9615 dog Australian Cattle Dog (Dog) Border Collie (Dog) Myotonia CLCN1 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 16 g.6344748_6344749insT c.2647_2648insA p.(R883Qfs*18) NM_001003124.2; NP_001003124.1; published as c.2665insA; p.(R889fs); coordinates in the table have been updated to a recent reference genome and / or transcript 2007 17552451
1041 OMIA:000698-9615 dog Labrador Retriever (Dog) Myotonia CLCN1 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 16 g.6348929T>A c.2275A>T p.(R759X) Quitt et al. (2018): "Chr16:6348929 T A CLCN1 ENSCAFG00000003619.3 stopgain" 2018 29934119
62 OMIA:000698-9615 dog Miniature Schnauzer (Dog) Myotonia CLCN1 missense Naturally occurring variant yes CanFam3.1 16 g.6366383G>A c.803C>T p.(T268M) 1999 10452529 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1364 OMIA:000698-9615 dog American Bulldog (Dog) Myotonia CLCN1 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 16 g.6369245_6369246insAGAG c.436_437insCTCT p.(Y146Sfs*49) cDNA and protein position based on NM_001003124.2 and NP_001003124.1 2020 33246886
1570 OMIA:000698-9615 dog Mixed Breed (Dog) Myotonia CLCN1 deletion, gross (>20) Naturally occurring variant yes CanFam3.1 16 g.[6367458_6367478del;6367482del;6367485A>C] c.[703T>G;706del;710_730del] p.[(F235V;V236fs)] NM_001003124.2; NP_001003124.1; published as c.[705T>G; 708del; 712_732del], coordinates in the table have been updated to the CanFam3.1 reference genome and reflect correction in PMID:37212506. 2023 37212506
161 OMIA:000698-9796 horse New Forest Pony (Horse) Myotonia CLCN1 missense Naturally occurring variant yes EquCab3.0 4 g.96518592A>C c.1775A>C p.(D592A) c.1775A>C, Genbank acc. XM_001915636); p.D592A, Genbank acc. XP_001915671 (Wijnberg et al., 2014) rs5334475185 2012 22197188 (FN thanks Izabela De Assis Rocha, who provided genomic location in EquCab3.0 and the Genbank acc IDs, working under the supervision of Professor Ernie Bailey; 15 April 2020) Revised genomic location kindly provided by Cord Drögemüller; 21 May 2021
1573 OMIA:000698-9685 domestic cat Domestic Longhair Myotonia CLCN1 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 A2 g.158967085_158967092del p.(L143Qfs3*) NP_001291956.1; published as chrA2:15897085‐15 897 092, coordinates in this table have been verified in Felis_catus_9.0 2022 35815860
1623 OMIA:000698-9685 domestic cat Myotonia CLCN1 missense Naturally occurring variant yes Felis_catus_9.0 A2 g.158976314G>C c.991G>C p.(A331P) NM_001305027.1; NP_001291956.1 2023 37668104
408 OMIA:000698-9685 domestic cat Myotonia CLCN1 splicing Naturally occurring variant yes Felis_catus_9.0 A2 g.158986498G>T c.1930+1G>T NM_001305027.1 2014 25356766 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
245 OMIA:000698-9940 sheep Rasa Aragonesa, Spain (Sheep) Myotonia CLCN1 missense Naturally occurring variant yes Oar_rambouillet_v1.0 4 g.115541101G>A c.277G>A p.(E93K) Oar_v3.1 position is g.106140081G>A published as p.Gln93Lys. cDNA and protein position predicted using Variant Effect Predictor ENSOART00020002372.1 rs401726021 2015 25744800 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1365 OMIA:000698-9823 pig Myotonia CLCN1 deletion, gross (>20) Naturally occurring variant yes Sscrofa11.1 18 g.6912538_6916702del 2019 31666547
210 OMIA:001887-9913 taurine cattle Belgian Blue (Cattle) Osteopetrosis with gingival hamartomas CLCN7 missense Naturally occurring variant yes ARS-UCD1.2 25 g.[1139611G>T; 1139613A>G] c.[2248T>C;2250C>A] p.(Y750Q) 2014 24159188 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
648 OMIA:001135-9913 taurine cattle Japanese Black, Japan (Cattle) Renal dysplasia CLDN16 Type 1 deletion, gross (>20) Naturally occurring variant yes 1 37kb deletion of exons 1-4 2000 10810088
781 OMIA:001135-9913 taurine cattle Japanese Black, Japan (Cattle) Renal dysplasia CLDN16 Type 2 deletion, gross (>20) Naturally occurring variant yes 1 "a 56-kb deletion that eliminates exons 1-4 and 21-bp of exon 5" 200922: g. info moved to here (g.77528017_?) until can be standardised 2002 12047224 Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
593 OMIA:001482-9913 taurine cattle Devon (Cattle) Neuronal ceroid lipofuscinosis, 5 CLN5 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 12 g.52112732_52112733insG c.662_663insG p.(R221Gfs*6) 2006 16935476 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) 210909: after checking the genome assembly sequence, FN changed g.52461241insG to g.52461241_52461242insG; and c.662insG to c.662_663insG
279 OMIA:001482-9615 dog Australian Cattle Dog (Dog) Border Collie (Dog) Neuronal ceroid lipofuscinosis, 5 CLN5 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 22 g.30574637C>T c.619C>T p.(Q207*) rs1152388418 rs1152388418 2005 16033706 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool 30 Dec 2020: g. coordinate corrected, with thanks to Angelica K Kallenberg
541 OMIA:001482-9615 dog Golden Retriever (Dog) Neuronal ceroid lipofuscinosis, 5 CLN5 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 22 g.30574953_30574954del c.935_936del p.(E312Vfs*6) NM_001011556.1; NP_001011556.1,published as CLN5:c.934_935delAG; coordinates in the table have been updated to a recent reference genome and / or transcript 2015 25934231 Breed information obtained from Katz et al. (2017) Neurobiol Dis. doi: 10.1016/j.nbd.2017.08.017; Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
389 OMIA:001482-9940 sheep Borderdale, New Zealand (Sheep) Neuronal ceroid lipofuscinosis, 5 CLN5 splicing Naturally occurring variant yes Oar_rambouillet_v1.0 10 g.56313269G>A c.571+1G>A rs422165326 2008 17988881 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
68 OMIA:001443-9615 dog Australian Shepherd (Dog) Neuronal ceroid lipofuscinosis, 6 CLN6 missense Naturally occurring variant yes CanFam3.1 30 g.32247875A>G c.829T>C p.(W277R) ROS_Cfam_1.0:g.32443458A>G ENSCAFT00845033654.1:c.829T>C ENSCAFP00845026347.1:p.Trp277Arg rs1152388420 rs1152388420 2011 21234413 Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
1213 OMIA:001443-9685 domestic cat Domestic medium-haired Neuronal ceroid lipofuscinosis, 6 CLN6 nonsense (stop-gain) Naturally occurring variant yes Felis_catus_9.0 B3 g.39334330G>A c.668G>A p.(W223*) ENSFCAT00000025909:c.668G>A; XM_003987007.5:c.668G>A (Katz et al. (2020) rs5334475122 2020 32518081
671 OMIA:001443-9940 sheep South Hampshire, New Zealand (Sheep) Neuronal ceroid lipofuscinosis CLN6 deletion, gross (>20) Naturally occurring variant yes Oar_rambouillet_v1.0 7 deletion of exon 1 2013 23338040
234 OMIA:001443-9940 sheep Merino (Sheep) Neuronal ceroid lipofuscinosis, 6 CLN6 missense Naturally occurring variant yes Oar_rambouillet_v1.0 7 g.16039510G>A c.184C>T p.(R62C) protein and cDNA position based on NP_001035379.1 and NM_001040289.1, respectively rs399747319 2006 17046213 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1030 OMIA:001962-9542 Japanese macaque Neuronal ceroid lipofuscinosis, 7 CLN7 deletion, small (<=20) Naturally occurring variant yes 4 c.769delA p.(I257Lfs*36) 2018 30048804
690 OMIA:001506-9615 dog Alpine Dachsbracke (Dog) Neuronal ceroid lipofuscinosis, 8 CLN8 deletion, gross (>20) Naturally occurring variant yes CanFam3.1 37 g.30852988_30902901del c.-14679_*18669del NM_001012343.1; a homozygous deletion encompassing the entire CLN8 gene 2017 28024876 g. information obtained from Katz et al. (2017) Neurobiol Dis. doi: 10.1016/j.nbd.2017.08.017
971 OMIA:001506-9615 dog Saluki (Dog) Neuronal ceroid lipofuscinosis, 8 CLN8 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 37 g.30874636dupT c.349dupT p.(E117*) "an insertion of 1 bp (T) in the CLN8 gene (Fig. S2) in a short T repeat, thereby changing the stretch of 9 T's to a stretch consisting of 10 T's. The exact position of the inserted base could obviously not be verified, given that this was an insertion of a single base in a stretch of nine repeats of the same base (CFA37:g.30874628–30874636). According to the recommended nomenclature, the T insertion was noted as a T duplication in the T farthest in the 3′ direction (g.30874636dupT; c.349dupT)" 2018 29446145
69 OMIA:001506-9615 dog English Setter (Dog) Neuronal ceroid lipofuscinosis, 8 CLN8 missense Naturally occurring variant yes CanFam3.1 37 g.30874779T>C c.491T>C p.(L164P) 2005 15629147 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
338 OMIA:001506-9615 dog Australian Shepherd (Dog) German Shorthaired Pointer (Dog) Neuronal ceroid lipofuscinosis, 8 CLN8 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 37 g.30883950G>A c.585G>A p.(W195*) NM_001012343: c.585G>A (Guo et al., 2014) 2014 24953404 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; confirmed by Guo et al. (2019, pages 3, 4, 5 and 6), assuming that the g. coordinate (g.30,895,648) in the abstract of Guo et al. (2019) is a typo.
431 OMIA:000119-9685 domestic cat Blood group system AB CMAH regulatory Naturally occurring variant no Felis_catus_9.0 B2 g.4934641C>T published as C-371T 2007 17553163
1432 OMIA:000119-9685 domestic cat Blood group system AB CMAH regulatory Naturally occurring variant no Felis_catus_9.0 B2 g.4934795G>A published as G-217A 2007 17553163
430 OMIA:000119-9685 domestic cat Blood group system AB CMAH insertion, small (<=20) Naturally occurring variant no Felis_catus_9.0 B2 g.4934941_4934942insAACGAGCAACCGAAGCTG published as "an indel in the exon 1 5' UTR"; Delta-53; Felis_catus_9.0 represents the deletion allele 2007 17553163 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1431 OMIA:000119-9685 domestic cat Blood group system AB CMAH missense Naturally occurring variant no Felis_catus_9.0 B2 g.4935345C>T c.139C>T p.(R47C) NM_001244985.1; NP_001231914.1; published as c.136C>T 2014 24697343 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
118 OMIA:000119-9685 domestic cat Blood group system AB CMAH missense Naturally occurring variant no Felis_catus_9.0 B2 g.4935348G>A c.142G>A p.(V48M) NM_001244985.1; NP_001231914.1; initially reported as Felis_catus_6.2: B2:4587414G>A; c.139G>A; p.(V47M) rs5334475157 2007 17553163 The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
800 OMIA:000119-9685 domestic cat 2019 TYPING PANEL CMAH missense Naturally occurring variant no Felis_catus_9.0 B2 g.4935385G>T c.179G>T p.(G60V) NM_001244985.1; NP_001231914.1 rs5334475140 2016 27755584 The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
801 OMIA:000119-9685 domestic cat Blood group system AB CMAH missense Naturally occurring variant no Felis_catus_9.0 B2 g.4935393A>G c.187A>G p.(I63V) NM_001244985.1; NP_001231914.1 2016 27755584
119 OMIA:000119-9685 domestic cat 2019 TYPING PANEL CMAH missense Naturally occurring variant no Felis_catus_9.0 B2 g.4938728T>A c.268T>A p.(Y90N) NM_001244985.1; NP_001231914.1; published as c.265T>A (2007); revised designation of c.268T>A was reported by Kehl et al. (2019) rs5334475138 2007 17553163 The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
1446 OMIA:000119-9685 domestic cat Blood group system AB CMAH missense Naturally occurring variant no Felis_catus_9.0 B2 g.4947482C>A c.327A>C p.(E109D) NM_001244985.1; NP_001231914.1; published as c.327A>C; variant is reported to be not causal for blood type B, but may impact Neu5GC levels (Omi et al.,2016). The Felis_catus_9.0 reference genome represents the C allele, while transcript NM_001244985.1 represents the A allele. 2016 27171395
799 OMIA:000119-9685 domestic cat Ragdoll (Cat) 2019 TYPING PANEL CMAH missense Naturally occurring variant no Felis_catus_9.0 B2 g.4947519C>T c.364C>T p.(P122S) NM_001244985.1; NP_001231914.1 rs5334475151 2016 27171395 The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
1413 OMIA:000119-9685 domestic cat Blood group system AB CMAH missense Naturally occurring variant no Felis_catus_9.0 B2 g.4953568G>A c.773G>A p.(R258Q) NM_001244985.1; NP_001231914.1 2021 34589535
1430 OMIA:000119-9685 domestic cat Blood group system AB CMAH deletion, small (<=20) Naturally occurring variant no Felis_catus_9.0 B2 g.4955359del c.933del p.(A312Hfs*6) NM_001244985.1; NP_001231914.1 2018 30235335 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1062 OMIA:000119-9685 domestic cat Ragdoll (Cat) 2019 TYPING PANEL CMAH deletion, small (<=20) Naturally occurring variant no Felis_catus_9.0 B2 g.4978934del c.1322del p.(L441*) NM_001244985.1; NP_001231914.1; published as c.1322delT 2018 30235335 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
120 OMIA:000119-9685 domestic cat Blood group system AB CMAH missense Naturally occurring variant no Felis_catus_9.0 B2 g.4985762G>A c.1603G>A p.(D535N) NM_001244985.1; NP_001231914.1; also published as c.1600G>A; p.(D534N) rs5334475141 2007 17553163 The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
547 OMIA:001977-9615 dog Shetland Sheepdog (Dog) Progressive retinal atrophy, due to CNGA1 mutations CNGA1 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 13 g.43831897_43831900del c.1752_1755del p.(T585Sfs*7) NM_001003222.1; published as c.1752_1755delAACT 2015 26202106 Genomic and protein coordinates in CanFam3.1 provided by Robert Kuhn
548 OMIA:001481-9615 dog Labrador Retriever (Dog) Achromatopsia-2 CNGA3 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 10 g.44234198_44234200del c.1931_1933del p.(V644del) NM_001301112.1; published as c.1931_1933delTGG rs852784090 rs852784090 2015 26407004 Genomic coordinates in CanFam3.1 and EVA ID provided by Robert Kuhn
97 OMIA:001481-9615 dog German Shepherd Dog (Dog) Achromatopsia-2 CNGA3 missense Naturally occurring variant yes CanFam3.1 10 g.44234861C>T c.1270C>T p.(R424W) NM_001301112.1; NP_001288041.1 2015 26407004 Genomic position in CanFam3.1 provided by Mateo Etcheveste.
1016 OMIA:001481-9940 sheep Awassi (Sheep) Achromatopsia-2 (day blindness) CNGA3 missense Naturally occurring variant yes Oar_rambouillet_v1.0 3 g.108958871C>T c.1618G>A p.(G540S) 2017 28282490 Genomic coordinate on Oar_v4.0 (g.102602387G>A) kindly provided by Eyal Seroussi via Elisha Gootwine. The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager & Shernae Woolley, EMAI, NSW Department of Primary Industries.
317 OMIA:001481-9940 sheep Awassi (Sheep) Achromatopsia-2 (day blindness) CNGA3 nonsense (stop-gain) Naturally occurring variant yes Oori1 scaffold00739 3 g.263324C>T c.706C>T p.(R236*) In a pers. comm. to FN via Elisha Gootwine, Eyal Seroussi advises that the Oar_v4.0 assembly has errors in the region of of this mutation, such that it cannot be mapped onto that assembly. It can, however, be mapped on to the Ovis aries musimon sequence: "Exon 8 mutation is at position 263,324 in Ovis aries musimon unplaced genomic scaffold, alternate assembly Oori1 scaffold00739 (Sequence ID: NW_011942977.1 Length: 1056687)" 2010 19874885
918 OMIA:002723-9615 dog Papillon (Dog) Phalène (Dog) Progressive retinal atrophy CNGB1 delins, small (<=20) Naturally occurring variant yes CanFam3.1 2 g.58622673_58622675delinsCTAGCTAC c.2387_2389delinsCTAGCTAC p.(Y796Sfs*7) NM_001284462.1; NP_001271391.1; published as c.2685delA2687_2688insTAGCTA and p.(Y889Sfs*5); coordinates in the table have been updated to a recent reference genome and / or transcript and updated to HGVS recommendations rs1152388403 2013 24015210
631 OMIA:001365-9615 dog Alaskan Malamute (Dog) Miniature Australian Shepherd Dog (Dog) Achromatopsia (cone degeneration, hemeralopia), AMAL CNGB3 cd^AMAL deletion, gross (>20) Naturally occurring variant yes 29 "deletion removing all exons of canine CNGB3" 2002 12140185
1400 OMIA:001365-9913 taurine cattle Brown Swiss (Cattle) Achromatopsia CNGB3 OH1 missense Naturally occurring variant yes ARS-UCD1.2 14 g.76011964G>A c.751G>A p.(D251N) XM_015474554.2: c.751G>A, XP_015330040.2: p.Asp251Asn ENSBTAT00000065296.2:c.751G>A ENSBTAP00000054173.2:p.Asp251Asn rs716218235 rs716218235 2021 34830323
27 OMIA:001365-9615 dog German Shorthaired Pointer (Dog) Achromatopsia (cone degeneration, hemeralopia), GSPT CNGB3 cd^GSPT missense Naturally occurring variant yes CanFam3.1 29 g.32837065C>T c.784G>A p.(D262N) 2002 12140185 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool 30 Dec 2020 Chromosome corrected, thanks to Angelica K Kallenberg
1502 OMIA:002591-9615 dog Dalmatian (Dog) Lysosomal storage disease, CNP-related CNP deletion, small (<=20) Naturally occurring variant yes Dog10K_Boxer_Tasha 9 g.20350240del c.1107del p.(K370Nfs*11) ENSCAFT00000102206 2022 35447247
1273 OMIA:002301-9615 dog Labrador Retriever (Dog) Leonberger (Dog) Pyrenean Shepherd (Dog) Saint Bernard (Dog) Laryngeal paralysis and polyneuropathy CNTNAP1 LPPN3 missense Naturally occurring variant yes CanFam3.1 9 g.20298261C>T c.2810G>A p.(G937E) XM_548083.6:c.2810G>A; XP_548083.3:p.Gly937Glu; variant initially identified in Labrador Retriever, Leonberger and Saint Bernard and later reported in a Pyrenean Shepherd (PMID: 37582787) rs24587752 rs24587752 2020 33261176
172 OMIA:001718-9823 pig Dwarfism, Schmid metaphyseal chondrodysplasia COL10A1 missense Naturally occurring variant yes Sscrofa11.1 1 g.81767089C>T c.1768G>A p.(G590R) rs5334475171 2000 11130976 The genomic and CDS position was determined by Stephanie Shields and the effect was confirmed with Ensembl VEP (27/05/2020)
1657 OMIA:002811-9615 dog Old English Sheepdog (Dog) Multiocular defect COL11A1 missense Naturally occurring variant yes CanFam3.1 6 g.47611886T>C c.1775T>C p.(F1592S) 2023 38153936
78 OMIA:001772-9615 dog Labrador Retriever (Dog) Skeletal dysplasia 2 (SD2) COL11A2 missense Naturally occurring variant yes CanFam3.1 12 g.2652874C>G c.143G>C p.(R48P) ROS_Cfam_1.0:g.2983602C>G ENSCAFT00845034709.1:c.143G>C ENSCAFP00845027184.1:p.Arg48Pro rs851399084 rs851399084 2013 23527306 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1634 OMIA:002793-9685 domestic cat American Shorthair (Cat) Epidermolysis bullosa, junctional, COL17A1-related COL17A1 splicing Naturally occurring variant yes F.catus_Fca126_mat1.0 D2 g.62124169del c.3019+1del XM_006938156.5; variant reported in a single affected cat 2023 37895184
1635 OMIA:002793-9685 domestic cat European Shorthair (Cat) Epidermolysis bullosa, junctional, COL17A1-related COL17A1 splicing Naturally occurring variant yes F.catus_Fca126_mat1.0 D2 g.62149308C>T c.769+5G>A p.([=,p.Val257Glyfs*82]) XM_006938156.5; XP_006938218.3, variant described in a single affected cat 2023 37895184
1031 OMIA:002127-9913 taurine cattle Red Angus (Cattle) Osteogenesis imperfecta, type II, COL1A1-related COL1A1 missense Naturally occurring variant yes ARS-UCD1.2 19 g.36463798G>A c.1063G>A p.(G355S) Petersen et al. (2019): "PolyPhen-2 predicted the mutation to be “probably damaging” with a score of 1.000 (sensitivity 0.00; specificity 1.00). Similarly, PROVEAN prediction classified the variant as “Deleterious” with a score of − 4.615, exceeding both the default (− 2.5) and stringent (− 4.1) thresholds for this classification." The genomic coordinate in the UMD3.1 assembly is g.37094333G>A (Petersen et al., 2019). The coding sequence coordinates are c.1063G>A (ENSBTAT00000017420.4) (Petersen, pers. comm.) rs3423092630 rs3423092630 2019 30788588
839 OMIA:002127-9913 taurine cattle Simmental (Cattle) Osteogenesis imperfecta, type II, COL1A1-related COL1A1 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.36470764_36470767delinsT c.3145_3148delinsT p.(A1049_P1050delinsS) UMD3.1 position is g.37101299_37101302delinsT; cDNA position based on ENSBTAT00000017420.4 rs876049195 rs876049195 2017 28904385 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1289 OMIA:002127-9913 taurine cattle Holstein (black and white) (Cattle) Osteogenesis imperfecta, type II, COL1A1-related COL1A1 missense Naturally occurring variant yes ARS-UCD1.2 19 g.36473359T>A c.3917T>A p.(V1306E) NM_001034039.2: c.3917T>A; XP_024835395.1: p.Val1306Glu (Jacinto et al., 2021) rs5334474947 2021 33672767
959 OMIA:002126-9615 dog Golden Retriever (Dog) Osteogenesis imperfecta, type III, COL1A1-related COL1A1 missense Naturally occurring variant yes CanFam3.1 9 g.26193593C>G c.1145G>C p.(G382A) NM_001003090.1; NP_001003090.1; published as c.1276G>C, p.(G208A); coordinates in the table have been updated to a recent reference genome and / or transcript rs1152388502 rs1152388502 2000 11147834
762 OMIA:002112-9615 dog Beagle (Dog) Osteogenesis imperfecta, COL1A2-related COL1A2 delins, small (<=20) Naturally occurring variant yes CanFam3.1 14 g.(19918265_19918268delinsTGTCATTGG) c.3656_3859delinsTGTCATTGG p.(L1286Cfs*31) NM_001003187.1; NP_001003187.1; "a mutation in which nucleotides 3991-3994 ("CTAG") were replaced with "TGTCATTGG." The first seven bases of the inserted sequence were identical to nucleotides 4002-4008 of the normal canine COL1A2 sequence. The resulting frameshift changed 30 amino acids and introduced a premature stop codon." The genomic information is presented in brackets as the variant was detected in cDNA and the genomic position is predicted. Coordinates in the table have been updated to a recent reference genome and or transcripts. 2001 11393792
1114 OMIA:002112-9615 dog Lagotto Romagnolo (Dog) Osteogenesis imperfecta, COL1A2-related COL1A2 duplication Naturally occurring variant yes CanFam3.1 14 g.19898279_19898281dup c.877_879dup p.(P293dup) NM_001003187.1; NP_001003187.1 2019 31468557
852 OMIA:002112-9615 dog Chow Chow (Dog) Osteogenesis imperfecta, COL1A2-related COL1A2 splicing Naturally occurring variant yes CanFam3.1 14 g.19898487G>A c.936+1G>A 2018 29036614
840 OMIA:001926-9913 taurine cattle Charolais (Cattle) Salers (Cattle) Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32301746G>A c.1791G>A p.(G600D) rs5334474917 2017 28904385 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1275 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) Bulldog calf COL2A1 deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 5 g.32301911_32308589del "Sanger sequencing revealed the precise breakpoints of the heterozygous deletion from position 32 301 911 located in intron 25 to 32 308 589 located within exon 45. The 6679 bp deletion includes the entire sequence of 18 exons (26–44) plus the first 36 nucleotides of exon 45" (Jacinto et al., 2020) 2021 33316082
1241 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) Bulldog calf COL2A1 delins, gross (>20) Naturally occurring variant yes ARS-UCD1.2 5 g.32303127_32306640delinsTCTGGGGAGC 2020 32894162
842 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32303739G>A c.2158G>A p.(G720S) rs455596159 2017 28904385 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
414 OMIA:001926-9913 taurine cattle Danish Holstein (Cattle) bulldog calf COL2A1 splicing Naturally occurring variant yes ARS-UCD1.2 5 g.32305226G>A c.2463+1G>A rs5334475095 2016 27296271 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
223 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32307658G>A p.(G960R) rs3423194986 2014 25017103
841 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32308008G>A c.2986G>A p.(G996S) rs876243579 rs876243579 2017 28904385 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1026 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32308734G>A c.3166G>A p.(G1056S) rs5334475093 2019 30378686
278 OMIA:002618-9615 dog English Springer Spaniel (Dog) Nephropathy COL4A4 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 25 g.39893376G>A c.2713C>T p.(Q905*) NM_001031818.1; NP_001026988.1; published as c.2806C>T and p.(Q904*) 2012 22369189
277 OMIA:002618-9615 dog English Cocker Spaniel (Dog) Nephropathy COL4A4 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 25 g.39953906T>A c.115A>T p.(K39*) 2007 17552442 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
471 OMIA:001112-9615 dog Navasota (mixed breed) (Dog) Nephritis, X-linked COL4A5 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 X g.82134508_82134517del c.513_522del p.(N172Ifs) XM_005640969.3; XP_005641026.1; a 10 base pair (TAATCCAGGA) deletion in exon 9 of COL4A5 2003 12879362
276 OMIA:001112-9615 dog Samoyed (Dog) Nephritis, X-linked COL4A5 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 X g.82196868G>T c.3079G>T p.(G1027*) 1994 8171024 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1124 OMIA:002165-9615 dog Labrador Retriever (Dog) Ehlers-Danlos syndrome, classic type, 1 COL5A1 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 9 g.50806169del c.3038del p.(G1013Vfs*260) XM_022423936.1; XP_022279644.1; published as c.3038delG - "variant arose by a de novo mutation event during the development of the mother." (Bauer et al., 2019) 2019 31546637
1125 OMIA:002165-9615 dog Mixed Breed (Dog) Ehlers-Danlos syndrome, classic type, 1 COL5A1 missense Naturally occurring variant yes CanFam3.1 9 g.50832936G>A c.4711G>A p.(G1571R) XM_022423936.1,c.4711G>A; XP_022279644.1,p.(Gly1571Arg) 2019 31546637
1465 OMIA:002165-9685 domestic cat Bombay (Cat) classical Ehlers-Danlos syndrome COL5A1 nonsense (stop-gain) Naturally occurring variant yes Felis_catus_9.0 D4 g.93209345T>A c.3514A>T p.(Lys1172*) XM_023242950.1; XP_023098718.1 2022 35627182
1025 OMIA:002165-9685 domestic cat Domestic Shorthair Ehlers-Danlos syndrome, classic type, 1 COL5A1 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 D4 g.93210344del c.3420del p.(L1141Sfs*134) XM_023242951.1; XP_023098719.1; published as c.3420delG 2018 30246406
1466 OMIA:002165-9685 domestic cat Domestic Shorthair classical Ehlers-Danlos syndrome COL5A1 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 D4 g.93215496del c.3066del p.(Gly1023Valfs*50) XM_023242950.1; XP_023098718.1 2022 35627182
1609 OMIA:002165-9685 domestic cat Domestic medium-haired classical Ehlers-Danlos syndrome COL5A1 splicing Naturally occurring variant yes Felis_catus_9.0 D4 g.93290016T>G c.501-2A>C XM_023242950.1 2023 37594181
1464 OMIA:002165-9685 domestic cat Bengal (Cat) classical Ehlers-Danlos syndrome COL5A1 deletion, gross (>20) Naturally occurring variant yes Felis_catus_9.0 D4 g.93331577_93331598del c.112_118+15del r.spl? XM_023242950.1 2022 35627182
1263 OMIA:002295-9913 taurine cattle Holstein (black and white) (Cattle) Ehlers-Danlos syndrome, classic type, 2 COL5A2 missense Naturally occurring variant yes ARS-UCD1.2 2 g.7331916G>T c.2366G>T p.(G789V) XM_024979774.1: c.2366G>T; XP_024835542.1: p.Gly789Val (Jacinto et al., 2020) rs5334475045 2020 33143196
1460 OMIA:002295-9615 dog Chihuahua (Dog) Ehlers-Danlos syndrome, classic type, 2 COL5A2 deletion, gross (>20) Naturally occurring variant yes CanFam3.1 36 g.30548697_30548723del c.3388_3414del p.(Lys1130_Asp1138del) XM_005640393.3; XP_005640450.1 2022 35627319
340 OMIA:001967-9615 dog Landseer (Dog) Muscular dystrophy, Ullrich type COL6A1 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 31 g.39303964G>T c.289G>T p.(E97*) XM_003434001.5; XP_003434049.2; previously incorrectly listed in this table as c.289C>T; p.(Q97*) - corrected 8/2/2022 2015 26438297
1184 OMIA:002260-9913 taurine cattle Holstein (black and white) (Cattle) de novo mutation in an AI sire COL6A3 missense Naturally occurring variant yes ARS-UCD1.2 3 g.116826597G>A p.(T1894M) Bourneuf et al. (2017) detected COL6A3 g.117453719G>A; p.T1894M as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Holstein AI bull. No information was provided on the descendants of this bull. rs5334475059 2017 28904385
1625 OMIA:002274-9615 dog American Staffordshire Terrier (Dog) Muscular dystrophy, COL6A3-related COL6A3 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 25 g.48005972del c.6398del p.(P2133Rfs*109) NM_001103215.1; NP_001096685.1; published as g.48287602CG>C in CanFam4 2023 37706358
1208 OMIA:002274-9615 dog Labrador Retriever (Dog) Muscular dystrophy, COL6A3-related COL6A3 splicing Naturally occurring variant yes CanFam3.1 25 g.48007994C>T c.6210+1G>A NM_001103215.1; CanFam3.1 chr25:48,007,994C > T; NM_001103215.1 c.6210 + 1G > A (Bolduc et al., 2020) 2020 32439203
1207 OMIA:002274-9615 dog Labrador Retriever (Dog) Muscular dystrophy, COL6A3-related COL6A3 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 25 g.48014962G>A c.4726C>T p.(R1576*) NM_001103215.1; NP_001096685.1; CanFam3.1 chr25:48,014,962G > A; NM_001103215.1 c.4726C > T, p.R1576* (Bolduc et al., 2020) 2020 32439203
292 OMIA:000341-9913 taurine cattle Rotes Höhenvieh, Germany (Cattle) Vorderwälder, Germany (Cattle) Epidermolysis bullosa, dystrophic COL7A1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 22 g.51301158C>T c.4762C>T p.(R1588*) rs876174537 rs876174537 2012 22715415 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed and some variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
357 OMIA:000341-9615 dog Central Asian Shepherd Dog (Dog) Epidermolysis bullosa, dystrophic COL7A1 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 20 g.40532043C>T c.4579C>T p.(R1527*) 2017 28493971 Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
38 OMIA:000341-9615 dog Golden Retriever (Dog) Epidermolysis bullosa, dystrophic COL7A1 missense Naturally occurring variant yes CanFam3.1 20 g.40538034G>A c.5716G>A p.(G1906S) rs1152388417 2003 12874109 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1276 OMIA:000341-9615 dog Basset Hound (Dog) Epidermolysis bullosa, dystrophic COL7A1 complex rearrangement Naturally occurring variant yes CanFam3.1 20 g.[40524302_40524308del;40524267_40524380dup] c.[2028_2034del;1993_2050+56dup] p.(V677Sfs*11) NM_001002980.1; NP_001002980.1; complex duplication event spanning parts of exon 15 and intron 15 of the COL7A1 gene, starting at position 40,524,267 and ending at 40,524,380 on chromosome 20 (CanFam3.1 assembly) (Garcia et al., 2020). 2020 33291836
641 OMIA:001523-9615 dog Samoyed (Dog) Oculoskeletal dysplasia 2 COL9A2 deletion, gross (>20) Naturally occurring variant yes 15 a 1,267 bp deletion that eliminates part of the 5’UTR, all of exon 1 and part of intron 1 2010 20686772
581 OMIA:001522-9615 dog Labrador Retriever (Dog) Oculoskeletal dysplasia 1 COL9A3 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 24 g.46653422_46653423insG c.10_11insG p.(A4Gfs*46) NM_001197171.1; NP_001184100.1; published as "a 1-base insertion (guanine) in exon 1 that changes a string of four guanines (CFA24: 49,699,847–49,699,850; CanFam2) to a string of five guanines (c.7–10insG). ... (p.A4GX46)" Goldstein et al. (2010). Information in this table has been changed in accordance to HGVS 3'rule and updated to the current reference genome. 2010 20686772
1092 OMIA:001522-9615 dog Northern Inuit Dog (Dog) Oculoskeletal dysplasia 1 COL9A3 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 24 g.46660067C>T c.700C>T p.(R234*) 2019 31415586
944 OMIA:001621-9685 domestic cat Devon Rex (Cat) Sphynx (Cat) Muscular dystrophy-dystroglycanopathy (limb-girdle) COLQ missense Naturally occurring variant yes Felis_catus_9.0 C2 g.135068287C>T c.1190G>A p.(C397Y) rs869320615 rs869320615 2015 26327126 26374066 Genomic location obtained via Ensembl's VEP
643 OMIA:001988-9615 dog Bedlington Terrier (Dog) Wilson disease, COMMD1 type COMMD1 deletion, gross (>20) Naturally occurring variant yes 10 deletion "breakpoints were positioned at 65.3091 and 65.3489 Mb of dog chromosome 10, in intron 1 and intron 2 of COMMD1 respectively, a deletion of 39.7 kb" 2005 16293123
1545 OMIA:002667-9031 chicken Feather colour, Inhibitor of gold COMTD1 IG insertion, small (<=20) Naturally occurring variant no GRCg6a 6 g.15675521_15675522insCT c.747_748insCT p.(Q250fs) XM_015288295.1; XP_015143781.1 2023 37068079
215 OMIA:001529-9913 taurine cattle Holstein (black and white) (Cattle) Dominant red COPA DR^DR missense Naturally occurring variant no ARS-UCD1.2 3 g.9361962C>T c.478C>T p.(R160C) rs3423151160 2017 28904385 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1506 OMIA:001274-452646 American mink Coat colour, black crystal COPA missense Naturally occurring variant unknown NNQGG.v01 FNWR01000261.1 g.4876673G>A c.478C>T p.(R160C) 2022 35729186
1012 OMIA:002159-9694 tiger Golden tiger CORIN missense Naturally occurring variant no c.1759C>T p.(H587Y) 2017 28281538
1463 OMIA:002159-9685 domestic cat British Shorthair (Cat) Copper (British recessive wideband) CORIN vwb^BSH nonsense (stop-gain) Naturally occurring variant no Felis_catus_9.0 B1 c.2425C>T p.(R809*) ON640807 2022 35703390
1456 OMIA:002159-9685 domestic cat Siberian (Cat) Extreme sunshine (Siberian recessive extreme wideband) CORIN vwb^eSIB missense Naturally occurring variant no Felis_catus_9.0 B1 g.167737406G>A c.839G>A p.(C280Y) XM_019829549.2; XP_019685108.1; reported as Genbank ID ON355336 2022 35574714
1313 OMIA:002159-9685 domestic cat Siberian (Cat) Sunshine (golden) CORIN vwb^SIB missense Naturally occurring variant no Felis_catus_9.0 B1 g.167809720C>T c.2383C>T p.(R795C) XM_019829551.2; XP_019685110.1 2021 33970502 Genomic position in Felis_catus_9.0 provided by Joshua Khamis.
358 OMIA:002111-9913 taurine cattle Holstein (red and white) (Cattle) Cataract, recessive, CPAMD8-related CPAMD8 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 7 g.6073556C>T c.220C>T p.(Q74*) rs5334474964 2017 28683140
1418 OMIA:002519-9913 taurine cattle Brown Swiss (Cattle) Haplotype with homozygous deficiency BH24 CPT1C BH24 missense Naturally occurring variant yes ARS-UCD1.2 18 g.56098048G>A c.158G>A p.(G53D) XM_002695120.5 rs719328437 2021 34915862
1428 OMIA:002533-9685 domestic cat Domestic Shorthair Osteogenesis imperfecta CREB3L1 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 D1 g.100436508_100436509del c.370_371del p.(C124Lfs) XM_003993204.4; XP_003993253.1; published as c.370_371delTG 2022 35168412
916 OMIA:000881-9685 domestic cat Abyssinian (Cat) Rod-cone dysplasia CRX Rdy deletion, small (<=20) Naturally occurring variant yes F.catus_Fca126_mat1.0 E2 g.9492897del c.546del p.(P185Lfs*2) XM_045045412.1; XP_044901347.1; published as CRX: n.546delC; in the Felis_catus_9.0 assembly the CRX gene is duplicated and genomic coordinates in this table are given for a more recent reference genome 2010 20053974
1491 OMIA:001643-10036 golden hamster duper Cry1 deletion, small (<=20) Naturally occurring variant unknown c.578del p.(P193fs) published as c.578delC 2022 35471909
1176 OMIA:000168-10141 domestic guinea pig Cataract Cryz splicing Naturally occurring variant yes "a 102-bp deletion towards the 3' end of the coding region. This deletion does not interfere with the reading frame but results in a protein 34 amino acids shorter." (Rodriguez et al., 1992) 1992 1390943
692 OMIA:000852-9925 goat Casein, alpha-S1, reduced concentration CSN1S1 insertion, gross (>20) Naturally occurring variant no 6 "a 457-bp insertion within exon 19 (last untranslated exon). This insert is a truncated long interspersed repeated element (LINE) containing part of the ORF-2, the 3' UTR and the poly(A) tail of the original retroposon." 1994 7926797
907 OMIA:001623-9925 goat Casein, alpha-S2, absence CSN1S2 nonsense (stop-gain) Naturally occurring variant no ARS1 6 g.86085134G>A c.763G>A p.(T110*) rs268293093 rs268293093 2001 11419340 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
220 OMIA:002033-9913 taurine cattle A2 milk CSN2 A2 missense Naturally occurring variant no ARS-UCD1.2 6 g.85451298T>G c.245A>C p.(H82P) Note that cattle cannot be genotyped for the A2 allele solely on the basis of the c.245A>C variant because this variant is common to 4 other alleles; see Table 2 of Caroli et al. (2009) J. Dairy Sci. 92, 5335-5352 (Matt McClure, pers. comm.) rs43703011 rs43703011 2013 23102962 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1312 OMIA:001424-9925 goat Absence of β‐casein CSN2 CSN2^0 deletion, small (<=20) Naturally occurring variant no ARS1 6 g.86008404del c.175del p.I59Sfs*10 Changed from g.86008401del to g.86008404del to adhere to the HGVS 3’rule [220110] ENSCHIT00000032661.1:c.175del ENSCHIP00000024801.1:p.Ile59SerfsTer10 Persuy et al. (1999): "allele CSN2^O had a one-nucleotide deletion in the 5' end of exon 7, which introduces a premature stop codon. The open reading frame of allele CSN2^O encodes a shortened polypeptide of 72 amino acids, compared to 223 amino acids for caprine pre beta-casein A." rs645737170 rs645737170 1999 10612234
1311 OMIA:001424-9925 goat Absence of β‐casein CSN2 CSN2^01 regulatory Naturally occurring variant no ARS1 6 g.86015651A>G Cosenza et al. (2016): "nucleotide C .... negatively affects the promoter activity of the CSN2 gene" Synonyms: dbSNP ss1245869815 rs654545998 rs654545998 2007 17931404 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
1186 OMIA:002262-9913 taurine cattle Montbéliarde (Cattle) de novo mutation in an AI sire CSNK1G2 missense Naturally occurring variant yes ARS-UCD1.2 7 g.44265842G>C p.(D164H) Bourneuf et al. (2017) detected Chr7 CSNK1G2 g.45885860G>C; p.D164H as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Montbéliarde AI bull. No information was provided on the descendants of this bull. rs5334475073 2017 28904385
66 OMIA:001505-9615 dog American Bulldog (Dog) Neuronal ceroid lipofuscinosis, 10 CTSD missense Naturally occurring variant yes CanFam3.1 18 g.46013354C>T c.597G>A p.(M199I) 2006 16386934 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
905 OMIA:001505-9940 sheep Roslagsfår, Sweden (Sheep) Neuronal ceroid lipofuscinosis, 10 CTSD missense Naturally occurring variant yes Oar_rambouillet_v1.0 21 g.51583020G>A c.883G>A p.(D295N) published as c.934G>A; protein and cDNA positions in this table based on XP_027815055.1 and XM_027959254.1, respectively 2000 10856224 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1517 OMIA:002607-9685 domestic cat Domestic Longhair Pyknodysostosis CTSK nonsense (stop-gain) Naturally occurring variant yes Felis_catus_9.0 C1 g.105945826G>A c.724C>T p.(R242*) ENSFCAT00000003643; variant is reported in a single affected cat 2022 36532681
529 OMIA:001786-9615 dog Beagle (Dog) Intestinal cobalamin malabsorption due to CUBN mutation CUBN deletion, small (<=20) Naturally occurring variant yes CanFam3.1 2 g.19796293del c.786del p.(D262Efs*47) NM_001003148.1; NP_001003148.1; deletion C rs1152388404 rs1152388404 2014 24164695
447 OMIA:001786-9615 dog Border Collie (Dog) Intestinal cobalamin malabsorption due to CUBN mutation CUBN deletion, small (<=20) Naturally occurring variant yes CanFam3.1 2 g.19974334del c.8392del p.(Q2798Rfs*3) NM_001003148.1; NP_001003148.1; deletion C 2013 23613799
1036 OMIA:001786-9615 dog Komondor (Dog) Intestinal cobalamin malabsorption, CUBN-related CUBN splicing Naturally occurring variant yes CanFam3.1 2 g.19981457G>A c.8746+1G>A NM_001003148.1 2018 30591068
287 OMIA:001697-9913 taurine cattle Jersey (Cattle) Abortion due to haplotype JH1 CWC15 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 15 g.15449431C>T c.163C>T p.(R55*) UMD3.1 position is g.15707169C>T, cDNA and protein positions based on XM_005215764.2 rs1115118696 rs1115118696 2013 23349982 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
850 OMIA:002131-9615 dog Mixed Breed (Dog) Methemoglobinaemia, CYB5R3-related CYB5R3 missense Naturally occurring variant yes CanFam3.1 10 g.22832963G>A c.214G>A p.(G72S) 2017 28963729 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
967 OMIA:002131-9615 dog Pomeranian (Dog) Methemoglobinaemia, CYB5R3-related CYB5R3 missense Naturally occurring variant yes CanFam3.1 10 g.22836951A>C c.580A>C p.(I194L) NM_001048084.1, NP_001041549.1 2018 29356095 Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
1548 OMIA:002131-9685 domestic cat Domestic Shorthair Methaemoglobinaemia, CYB5R3-related CYB5R3 splicing Naturally occurring variant yes F.catus_Fca126_mat1.0 B4 g.135605715C>T c.226+5G>A XM_045062469.1; two transcripts were observed in the cat with the splice variant resulting in two predicted protein variants: XP_044918404.1:p.(G76_Q77insERSPDPARVEPG) and XP_044918404.1:p.(V52Afs*58), 2023 37048064
1155 OMIA:002131-9685 domestic cat Domestic Shorthair Methaemoglobinaemia, CYB5R3-related CYB5R3 missense Naturally occurring variant yes Felis_catus_9.0 B4 g.137967506C>T c.625G>A p.(G209S) Jaffey e al. (2019): "p.Gly209Ser amino acid change in transcript CYB5R3-202 (ENSFCAT00000056925) at position B4:137967506" 2019 31650629
1156 OMIA:002131-9685 domestic cat Domestic Shorthair Methaemoglobinaemia, CYB5R3-related CYB5R3 splicing Naturally occurring variant yes Felis_catus_9.0 B4 g.137970815C>G c.232-1G>C Jaffey et al. (2019): "a putative loss of function splice acceptor variant at c.232-1G>C in the CYB5R3-202 transcript (ENSFCAT00000056925) at position B4:137970815 that is in the acceptor site for exon 4, which likely affects downstream translation of the protein." 2019 31650629
629 OMIA:000017-9986 rabbit Adrenal hyperplasia, congenital CYP11A1 deletion, gross (>20) Naturally occurring variant yes "a large deletion mutation in the P450scc gene" 1993 7682938
117 OMIA:001661-9685 domestic cat Adrenal hyperplasia, congenital, due to 11-beta hydroxylase deficiency CYP11B1 missense Naturally occurring variant yes Felis_catus_9.0 F2 g.84247412G>A c.1151G>A p.(R384Q) XM_004000154.3; XP_004000203.1 published as "a guanosine-to-adenosine mutation in exon 7 that results in an arginine to glutamine amino acid substitution; this latter mutation results in 11β-hydroxylase deficiency-associated CAH in people [Parajes et al. (2010) J Clin Endocrinol Metab 95:779–788]. 2012 22827537 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
720 OMIA:000452-9031 chicken Campine (Chicken) Sebright Bantams, United Kingdom of Great Britain and Northern Ireland (Chicken) Henny feathering CYP19A1 insertion, gross (>20) Naturally occurring variant no GRCg6a 10 g.9683879_9683880insN[7524] The insertion is 7524bp and "contains an intact endogenous retrovirus that was not found in chickens representing 31 different breeds not showing henny feathering or in samples of the ancestral red junglefowl. The sequence shows over 99% sequence identity to the avian leukosis virus ev-1 and ev-21 strains, suggesting a recent integration. The ERV 3’LTR, containing a powerful transcriptional enhancer and core promoter with TATA box together with binding sites for EFIII and Ig/EBP inside the CYP19A1 5′ untranslated region" (Li et al., 2019) 1991 1939054 Genomic location and size of the insertion provided by Li et al. (2019)
274 OMIA:001405-9615 dog Beagle (Dog) Metabolizer of a cognitive enhancer CYP1A2 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 30 g.37821686C>T c.1117C>T p.(R373*) rs852922442 rs852922442 2004 15564884 Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
1251 OMIA:002288-9913 taurine cattle Hereford (Cattle) Mandibulofacial dysostosis CYP26C1 missense Naturally occurring variant yes ARS-UCD1.2 26 g.14404993T>C c.563T>G p.(L188P) ENSBTAT00000056396.3:c.563T>G; ENSBTAP00000050244.2:p.Leu188Arg rs431913023 rs431913023 2020 33105751
656 OMIA:000837-9823 pig Vitamin D-deficiency rickets, type I CYP27B1 deletion, gross (>20) Naturally occurring variant yes 5 the first of two deletions (173 bp or 329 bp) in the gene for cytochromome P450C1 (otherwise known as CYP27B1) 2003 12915218
657 OMIA:000837-9823 pig Vitamin D-deficiency rickets, type I CYP27B1 deletion, gross (>20) Naturally occurring variant yes 5 the second of two deletions (173 bp or 329 bp) in the gene for cytochromome P450C1 (otherwise known as CYP27B1) 2003 12915218
502 OMIA:000837-9685 domestic cat Vitamin D-deficiency rickets, type I CYP27B1 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 B4 g.86180281del c.731del p.(R244Pfs*32) XM_003988966.3; XP_003989015.1; published as c.731delG 2009 19138382 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
315 OMIA:000837-9685 domestic cat Siamese (Cat) Vitamin D-deficiency rickets, type I CYP27B1 nonsense (stop-gain) Naturally occurring variant yes Felis_catus_9.0 B4 g.86180375C>A c.637G>T p.(E213*) XM_003988966.3; XP_003989015.1; rs5334475145 2012 22553308 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1576 OMIA:000837-9615 dog Pug (Dog) Vitamin D-deficiency rickets, type IA CYP27B1 nonsense (stop-gain) Naturally occurring variant yes UU_Cfam_GSD_1.0 10 g.2182971G>T c.261C>A p.(Y87*) XM_038549826.1; XP_038405754.1 2023 37293695
1411 OMIA:002508-9913 taurine cattle Simmental (Cattle) Haplotype with homozygous deficiency SH8 CYP2B6 SH8 missense Naturally occurring variant yes ARS-UCD1.2 18 g.50296371A>T c.938T>A p.(I313N) NM_001075173.1 rs5352006042 2021 34944310
1137 OMIA:002221-9685 domestic cat Domestic Shorthair Vitamin D-deficiency rickets, type Ib CYP2R1 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 D1 g.72977336del c.1386del p.(F462Lfs*20) XM_003993015.5; XP_003993064.1; genomic position in accordance with HGVS 3'-rule 2019 30777056 Genomic position in Felis_catus_9.0 provided by Joshua Khamis.
52 OMIA:002684-9615 dog Australian Cattle Dog (Dog) Shetland Sheepdog (Dog) Leucodystrophy CYTB missense Naturally occurring variant yes CanFam3.1 M m.14474G>A c.14474G>A p.(V98M) 2006 16026996 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
784 OMIA:001986-9823 pig Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive, with sensitivity to ionizing radiation DCLRE1C splicing Naturally occurring variant yes Sscrofa11.1 10 g.46845535G>A rs5334475180 2015 26320255
785 OMIA:001986-9823 pig Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive, with sensitivity to ionizing radiation DCLRE1C nonsense (stop-gain) Naturally occurring variant yes Sscrofa11.1 10 g.46851262G>A p.(Trp267*) rs5334475181 2015 26320255
167 OMIA:000735-9796 horse Belgian Draft (Horse) Connemara Pony (Horse) Haflinger (Horse) Rocky Mountain, United States of America (Bighorn sheep) Ocular squamous cell carcinoma DDB2 missense Naturally occurring variant yes EquCab3.0 12 g.11726667C>T c.1013C>T p.(T338M) The EquCab2 coordinates, obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool, are g.11608667, c.1013C>T and p.T338M rs1139682898 rs1139682898 2017 28425625 The EquCab3 g. coordinates were provided by by Meredith O’Connell, working under the guidance of Professor Ernie Bailey, 5 March 2019
1624 OMIA:002582-9913 taurine cattle Japanese Black, Japan (Cattle) Hepatic fibrinogen storage disease DGKG missense Genome-editing (CRISPR-Cas9) yes ARS-UCD1.3 1 g.81082187C>T c.2162C>T p.T721I XM_002684869.5; XP_002684915.3 2023 37681469
1335 OMIA:002377-8845 swan goose Lion Head (Goose (domestic)) Sichuan White, China (Goose (domestic)) Knob, basal DIO2 missense Naturally occurring variant no AnsCyg_PRJNA183603_v1.0 NW_013185827.1 g.642923G>A p.(P265L) 2021 34193033
565 OMIA:002095-9615 dog Rhodesian Ridgeback (Dog) Epilepsy, generalized myoclonic, with photosensitivity DIRAS1 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 20 g.56474668_56474671del c.564_567del p.(D189Afs*11) XM_005633100.3; XP_005633157.1; published as DIRAS1:c.564_567delAGAC 2017 28223533 Genomic and protein coordinates in CanFam3.1 provided by Robert Kuhn
1412 OMIA:002505-9913 taurine cattle Simmental (Cattle) Haplotype with homozygous deficiency SH5 DIS3 SH5 insertion, small (<=20) Naturally occurring variant unknown ARS-UCD1.2 12 g.47511687_47511687insT c.2032dup p.(I678N*2) NP_025000110.1, XM_025000110.1 2021 34944310
1308 OMIA:001484-9685 domestic cat Abyssinian (Cat) Burmese (Cat) Maine Coon (Cat) Oriental Shorthair (Cat) Ticked DKK4 Ti^CK missense Naturally occurring variant no Felis_catus_9.0 B1 g.42620835C>T c.53C>T p.(A18V) rs5334475164 2021 33780570 ENSFCAT00000034752:c.53C>T; XM_023252567.1:c53C>T
1307 OMIA:001484-9685 domestic cat Abyssinian (Cat) Ticked DKK4 Ti^A missense Naturally occurring variant no Felis_catus_9.0 B1 g.42621481G>A c.188G>A p.(C63Y) published as g.41621481G>A rs785541575 2021 33780570 (XM_023252567.1; ENSFCAT00000034752: c.188G>A)
914 OMIA:001354-9940 sheep Muscular hypertrophy (double muscling), Callipyge DLK1 regulatory Naturally occurring variant unknown Oar_rambouillet_v1.0 18 g.66187430A>G "a single A/G polymorphism located at position 103,894 of GenBank AF354168 and position 267 of the GenBank STS AF401294" (Freking et al., 2002) "the CLPG mutation, an A to G transition in a highly conserved dodecamer motif located in the 90-Kb intergenic region separating the Delta-like 1 homologue (DLK1) and Gene trap locus 2 (GTL2) genes in the eponymous imprinted domain" (Xu et al., 2015; PubMed 26474044) In relation to the Oar_v4.0/oviAri4 genome assembly, the location of the causative SNP is OAR18:g.64294536A>G (Ross Tellam, pers. comm. to FN 5 Nov 2020) rs10721113 2002 12368241 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager & Shernae Woolley, EMAI, NSW Department of Primary Industries.
615 OMIA:002109-9913 taurine cattle Brown Swiss (Cattle) Tricho-dento-osseous-like syndrome DLX3 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.36665831_36665832insGGAGCACA c.584_585insGGAGCACAGG p.(S198Rfs*99) NM_001081622 position is g.37298375_37298376insGGAGCACA rs5334475096 2017 28670783 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
728 OMIA:001919-9615 dog Nova Scotia Duck Tolling Retriever (Dog) Cleft palate 1 DLX6 insertion, gross (>20) Naturally occurring variant yes CanFam3.1 14 g.22068082_22068083insN[2056] "2056 bp insertion [including LINE1] . . within a highly conserved region of DLX6 intron 2 at cfa14.25016716"[CanFam2.0] 2014 24699068
1395 OMIA:001081-9823 pig Duchenne muscular dystrophy DMD DMD^ex52del delins, gross (>20) Transgenesis via somatic cell nuclear transfer (SCNT) yes X gene targeting and somatic cell nuclear transfer was used to replace DMD exon 52 with a neomycin resistance cassette 2013 23784375
680 OMIA:001081-9615 dog German Shorthaired Pointer (Dog) Muscular dystrophy, Duchenne type DMD deletion, gross (>20) Naturally occurring variant yes X a "deletion encompassing the entire dystrophin [DMD] gene" 1999 10407848
536 OMIA:001081-9615 dog Cocker Spaniel (Dog) Muscular dystrophy, Duchenne type DMD deletion, small (<=20) Naturally occurring variant yes X deletion of four nucleotides in exon 65, with a reading frame shift predicting a premature stop codon at the site of the deletion 2012 22218699
681 OMIA:001081-9615 dog Tibetan Terrier (Dog) Muscular dystrophy, Duchenne type DMD deletion, gross (>20) Naturally occurring variant yes X "a large deletion of exons 8-29" 2012 22218699
729 OMIA:001081-9615 dog Labrador Retriever (Dog) Muscular dystrophy, Duchenne type DMD insertion, gross (>20) Naturally occurring variant yes X "184 nucleotide [pseudoexon] insertion between exon 19 and exon 20, which results in a premature stop codon at the next codon downstream of the insertion" 2012 22218699 Reference not in PubMed; see OMIA 001081-9615 for reference details
957 OMIA:001081-9615 dog Rottweiler (Dog) Muscular dystrophy, Duchenne type DMD nonsense (stop-gain) Naturally occurring variant yes X "nonsense mutation in exon 58" 1994 Reference not in PubMed; see OMIA 001081-9615 for reference details
989 OMIA:001081-9615 dog Poodle, Miniature (Dog) Muscular dystrophy, Duchenne type DMD deletion, gross (>20) Naturally occurring variant yes X "a >5 Mb deletion on the X chromosome, encompassing the entire DMD gene" 2018 29474464
922 OMIA:001081-9685 domestic cat Domestic Shorthair Muscular dystrophy, Duchenne type DMD deletion, gross (>20) Naturally occurring variant yes X A deletion of the muscle promoter and first exon and the Purkinje neuronal first exon of the DMD gene 1994 7881288
923 OMIA:001081-9685 domestic cat Domestic Shorthair Muscular dystrophy, Duchenne type DMD deletion, gross (>20) Naturally occurring variant yes X A large deletion that "involved regions of the dystrophin gene that are poorly characterized, including the cortical neuronal promoter and its first exon and the skeletal neuronal promoter and its first exon" 2014 24446404
367 OMIA:001081-9615 dog Cavalier King Charles Spaniel (Dog) Muscular dystrophy, Duchenne type DMD splicing Naturally occurring variant yes CanFam3.1 X g.26956239G>A c.7294+5G>T NM_001003343.1; NP_001003343.1; experimentally confirmed splice defect; a single nucleotide variant in the 5'-splice site of intron 51 that results in skipping of exon 50 in mRNA transcripts and a predicted premature truncation of the translated protein 2010 20072625
562 OMIA:001081-9615 dog Cavalier King Charles Spaniel (Dog) Muscular dystrophy, Duchenne type DMD deletion, small (<=20) Naturally occurring variant yes CanFam3.1 X g.27442996_27443002del c.6057_6063del p.(N2021Pfs) NM_001003343.1; NP_001003343.1; published as c.6051_6057delTCTCAAT based on different transcript 2016 28028563
542 OMIA:001081-9615 dog Norfolk Terrier (Dog) Muscular dystrophy, Duchenne type DMD deletion, small (<=20) Naturally occurring variant yes CanFam3.1 X g.27606021del c.3084delG p.(G1029Nfs*30) 2015 26401335
1249 OMIA:001081-9615 dog Jack Russell Terrier (Dog) Duchenne-type muscular dystrophy DMD deletion, gross (>20) Naturally occurring variant yes CanFam3.1 X g.27615280_27982912del c.94-10346_2807-6207del XM_005641029.1 2020 33049940
1236 OMIA:001081-9615 dog Australian Labradoodle (Dog) Australian Labradoodle dystrophinopathy DMD nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 X g.27621845G>A c.2668C>T p.(R890*) NM_001003343.1; NP_001003343.1; "a C to T transition at base pair 43 in exon 21 of the dystrophin gene" (Shrader et al., 2018) 2018 30286978
1234 OMIA:001081-9615 dog Labrador Retriever (Dog) Labrador Retriever muscular dystrophy (LRMD) DMD inversion Naturally occurring variant yes CanFam3.1 X g.27622834_29823788inv c.-1490357_2626-947inv XM_005641029.1 2020 32767978
1235 OMIA:001081-9615 dog Border Collie (Dog) Muscular dystrophy, Duchenne DMD deletion, small (<=20) Naturally occurring variant yes CanFam3.1 X g.27626466del c.2841delT 2018 29843823
750 OMIA:001081-9615 dog Japanese Spitz (Dog) Muscular dystrophy, Duchenne type DMD inversion Naturally occurring variant yes CanFam3.1 X g.27631972_33069482inv c.-4736051_2384-5339inv XM_005641029.1; "an inversion of a 5.4-Mb fragment of the X chromosome, with one break point (BP1) in the DMD gene . . . and a second break point (BP2) in a gene farther toward the centromere, the RPGR gene". 2015 25644216
708 OMIA:001081-9615 dog Pembroke Welsh Corgi (Dog) Muscular dystrophy, Duchenne type DMD insertion, gross (>20) Naturally occurring variant yes CanFam3.1 X g.27721607_27721608insN[(4800)] "a long interspersed repetitive element-1 (LINE-1) insertion in intron 13, which introduced a new exon containing an in-frame stop codon" 2011 20714321
1492 OMIA:001081-9615 dog Labrador Retriever (Dog) Muscular dystrophy, Duchenne type DMD duplication Naturally occurring variant yes CanFam3.1 X g.27851768_28247504dup Shelton et al. (2022): "chrX:27,851,768-27,852,122 bp position (Intron 7 . . .) and chrX:28,247,150-28,247,504 bp position (Intron 1 . . .)" 2022 36041985
366 OMIA:001081-9615 dog Golden Retriever (Dog) Muscular dystrophy, Duchenne type DMD splicing Naturally occurring variant yes CanFam3.1 X g.27926946T>C c.531-2A>G NM_001003343.1; a point mutation in the consensus splice acceptor site in exon 6 , such that exon 7 is skipped rs1152388423 rs1152388423 1992 1577476
1656 OMIA:001081-9685 domestic cat Domestic Shorthair Muscular dystrophy, Duchenne type DMD nonsense (stop-gain) Naturally occurring variant yes F.catus_Fca126_mat1.0 X g.27949145C>T c.4849C>T p.(Q1617*) XM_023249210.1 2024 38180235
1531 OMIA:001888-9685 domestic cat Becker muscular dystrophy DMD missense Naturally occurring variant yes F.catus_Fca126_mat1.0 X g.27988938G>A c.4186C>T p.(H1396Y) XM_045050787.1; XP_044906722.1 2023 36834603
1510 OMIA:001081-9685 domestic cat Maine Coon (Cat) Muscular dystrophy, Duchenne type DMD nonsense (stop-gain) Naturally occurring variant yes F.catus_Fca126_mat1.0 X g.28208148G>A c.1180C>T p.(R394*) XM_045050794.1; XP_044906729.1 2022 36359052
1457 OMIA:001888-9823 pig Becker muscular dystrophy DMD insertion, gross (>20) Naturally occurring variant yes Sscrofa11.1 X Aihara et al. (2022): "Analysis of dystrophin mRNA showed a 62 base pair insertion between exons 26 and 27. The insertion was derived from intron 26." 2022 35220848
179 OMIA:001685-9823 OMIA:001888-9823 pig Stress syndrome DMD missense Naturally occurring variant yes Sscrofa11.1 X g.28309227G>A c.5872C>T p.(R1958W) Ensembl VEP was used to identify cDNA position in transcript ENSSSCT00000089893.1, SIFT score 0.01 rs196952080 rs196952080 2012 22691118
1615 OMIA:001081-9615 dog Brittany Spaniel (Dog) Muscular dystrophy, Duchenne DMD insertion, gross (>20) Naturally occurring variant yes UU_Cfam_GSD_1.0 X RSPYR1 retrogene insertion in intron 20; reported in a single dog; reported in a single dog 2023 37628610
1614 OMIA:001081-9615 dog Brittany Spaniel (Dog) Muscular dystrophy, Duchenne DMD nonsense (stop-gain) Naturally occurring variant yes UU_Cfam_GSD_1.0 X g.26939052G>A c.8059C>T p.(Q2687*) NM_001003343.1; NP_001003343.1; reported in 2 related dogs 2023 37628610
1616 OMIA:001081-9615 dog French Bulldog (Dog) Muscular dystrophy, Duchenne DMD insertion, small (<=20) Naturally occurring variant yes UU_Cfam_GSD_1.0 X g.27774668_27774669insT c.3371_3372insA p.(F1125fs) NM_001003343.1; NP_001003343.1; published as p.(F1125*), reported in a single dog 2023 37628610
908 OMIA:001542-9940 sheep Corriedale (Sheep) Hypophosphatemic rickets, autosomal recessive, 1 DMP1 nonsense (stop-gain) Naturally occurring variant yes Oar_rambouillet_v1.0 6 g.112910614C>T c.433C>T p.(R145*) Published as g.112213795C>T / c.250C>T. Protein and cDNA positions in this table are based on XP_012035717.1 and XM_012180327.3. 2011 21747952 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1352 OMIA:002442-9823 pig Large White (Pig) Sperm flagella defect DNAH17 deletion, small (<=20) Naturally occurring variant yes Sscrofa11.1 12 g.3556402_3556414del Nosková et al. (2021): "intronic 13-bp deletion ... causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17" rs5334475172 2021 33724408
39 OMIA:001466-9615 dog Chesapeake Bay Retriever (Dog) Curly Coated Retriever (Dog) Labrador Retriever (Dog) Exercise-induced collapse DNM1 missense Naturally occurring variant yes CanFam3.1 9 g.55282762C>A c.767G>T p.(R256L) ROS_Cfam_1.0:g.56204742C>A ENSCAFT00845051951.1:c.767G>T ENSCAFP00845040760.1:p.Arg256Leu rs852832685 rs852832685 2008 18806795 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1434 OMIA:002534-9615 dog Border Collie (Dog) Centronuclear myopathy 1 DNM2 missense Naturally occurring variant yes CanFam3.1 20 g.50423497G>A c.1393C>T p.(R465W) XM_005632882.3; XP_005632939.1. 2022 35244154
125 OMIA:001776-9685 domestic cat Dihydropyrimidinase deficiency DPYS missense Naturally occurring variant yes Felis_catus_9.0 F2 g.52064442C>T c.1303G>A p.(G435R) XM_023248231.1; XP_023103999.1 2012 23430934 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1194 OMIA:002266-9615 dog Rottweiler (Dog) Hyperkeratosis, palmoplantar, DSG1-related DSG1 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 7 g.58163636_58163640del c.2541_2545del p.(G848Wfs*2) NM_001002939.1; NP_001002939.1; published as c.2541_2545delGGGCT 2020 32344723
1392 OMIA:002452-9685 domestic cat Domestic Shorthair Hair shaft dysplasia DSG4 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 D3 g.55315010del c.76del p.(I26Lfs*4) XM_019815116.1; XP_019670675.1 2022 34878611
1393 OMIA:002452-9685 domestic cat Domestic Shorthair Hair shaft dysplasia DSG4 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 D3 g.55336127del c.1777del p.(H593Tfs*23) XM_019815116.1; XP_019670675.1 2022 34878611
1408 OMIA:002243-9913 taurine cattle Highland (Cattle) Ichthyosis, DSP-related DSP missense Naturally occurring variant yes ARS-UCD1.2 23 g.47826600G>T c.6893C>A p.(A2298D) NM_001192368.2; NP_001179297.1 rs5385033307 2022 34996433
1115 OMIA:002210-9823 pig Bama Xiang Zhu, China (Pig) Congenital hypothyroidosis DUOX2 missense Naturally occurring variant yes Sscrofa11.1 1 g.126625620A>G c.1226A>G p.(D409G) ENU mutagenesis was used to create these pigs, the mutation is located within an exonic splicing enhancer motif and causes aberrant splicing of DUOX2 transcripts (Cao et al., 2019) rs5334475175 2019 30651277
1056 OMIA:002186-9615 dog Boston Terrier (Dog) Bulldog (Dog) French Bulldog (Dog) Screw tail DVL2 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 5 g.32195051del c.2051del p.(P684Lfs*26) XM_005619960.3; XP_005620017.1; published as g.32195043_32195044del; c.2044delC and changed to HGVS nomenclature in this table 2018 30521570
711 OMIA:000543-9913 taurine cattle Danish Holstein (Cattle) Anhidrotic ectodermal dysplasia EDA HED6 insertion, gross (>20) Naturally occurring variant yes X "a LINE1-derived pseudoexon between EDA exons 1 and 2. The 161-bp-long pseudoexon introduces a shift in reading frame and a premature stop codon early in EDA exon 2" 2011 22034998 Allele id was copied from Table 1 of Capuzzello et al. (2022)
645 OMIA:000543-9913 taurine cattle Deutsche Holstein Schwarzbunt, Germany (Cattle) Anhidrotic ectodermal dysplasia EDA HED1 deletion, gross (>20) Naturally occurring variant yes X c.397_502del p.(M133Vfs*111) a large deletion including exon 3 in the gene for ectodysplasin (ED1; now called EDA) 200922: g. info moved to here (g.85821470) until it can be standardised 2001 11591646 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 Allele id and p. information were copied from Table 1 of Capuzzello et al. (2022)
1120 OMIA:000543-9913 taurine cattle Prim'Holstein, France (Cattle) Generalized hypohidrotic ectodermal dysplasia EDA HED8 inversion Naturally occurring variant yes ARS-UCD1.2 X g.77174882_80737442inv Escouflaire et al. (2019): The "first breakpoint . . . [is] between positions 82,271,052 and 82,271,053 bp on chromosome X . . . The second breakpoint is situated at position 86,034,441 bp within the EDA intron 1" 2019 31533624 Allele id was copied from Table 1 of Capuzzello et al. (2022).
1293 OMIA:000543-9913 taurine cattle Red Angus-Simmental cross Hypohidrotic ectodermal dysplasia EDA HED9 deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 X g.80382423_80435202del GCF_002263795.1 (O'Toole et al., 2021) 2021 33801223 Allele id was copied from Table 1 of Capuzzello et al. (2022).
373 OMIA:000543-9913 taurine cattle Deutsche Holstein Schwarzbunt, Germany (Cattle) Anhidrotic ectodermal dysplasia EDA HED2 splicing Naturally occurring variant yes ARS-UCD1.2 X g.80411671A>C c.924+2T>G c.DNA position is based on NM_001081743.2 rs5334474632 2002 12021844 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. Allele id was copied from Table 1 of Capuzzello et al. (2022)
1295 OMIA:000543-9913 taurine cattle Holstein Friesian (Cattle) Anhidrotic ectodermal dysplasia EDA HED5 splicing Naturally occurring variant yes ARS-UCD1.2 X g.80411795C>A c.802C>A "a single nucleotide polymorphism (SNP) G/A at the 9th base of exon 8 [GenBank: AJ278907.1 position 30.549] ... Sequencing of the RT-PCR products revealed that the amplified fragment of the affected animals lacked ... exon 8. At the protein level, the exon skipping leads to a frameshift and consequently to a premature stop codon." (Gargani et al., 2011) rs5334475058 2011 21740563 Allele id and c. information were copied from Table 1 of Capuzzello et al. (2022)
1294 OMIA:000543-9913 taurine cattle Red Angus-Charolais-Simmental cross Anhidrotic ectodermal dysplasia EDA HED3 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 X g.80415626G>A c.730C>T p.(R244*) rs5334474792 2007 17616058 Reference not in PubMed; see OMIA 000543-9913 for reference details The g. coordinate for the named reference genome assembly, together with the c. coordinate, were kindly provided by Tosso Leeb (22 March 2021). Allele id was copied from Table 1 of Capuzzello et al. (2022).
1484 OMIA:000543-9913 taurine cattle British Blue x Holstein-Friesian cross Anhidrotic ectodermal dysplasia, EDA-related EDA HED10 deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 X g.80516615_80538514del c.397_502del p.(M133Vfs*111) NM_001081743.2; NP_001075212.1 2022 36068608 Allele id was copied from Table 1 of Capuzzello et al. (2022).
586 OMIA:000543-9913 taurine cattle Japanese Black, Japan (Cattle) Anhidrotic ectodermal dysplasia EDA HED7 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 X g.80802800_80802801insCCCT c.280_281insAGGG p.(G94Qfs*49) rs5334475024 2012 22497423 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. Allele id was copied from Table 1 of Capuzzello et al. (2022).
482 OMIA:000543-9913 taurine cattle Holstein (black and white) (Cattle) Anhidrotic ectodermal dysplasia EDA HED4 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 X g.80803015_80803033del c.48_66del p.(A16S22fs*55) "a 19-bp deletion at nucleotides c.48_66 in exon 1 ... . This mutation is predicted to generate a truncated 49 aa protein." rs5334474984 2011 21410470 Allele id and p. information were copied from Table 1 of Capuzzello et al. (2022)
1661 OMIA:000543-9913 taurine cattle Limousin (Cattle) Hypohidrotic ectodermal dysplasia, X-linked EDA HED11 missense Naturally occurring variant yes ARS-UCD1.3 X g.80411716T>C c.881A>G p.(E294G) NM_001081743.2; NP_001075212.1 rs439722471 2024 38252617
1665 OMIA:000543-9913 taurine cattle Fleckvieh-Simmental, Germany (Cattle) Hypohidrotic ectodermal dysplasia, X-linked EDA missense Naturally occurring variant yes ARS-UCD1.3 X g.80417567C>T c.679G>A p.(G227R) NM_001081743.2; NP_001075212.1; published as g.85716041G>A in ARS-UCD2.0 rs1114816375 2023 38275590
1458 OMIA:000543-9615 dog Mixed Breed (Dog) X-linked hypohidrotic ectodermal dysplasia EDA splicing Naturally occurring variant yes CanFam3.1 X r.385_487del p.M129fs*112 NM_001014770.2; NP_001014770.1; EDA transcript lacks 103 nucleotides encoded by exon 2, exon skipping is likely to be caused by an intronic splice variant 2016 27449516
1017 OMIA:000543-9615 dog Dachshund (Dog) X-linked hypohidrotic ectodermal dysplasia EDA deletion, small (<=20) Naturally occurring variant yes CanFam3.1 X g.54509504del c.842delT p.(L281Hfs*22) 2018 30276836
361 OMIA:000543-9615 dog German Shepherd Dog (Dog) Anhidrotic ectodermal dysplasia EDA splicing Naturally occurring variant yes CanFam3.1 X g.54511433G>A c.910-1G>A NM_001014770.2 rs1152388425 rs1152388425 2005 16151697 Genomic coordinates in CanFam3.1 und EVA Id provided by Zoe Shmidt and Robert Kuhn.
724 OMIA:001695-8090 Japanese medaka Reduced scale-3 edar insertion, gross (>20) Naturally occurring variant yes "several kb of extra sequence in the 5' UTR that . . . contains out-of-frame start codons and stop codons, [and consequently] the mutant transcript is likely to result in premature initiation and termination of translation and, as a result, the EDAR protein is not synthesized" 2001 11516953
843 OMIA:002128-9913 taurine cattle Charolais (Cattle) Anhidrotic ectodermal dysplasia, EDAR-related EDAR insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 11 g.44599876_44599877insC p.(P161Rfs*97) UMD3.1 position is g.44462236_44462237insC 2017 28904385 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1550 OMIA:002687-9940 sheep Fleece variation, wool density EDAR regulatory Naturally occurring variant no Oar_v4.0 3 g.61927840T>C the T allele is associated denser wool production in fine wool sheep rs408766096 rs408766096 2023 37137429
1474 OMIA:002560-9913 taurine cattle Lidia, Spain (Cattle) Growth and respiratory lethal syndrome EDN2 missense Naturally occurring variant yes ARS-UCD1.2 3 g.104701617G>A c.149G>A p.(C50Y) ENSBTAG00000021434; ENSBTAT00000028571.3 2022 35912509
722 OMIA:001671-9031 chicken Bohuslän - Dals svarthöna, Sweden (Chicken) H'mong, Viet Nam (Chicken) Kedu, Indonesia (Chicken) Silkie (Chicken) Silky/Silkie pigmentation (Fibromelanosis) EDN3 FM complex rearrangement Naturally occurring variant no 20 the FM mutation actually involves "the duplication of two genomic regions, each larger than 100 kb and separated by 417 kb on wild-type [GGA20] chromosomes" 2011 22216010
760 OMIA:002164-9925 goat Coat colour, white spotting, EDNRA-related EDNRA repeat variation Naturally occurring variant no 17 "a 1Mb copy number variant (CNV) harboring 5 genes including EDNRA. The analysis of 358 Boer goats revealed 3 alleles with one, two, and three copies of this CNV. The copy number is correlated with the degree of white spotting in goats" 2016 27329507
160 OMIA:000629-9796 horse American Paint (Horse) Miniature Horse (Horse) Quarter Horse (Horse) Thoroughbred (Horse) Megacolon EDNRB frame overo delins, small (<=20) Naturally occurring variant yes EquCab3.0 17 g.50503041_50503042delinsCT c.353_354delinsAG p.(I118K) NM_001081837.2; NP_001075306.2 1998 9530628
930 OMIA:001765-9940 sheep West African Dwarf (Sheep) Waardenburg syndrome, type 4A EDNRB deletion, gross (>20) Naturally occurring variant yes Oar_rambouillet_v1.0 10 "a deletion of about 110 kb on sheep chromosome [OAR]10, comprising the entire EDNRB gene" 2012 23300849
1632 OMIA:000375-8932 rock pigeon Piebald EDNRB2 Group 4 duplication Naturally occurring variant yes tandem duplication of a 37-kb region spanning from intron 1 of VAMP7 to just 5’ of EDNRB2 2023 37546953
1631 OMIA:000375-8932 rock pigeon Piebald EDNRB2 Group2 missense Naturally occurring variant yes p.(A42E) 2023 37546953
1630 OMIA:000375-8932 rock pigeon Piebald EDNRB2 Group1 missense Naturally occurring variant yes p.(R290C) 2023 37546953
1562 OMIA:002701-51751 ball python Skin colour, EDNRB2-related EDNRB2 yellowbelly deletion, small (<=20) Naturally occurring variant unknown c.1646del OP589186.1; 1-bp deletion introduces a frameshift, which removes or alters three of the seven transmembrane helices 2023 37191439
1563 OMIA:002701-51751 ball python Skin colour, EDNRB2-related EDNRB2 yellowbelly deletion, small (<=20) Naturally occurring variant unknown c.1747_1763del OP589186.1; "17-bp deletion introduces a frameshift into the transcript, which removes or alters two of the seven transmembrane helices" 2023 37191439
1564 OMIA:002701-51751 ball python Skin colour, EDNRB2-related EDNRB2 specter missense Naturally occurring variant unknown c.2601G>C p.(R315P) OP589186.1 2023 37191439
1567 OMIA:002701-51751 ball python Skin colour, EDNRB2-related EDNRB2 asphalt splicing Naturally occurring variant unknown c.3118G>A OP589186.1; G-to-A substitution in the sixth splice donor for the sixth intron 2023 37191439
1565 OMIA:002701-51751 ball python Skin colour, EDNRB2-related EDNRB2 spark missense Naturally occurring variant unknown c.481G>C p.(L152F) OP589186.1 2023 37191439
1566 OMIA:002701-51751 ball python Skin colour, EDNRB2-related EDNRB2 gravel splicing Naturally occurring variant unknown c.499G>A OP589186.1; G-to-A substitution at the splice donor for the first intron 2023 37191439
257 OMIA:000375-93934 Japanese quail Feather colour, panda/dotted white EDNRB2 missense Naturally occurring variant no c.995G>A p.(R332H) 2007 17313575
1633 OMIA:000375-8932 rock pigeon Recessive white and bull eye EDNRB2 missense Naturally occurring variant no scaffold 507 g.11167700C>T p.(E256K) 2023 37546953
1164 OMIA:001252-8843 domestic goose Gang, China (Goose (domestic)) Feather colour, recessive white EDNRB2 insertion, small (<=20) Naturally occurring variant no AnsCyg_PRJNA183603_v1.0 g.750748_750735insCACAGGTGAGCTCT "NW_013185915.1: g. 750,748-750,735 insertion. CACAGGTGAGCTCT" (Xi et al., 2020) 2020 32066369
16 OMIA:001904-9031 chicken Feather colour, recessive white EDNRB2 mo^w missense Naturally occurring variant no GRCg6a 4 g.11164302G>T c.731G>T p.(C244F) NM_204120.1; NP_989451.1; published as c.1008G>T and p.(C244F); coordinates in the table have been updated to a recent reference genome and / or transcript 2014 24466053 Genomic position in GRCg6a provided by Joshua Khamis.
17 OMIA:001904-9031 chicken Feather colour, mottled EDNRB2 mo missense Naturally occurring variant no GRCg6a 4 g.11166001G>A c.999G>A p.(R332H) NM_204120.1; NP_989451.1; published as c.1272G>A and p.(R332H); coordinates in the table have been updated to a recent reference genome and / or transcript 2014 24466053 Genomic position in GRCg6a provided by Joshua Khamis.
1483 OMIA:002564-9615 dog Labrador Retriever (Dog) Congenital dyserythropoietic anemia and polymyopathy EHBP1L1 nonsense (stop-gain) Naturally occurring variant yes CanFam4 18 g.52128140G>A c.388C>T p.(R130*) XM_038563927.1; 2022 36011338
1481 OMIA:002564-9615 dog English Springer Spaniel (Dog) Dyserythropoietic anemia and myopathy syndrome (DAMS) EHBP1L1 deletion, small (<=20) Naturally occurring variant yes UU_Cfam_GSD_1.0 18 g.52123541delG c.3120delC p.(F1041Sfs*30) XM_038563927.1; XP_038419855.1 2022 36140701
1044 OMIA:001805-9615 dog Parson Russell Terrier (Dog) Amelogenesis imperfecta ENAM missense Naturally occurring variant yes CanFam3.1 13 g.59945218C>T c.716C>T p.(P239L) XM_539305.4; XP_539305.3 2019 30877375 Genomic coordinates in CanFam3.1 provided by Robert Kuhn and Zoe Shmidt.
452 OMIA:001805-9615 dog Italian Greyhound (Dog) Amelogenesis imperfecta ENAM deletion, small (<=20) Naturally occurring variant yes CanFam3.1 13 g.59946493_59946497del c.1991_1995delTTTCC p.(F665Rfs*3) XM_539305.4; XP_539305.3; published as c.1991_1995delTTTCC 2013 23638899 Genomic coordinates in CanFam3.1 provided by Robert Kuhn
759 OMIA:000296-9031 chicken Duplex comb EOMES duplication Naturally occurring variant no 2 "a 20 Kb tandem duplication containing several conserved putative regulatory elements located 200 Kb upstream of the eomesodermin gene (EOMES)" 2015 25789773
1 OMIA:000240-8932 rock pigeon Crest EPHB2 cr missense Naturally occurring variant no c.???C>T p.(R758C) 2013 23371554
1454 OMIA:002550-9615 dog Rhodesian Ridgeback (Dog) Early onset adult deafness EPS8L2 deletion, small (<=20) Naturally occurring variant yes UMICH_Zoey_3.1/canFam5 18 g.25868739_25868750del c.1033_1044del p.(V345_L348del) XM_038500406.1; XP_038356334.1; published as 12-bp inframe deletion in EPS8L2 (CFA18:25,868,739-25,868,751 in the UMICH_Zoey_3.1) corresponding to deletion of amino acids VHFL 2022 35385474
191 OMIA:001716-9913 taurine cattle Holstein (black and white) (Cattle) Ehlers-Danlos syndrome, Holstein variant EPYC missense Naturally occurring variant yes ARS-UCD1.2 5 g.20856381C>A c.258G>T p.(S87N) rs5334475097 1999 10357109 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
1161 OMIA:000483-9925 goat Polled intersex syndrome ERG PIS complex rearrangement Naturally occurring variant yes 1 "a deletion with a total length of 10 159 bp and an inversely inserted approximately 480 kb-sized duplicated segment of a region located approximately 21 Mb further downstream on chromosome 1 containing two genes, KCNJ15 and ERG" (Simon et al., 2020) 2020 32060960
1169 OMIA:002543-9031 chicken Cleft primary palate ESRP2 deletion, small (<=20) Naturally occurring variant yes GRCg6a 11 g.3284041del ss5200091912 rs3386590816 2020 32162363
1439 OMIA:001457-9685 domestic cat Multiple acyl-CoA dehydrogenase deficiency ETFDH missense Naturally occurring variant yes Felis_catus_9.0 B1 g.71374631A>C c.692T>G p.(F231C) NM_001290236.1; NP_001277165.1 2014 24142280 Thanks to Heidi Anderson for alerting OMIA to this paper; 31 March 2022
375 OMIA:002540-9913 taurine cattle Japanese Brown, Japan (Cattle) Chondrodysplasia EVC2 splicing Naturally occurring variant yes ARS-UCD1.2 6 g.103594013C>T c.1356C>T Variant creates a cryptic splice donor site in exon 11 which is leading to improper splicing at position c.1355 and resulting in the 56-base RNA deletion between 1355 and 1410. The deletion causes a frameshift and premature termination. rs5334475072 2002 12136126 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
617 OMIA:002540-9913 taurine cattle Japanese Brown, Japan (Cattle) Chondrodysplasia EVC2 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 6 g.103609778_103609779delinsG c.2327_2328delinsG p.(A776Gfs*22) Published as c.2054_2055delCAinsG, cDNA and protein position in this table based on ENSBTAT00000005613.6 rs5334475076 2002 12136126 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
534 OMIA:002540-9913 taurine cattle Tiroler Grauvieh (Cattle) Chondrodysplasia EVC2 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 6 g.103651709_103651710del c.2993_2994del p.(D998Efs*13) rs5334475061 2014 24733244 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. 210909 FN: given that the variant is a 2bp del (AC), g.103651710_103651710del needs to be changed. BLASTing with AGAGGAGCAAGAAGAC from Fig.4 indicates that it is 719 and 710 that are deleted. THus the entry is changed to g.103651709_103651710del; and AC is removed from the c. entry.
346 OMIA:002042-9913 taurine cattle Belgian Blue (Cattle) Abortion (embryonic lethality), EXOSC4 EXOSC4 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 14 g.755826G>A c.190G>A p.(R64*) rs3423357300 2016 27646536 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1467 OMIA:002554-9685 domestic cat Osteochondromatosis (feline leukemia virus-negative) EXT1 duplication Naturally occurring variant yes F.catus_Fca126_mat1.0? F2 g.61870704dup c.1468dup p.(L490Pfs*31) XM_023248762.2; 2022 35719100
980 OMIA:001214-9615 dog American Staffordshire Terrier (Dog) Osteochondromatosis EXT2 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 18 g.45101754G>T c.924C>A p.(Y308*) XM_014121199.2; XP_013976674.1; published as c.969C>A and p.(Y323*); coordinates in the table have been updated to a recent reference genome and / or transcript 2018 29485212
713 OMIA:000363-9913 taurine cattle Holstein (black and white) (Cattle) Sahiwal (Cattle) Factor XI deficiency F11 insertion, gross (>20) Naturally occurring variant yes 27 a 76-bp insertion in exon 12 of the Factor XI gene 200922: g. and c. info moved here (g.15367048; c.1406ins76) until can be standardised 2004 15566468 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
591 OMIA:000363-9913 taurine cattle Japanese Black, Japan (Cattle) Sahiwal (Cattle) Factor XI deficiency F11 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 27 g.16305660delinsATATGTGCAGAATATA c.870delinsATATGTGCAGAATATA P.(F290delinsLYVQNI) rs5334474726 2005 16104386 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
702 OMIA:000363-9615 dog Kerry Blue Terrier (Dog) Factor XI deficiency F11 insertion, gross (>20) Naturally occurring variant yes CanFam3.1 16 g.44477343_44477344ins90 c.819_820ins90 NM_001135123.1 "an insertion of 90 bp (SINE) inside of coding exon 7" resulting in a "30 amino acids insertion in the A3 domain of FXI serine protease" (Tcherneva et al., 2007). 2007 Reference not in PubMed; see OMIA 000363-9615 for reference details g. and c. coordinates kindly provided by Professor Urs Giger (27 August 2022)
1472 OMIA:000363-9685 domestic cat Maine Coon (Cat) Factor XI deficiency F11 missense Naturally occurring variant yes Felis catus 9.0 B1 g.17176154G>A c.1546G>A p.(V516M) XM_003984601.5; XP_003984650.2 2022 35627175
533 OMIA:000364-9685 domestic cat Factor XII deficiency F12 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 A1 g.175381114del c.1321del p.(L441Cfs*119) NM_001168212.2; NP_001161684.2; published as c.1321delC 2015 24793828 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
147 OMIA:000364-9685 domestic cat Domestic Shorthair Factor XII deficiency F12 missense Naturally occurring variant yes Felis_catus_9.0 A1 g.175382065G>C c.1631G>C p.(G544A) NM_001168212.2; NP_001161684.2 rs5334475144 2017 28392508 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1532 OMIA:001818-9913 taurine cattle Japanese Black, Japan (Cattle) Japanese Brown, Japan (Cattle) Factor XIII deficiency F13A1 missense Naturally occurring variant yes UMD_3.1.1 23 g.48649432T>C c.248T>C p.(F83S) NM_001167894.1; NP_001161366.1; reported in Japanese Brown in PMID: 1996 Reference not in PubMed; see OMIA 001818-9913 for reference details Variant was first reported by Ogawa and Iga (1996). Variant information in this table is based on supplementary table 1 by Shibutani et al. (2023).
148 OMIA:000361-9783 Asiatic elephant Factor VII deficiency F7 missense Naturally occurring variant yes c.202A>G p.(R68G) 2017 28118558
40 OMIA:000361-9615 dog Airedale Terrier (Dog) Alaskan Klee Kai (Dog) American Foxhound (Dog) Beagle (Dog) Finnish Hound (Dog) German Wirehaired Pointer (Dog) Giant Schnauzer (Dog) Irish Water Spaniel (Dog) Japanese Spitz (Dog) Miniature Schnauzer (Dog) obsolete Alaskan Sled Dog (Dog) Papillon (Dog) Scottish Deerhound (Dog) Sealyham Terrier (Dog) Welsh Springer Spaniel (Dog) Factor VII deficiency F7 missense Naturally occurring variant yes CanFam3.1 22 g.60578895G>A c.407G>A p.(G136E) 2006 16961583 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; variant initially identified in Beagle and later reported in additional breeds: PMID:17939552; PMID: 27525650; PMID:34544496
363 OMIA:000437-9615 dog Irish Setter (Dog) Miniature Schnauzer (Dog) Haemophilia A F8 splicing Naturally occurring variant yes X intronic inversion that results in "aberrant splicing and premature termination" 2002 12008949
1038 OMIA:000437-9913 taurine cattle Fleckvieh-Simmental, Germany (Cattle) Haemophilia A F8 missense Naturally occurring variant yes ARS-UCD1.2 X g.36017426A>T c.134A>T p.(H45L) ENSBTAT00000036726.5:c.134A>T; ENSBTAP00000036581.4:p.His45Leu rs1117392179 rs1117392179 2018 29774585
194 OMIA:000437-9913 taurine cattle Japanese Brown, Japan (Cattle) Haemophilia A F8 missense Naturally occurring variant yes ARS-UCD1.2 X g.36145188T>A c.6458T>A p.(L2153H) rs456129807 2009 19456318 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1655 OMIA:000437-9615 dog Border Collie (Dog) Haemophilia A F8 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 X g.122956942delA c.3206delA NM_001003212.1 2023 38104983
350 OMIA:000437-9615 dog Old English Sheepdog (Dog) Haemophilia A F8 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 X g.122973422G>A c.1786C>T p.(R596*) 2016 27780008 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
100 OMIA:000437-9615 dog German Shepherd Dog (Dog) Haemophilia A F8 missense Naturally occurring variant yes CanFam3.1 X g.122975611C>T c.1700G>A p.(C567Y) NM_001003212.1; NP_001003212.1; published as c.1643G>A & p.(C548Y); coordinates in the table have been updated to a recent reference genome and / or transcript. 2014 25040606
99 OMIA:000437-9615 dog Boxer (Dog) Haemophilia A F8 missense Naturally occurring variant yes CanFam3.1 X g.122981181G>C c.1469C>G p.(P490R) NM_001003212.1; NP_001003212.1; published as c.1412C>G & p.(P471R); coordinates in the table have been updated to a recent reference genome and/ or transcript 2014 25040606
272 OMIA:000437-9615 dog German Shepherd Dog (Dog) Haemophilia A F8 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 X g.123043081C>T c.98G>A p.(W33*) 2011 21949058 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
621 OMIA:000437-9940 sheep Weißes Alpenschaf, Switzerland (Sheep) Haemophilia A F8 delins, small (<=20) Naturally occurring variant yes Oar_rambouillet_v1.0 X g.86301507_86301516delinsTAATTAATACC c.3108_3117delinsGGTATTAATTA The 11 bp region in exon 14 that differed between the wild-type and the hemophiliac introduced a premature stop codon 2010 19943872 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. 210906 After checking the cDNA sequence in Fig. 3 of the paper, FN concluded that the 10bp deletion starts at c.3108 and ends at c.3117 and that the 11bp inserted sequence is GGTATTAATTA. Thus the HGVS-consistent notation is c.3108_3117delinsGGTATTAATTA, instead of c.3107del10ins11.
1284 OMIA:000437-9615 dog Rhodesian Ridgeback (Dog) Haemophilia A F8 insertion, gross (>20) Naturally occurring variant yes UU_Cfam_GSD_1.0 X g.124073876_124073877insN[221] c.4824_4825insN[221] NM_001003212.1; published as c.4824_25ins221, genomic coordinates published as chrX: 1240738676_77. After review of the position in the reference genome on the 17/7/2023 the genomic coordinates have been updated to g.124073876_124073877insN[221] in this table. 2021 33494213
1588 OMIA:000437-9615 dog Labrador Retriever (Dog) Haemophilia A F8 deletion, small (<=20) Naturally occurring variant yes UU_Cfam_GSD_1.0 X g.124075777_124075778del c.2923_2924del p.(E975Kfs*8) NM_001003212.1; NP_001003212 2023 37438956
636 OMIA:000438-9615 dog Labrador Retriever (Dog) Haemophilia B F9 deletion, gross (>20) Naturally occurring variant yes X a deletion of the entire gene 1997 9394892
637 OMIA:000438-9615 dog obsolete Pit Bull Terrier (Dog) Haemophilia B F9 deletion, gross (>20) Naturally occurring variant yes X Gu et al. (1999): "A large deletion mutation was found in 1 breed variant, spanning the entire 5' region of the factor IX gene extending to exon 6". 1999 10544912 Following Table 3 from Kuder et al. (2021), the breed for this variant has been changed to Pit Bull Terrier. (18th October 2021)
1039 OMIA:000438-9615 dog Hovawart (Dog) Haemophilia B F9 regulatory Naturally occurring variant yes CanFam3.1 X g.109501492del c.-73del NM_001003323.2; Brenig et al. (2019): NC_006621.3:g.109501492delC; "The deletion is located 73 bp upstream of the F9 start codon in the conserved overlapping DNA binding sites of hepatocyte nuclear factor 4alpha and androgen receptor." 2019 30846504
705 OMIA:000438-9615 dog German Wirehaired Pointer (Dog) Haemophilia B F9 insertion, gross (>20) Naturally occurring variant yes CanFam3.1 X g.109521130_109521131insN[(1500)] NM_001003323.2; published as "insert consists of a 5' truncated canine Line-1 followed by an approximately 200-bp 3' poly (A) tract, flanked by a 15-bp direct repeat"; g. coordinate of insertion obtained from Brenig et al. (2019) 2003 14722728 CanFam3.1 coordinates copied from Table 3 of Kuder et al. (2021) (18 Oct 2021)
467 OMIA:000438-9615 dog Lhasa Apso (Dog) Haemophilia B F9 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 X g.109521356_109521361delinsT c.548_553delinsT p.(R183Lfs*3) NM_001003323.2; NP_001003323.1; published as "a deletion including nucleotides 772-776 and a C-->T transition at nucleotide 777", coordinates in the table have been updated to a recent reference genome and / or transcript and to HGVS nomenclature 1996 8896410 CanFam3.1 coordinates copied from Table 3 of Kuder et al. (2021) (18 Oct 2021)
47 OMIA:000438-9615 dog Rhodesian Ridgeback (Dog) Haemophilia B F9 missense Naturally occurring variant yes CanFam3.1 X g.109530868G>A c.731G>A p.(G244E) NM_001003323.2; NP_001003323.1; published as p.(G244E) by Mischke et al. (2011), g. and p. coordinates were copied on the 18th October 2021 from Table 3 of Kuder et al. (2021) (relating to NP_001003323.1 ) as g.109530847G>A and p.(G237E). These g. and p. positions were incorrect. After review of Figure 1 published by Mischke et al. (2011) it was confirmed that the published p. coordinates are consistent with NM_001003323.2:c.731G>A and NP_001003323.1:p.(G244E). The g. coordinates have been updated to a recent reference genome (5th April 2022) 2011 20303304 Thank you to Agustín Arasanz for identifying that the coordinates published by Kuder et al. (2021) were inconsistent with the originally published information by Mischke et al. (2011) (5th April 2022).
1363 OMIA:000438-9615 dog Newfoundland (Dog) Haemophilia B F9 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 X g.109531586_109531587insA c.821_822insA p.(N274Kfs*23) NM_001003323.2; NP_001003323.1 2021 34680886
704 OMIA:000438-9615 dog Airedale Terrier (Dog) Haemophilia B F9 insertion, gross (>20) Naturally occurring variant yes CanFam3.1 X g.109532012_109532013insN[(5000)] c.1247_1248insN[(5000)] NM_001003323.2; Gu et al. (1999): "An approximately 5 kb insertion disrupted exon 8 ... associated with alternative splicing between a donor site 5' and acceptor site 3' to the normal exon 8 splice junction, with introduction of a new stop codon. The resultant transcript lacked most of the factor IX catalytic domain and 3' untranslated region." 1999 10544912 CanFam3.1 coordinates copied from Table 3 of Kuder et al. (2021) (18 Oct 2021)
46 OMIA:000438-9615 dog Cairn Terrier (Dog) Haemophilia B F9 missense Naturally occurring variant yes CanFam3.1 X g.109532018G>A c.1253G>A p.(G418E) NM_001003323.2; NP_001003323.1, published as p.(G379E) by Evans et al. (1989), coordinates in the table have been updated to a recent reference genome and / or transcript 1989 2481310 c. and p. coordinates updated from Kuder et al. (2021)
127 OMIA:000438-9685 domestic cat Domestic Longhair Haemophilia B F9 missense Naturally occurring variant yes Felis_catus_9.0 X g.117091961G>A c.383G>A p.(C128Y) NM_001009377.3; NP_001009377.1; published as p.(C82Y); coordinates in the table have been updated to a recent reference genome and / or transcript 2005 15822564 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
310 OMIA:000438-9685 domestic cat Haemophilia B F9 nonsense (stop-gain) Naturally occurring variant yes Felis_catus_9.0 X g.117111577C>T c.1150C>T p.(R384*) NM_001009377.3; NP_001009377.1; published as p.(R338*); coordinates in the table have been updated to a recent reference genome and / or transcript 2005 15822564 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1360 OMIA:002450-9913 taurine cattle Chianina (Cattle) Ichthyosis congenita FA2H insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 18 g.2205625_2205626insG c.9dupC p.(A4Rfs*142) NM_001192455.1; NP_001179384.1 2021 34599683
752 OMIA:002032-9615 dog Border Collie (Dog) Mixed Breed (Dog) Neuropathy, sensory FAM134B inversion Naturally occurring variant yes CanFam3.1 4 g.80439639_86910352inv "6.47 Mb inversion was identified with breakpoints in intron 3 of FAM134B (chr4:86,910,352) and in an upstream intergenic region (chr4:80,439,639) ... … Analysis of RNAseq data revealed FAM134B was majorly disrupted by the inversion, with novel exons occurring 3′ of the final normally transcribed exon before the inversion, due to cryptic splicing." 2016 27527794
1342 OMIA:002032-9615 dog Mixed Breed (Dog) Neuropathy, sensory FAM134B missense Naturally occurring variant yes CanFam3.1 4 g.86916562C>T c.656C>T p.(P219L) NM_001314111.1; NP_001301040.1 2021 34387380
925 OMIA:001918-9615 dog Tibetan Spaniel (Dog) Tibetan Terrier (Dog) Progressive retinal atrophy, type 3, FAM161A-related FAM161A insertion, gross (>20) Naturally occurring variant yes CanFam3.1 10 g.61822372_61822373insN[(230)] A ~230bp insertion containing a 132bp short interspersed nuclear element (SINE), near the splice acceptor site of exon 5 CanFam2.0 coordinate published as g.64974130 2014 24705771
1183 OMIA:002259-9913 taurine cattle Montbéliarde (Cattle) de novo mutation in an AI sire FAM189A1 missense Naturally occurring variant yes ARS-UCD1.2 21 g.28112913T>C p.(N192S) Bourneuf et al. (2017) detected FAM189A1 g.28644665T>C; p.N192S as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Montbéliarde AI bull. No information was provided on the descendants of this bull. rs5334475108 2017 28904385
102 OMIA:002015-9615 dog Border Collie (Dog) Dental hypomineralization FAM20C missense Naturally occurring variant yes CanFam3.1 6 g.16452327G>A c.899C>T p.(A300V) 2016 27187611 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
89 OMIA:001327-9615 dog Irish Terrier (Dog) Kromfohrlander (Dog) Hyperkeratosis, palmoplantar FAM83G missense Naturally occurring variant yes CanFam3.1 5 g.41055619G>C c.155G>C p.(R52P) 2014 24832243 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1511 OMIA:002600-9986 rabbit New Zealand White (Rabbit) Amelogenesis imperfecta FAM83H deletion, gross (>20) Genome-editing (CRISPR-Cas9) yes large deletion of more then 900bp in exon 5 2022 36300761
460 OMIA:001683-9615 dog Cavalier King Charles Spaniel (Dog) Congenital keratoconjunctivitis sicca and ichthyosiform dermatosis FAM83H deletion, small (<=20) Naturally occurring variant yes CanFam3.1 13 g.37328057del c.977del p.(P326Hfs*258) NM_001289427.1; NP_001276356.1; genomic position in accordance with HGVS 3'-rule 2012 22253609 Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
683 OMIA:002683-9615 dog Basenji (Dog) Fanconi syndrome FAN1 deletion, gross (>20) Naturally occurring variant yes 3 "317 bp of exon 14 were deleted starting at the second exon14 nucleotide and extending into the 3' untranslated region of FAN1" 2011 Reference not in PubMed; see OMIA 002683-9615 for reference details
646 OMIA:000151-9913 taurine cattle Holstein (black and white) (Cattle) Brachyspina FANCI deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 21 g.20773899_20777226del p.(V877Lfs*27) 2012 22952632 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
613 OMIA:002064-9685 domestic cat British Shorthair (Cat) Autoimmune lymphoproliferative syndrome FASLG duplication Naturally occurring variant yes Felis_catus_9.0 F1 g.16871916dup c.418dup p.(R140Kfs*37) NM_001009352.1; NP_001009352.1; published as c.413_414insA "insertion of an adenine at position 14,607,400 [Felis_Catus_6.2]" (Aberdein et al., 2017); changed in this table to a recent reference genome and HGVS nomenclature 2017 27770190
201 OMIA:000628-9913 taurine cattle Limousin (Cattle) Marfan syndrome FBN1 missense Naturally occurring variant yes ARS-UCD1.2 10 g.61831200G>A c.3598G>A p.(E1200K) rs5334475103 2005 15776436 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
377 OMIA:000628-9913 taurine cattle Japanese Black, Japan (Cattle) Marfan syndrome FBN1 splicing Naturally occurring variant yes ARS-UCD1.2 10 g.61917867G>A c.8227-1G>A rs5334475078 2012 22221020 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
1402 OMIA:000628-9823 pig Marfan syndrome FBN1 deletion, small (<=20) Genome-editing (ZFN) yes Sscrofa11.1 1 g.123246159del p.(E433Nfs98*) 2016 27074716
910 OMIA:000836-9913 taurine cattle Blonde d'Aquitaine (Cattle) Limousin (Cattle) Protoporphyria FECH extension (stop-lost) Naturally occurring variant yes ARS-UCD1.2 24 g.56787697C>A c.1250G>T p.(*417Lext*27) rs5334474668 1998 9784594 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
576 OMIA:001525-9615 dog German Shepherd Dog (Dog) Leukocyte adhesion deficiency, type III FERMT3 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 18 g.52835932_52835933insGGCAGCCGTCTT c.1349_1350insAAGACGGCTGCC p.(L450_A451insRRLP) XM_038425194.1; XP_038281122.1; 12-base pair insertion 2010 20126836
1336 OMIA:002382-9615 dog Dachshund, Miniature Wire-Haired (Dog) Afibrinogenaemia FGA deletion, small (<=20) Naturally occurring variant yes CanFam3.1 15 g.52240694del c.1665delT p.(I555Mfs*33) Transcript XM_532697.6 / ENSCAFT00000043702.3 rs1152388481 rs1152388481 2021 34356081
1529 OMIA:002625-9913 taurine cattle Japanese Black, Japan (Cattle) Skeletal dysplasia, FGD3 related FGD3 delins, small (<=20) Naturally occurring variant yes UMD_3.1.1 8 g.85826989_85826990delinsTG p.(H171C) 2015 26306008
1326 OMIA:002374-9913 taurine cattle Holstein Friesian (Cattle) Jersey (Cattle) Charcot Marie Tooth disease FGD4 splicing Naturally occurring variant yes ARS-UCD1.2 5 g.77262490C>T c.1671+1G>A Splice donor mutation based on XM_005206883.3 rs5334475069 2021 34045765
941 OMIA:001723-9940 sheep Romney Marsh (Sheep) Familial episodic ataxia FGF14 nonsense (stop-gain) Naturally occurring variant yes Oar_rambouillet_v1.0 10 g.88095843G>A c.46C>T p.(Q16*) Oar_v3.1 position is g.77593415 2017 29253853 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
327 OMIA:000889-9031 chicken Israeli experimental line, Israel (Chicken) Storrs Connecticut scaleless low line, United States of America (Chicken) UC Davis line, United States of America (Chicken) Scaleless FGF20 nonsense (stop-gain) Naturally occurring variant yes GRCg6a 4 g.63270401A>T c.535A>T p.(R179*) 2012 22712610 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
929 OMIA:000272-9615 dog Rhodesian Ridgeback (Dog) Thai Ridgeback (Dog) Ridge & dermoid sinus FGF3 Ridge allele duplication Naturally occurring variant yes CanFam3.1 18 g.48372578_48505893dup133316 A large ~133,000 bp duplication on chromosome 18, encompassing three FGF genes (FGF3, FGF4, FGF19) and another gene ORAOV1. There is an additional single T inserted between the two copies of the duplication. This is not indicated in the genomic variant designation. 2007 17906623
694 OMIA:002542-9615 dog Basset Hound (Dog) Cairn Terrier (Dog) Cardigan Welsh Corgi (Dog) Dachshund (Dog) Dandie Dinmont Terrier (Dog) Lancashire Heeler (Dog) Norwich Terrier (Dog) Pekingese (Dog) Pembroke Welsh Corgi (Dog) Petit Basset Griffon Vendeen (Dog) Shih Tzu (Dog) Skye Terrier (Dog) Swedish Vallhund (Dog) Tibetan Spaniel (Dog) West Highland White Terrier (Dog) Chondrodysplasia FGF4 retrogene CFA18 FGF4L1 insertion, gross (>20) Naturally occurring variant yes 18 a 5kb insertion containing a FGF4 retrogene, i.e. a processed pseudogene of FGF4: The insertion containing the FGF4 retrogene starts at 23,431,136 on CFA18, which is 25Mb away from the complete (original) FGF4 gene, which is located at CFA18 48413479-48415205 2009 19608863
855 OMIA:000157-9615 dog American Cocker Spaniel (Dog) Basset Hound (Dog) Beagle (Dog) Cardigan Welsh Corgi (Dog) Chesapeake Bay Retriever (Dog) Chihuahua (Dog) Coton de Tulear (Dog) Dachshund (Dog) English Springer Spaniel (Dog) French Bulldog (Dog) Nova Scotia Duck Tolling Retriever (Dog) Intervertebral disc disease, type I FGF4 retrogene in CFA12 FGF4L2 insertion, gross (>20) Naturally occurring variant yes CanFam3.1 12 " the insertion on CFA12 is 3,209 bp long (GenBank accession no. MF040221) and includes parental FGF4 cDNA (i.e., FGF4 exons spliced without introns) . . . ." 200922: g. info moved here (g.33710178_33710179insMF040221) until it can be standardised 2017 29073074
853 OMIA:002133-9615 dog Nova Scotia Duck Tolling Retriever (Dog) Skeletal dysplasia, FGF4-retrogene-related FGF4 retrogene on CFA12 FGF4L2 insertion, gross (>20) Naturally occurring variant yes CanFam3.1 12 " the insertion on CFA12 is 3,209 bp long (GenBank accession no. MF040221) and includes parental FGF4 cDNA (i.e., FGF4 exons spliced without introns) . . . ." 200922: g. info moved here (g.33710178_33710179insMF040221) until can be standardised 2017 29073074
983 OMIA:000439-9844 llama Long hair FGF5 complex rearrangement Naturally occurring variant no A "a single base deletion (c.348delA), [and] a 12-bp insertion (c.351_352insCATATAACATAG)" that comprise a single likely causal variant 2017 29024003
347 OMIA:000439-9793 ass (donkey) Hair, long FGF5 nonsense (stop-gain) Naturally occurring variant no c.245G>A 2014 25927731
982 OMIA:000439-10141 domestic guinea pig Long hair Fgf5 nonsense (stop-gain) Naturally occurring variant no c.403C>T p.(R135*) "The data were submitted to the European Variation Archive (accession no. PRJEB24997)" 2018 29603294
560 OMIA:000439-9793 ass (donkey) Hair, long FGF5 deletion, small (<=20) Naturally occurring variant no c.433_434delAT 2014 25927731
984 OMIA:000439-9844 llama Long hair FGF5 nonsense (stop-gain) Naturally occurring variant no c.499C>T 2017 29024003
559 OMIA:000439-10036 golden hamster Hair, long Fgf5 deletion, small (<=20) Naturally occurring variant no c.546delG p.(R184GfsX6) 2015 26481120
1343 OMIA:000439-9838 Arabian camel Long hair FGF5 missense Naturally occurring variant no CamDro3 2 g.76625546C>T c.779C>T p.(P260L) cDNA and protein positions based on transcript ENSCDRT00005003721.1 2021 34432312
48 OMIA:000439-9615 dog Afghan Hound (Dog) Border Collie (Dog) Cocker Spaniel (Dog) Collie (Dog) Dachshund (Dog) German Shepherd Dog (Dog) Golden Retriever (Dog) obsolete Corgi (Dog) Pomeranian (Dog) Samoyed (Dog) Long hair FGF5 missense Naturally occurring variant no CanFam3.1 32 g.4509367G>T c.284G>T p.(C95F) ROS_Cfam_1.0:g.4533621G>T ENSCAFT00845031580.1:c.290G>T ENSCAFP00845024720.1:p.Cys97Phe rs851828354 rs851828354 2006 16879338 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
418 OMIA:000439-9615 dog Afghan Hound (Dog) Long hair FGF5 splicing Naturally occurring variant no CanFam3.1 32 g.4517257T>A c.368-11T>A ROS_Cfam_1.0:g.4541511T>A ENSCAFT00845031580.1:c.368-11T>A rs397511324 rs397511324 2013 23384345 30 Dec 2020: g. coordinate corrected: thanks to Angelica K Kallenberg
952 OMIA:000439-9615 dog Eurasier (Dog) Long hair FGF5 deletion, small (<=20) Naturally occurring variant no CanFam3.1 32 g.4528617_4528632del c.556_571del p.(A186Tfs*71) NM_001048129.1; NP_001041594.1; published as c.556_571del16; p.(A186Tfs*69) rs397509816 rs397509816 2013 23384345 Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
950 OMIA:000439-9615 dog Afghan Hound (Dog) Eurasier (Dog) Long hair FGF5 duplication Naturally occurring variant no CanFam3.1 32 g.4528620_4528621dup c.559_560dup p.(R188Afs*75) NM_001048129.1; NP_001041594.1; published as c.559_560dupGG and p.(R188Afs*73) rs397512451 2013 23384345 Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
104 OMIA:000439-9615 dog Akita (Dog) Samoyed (Dog) Long hair FGF5 missense Naturally occurring variant no CanFam3.1 32 g.4528639C>T c.578C>T p.(A193V) NM_001048129.1; NP_001041594.1 2013 23384345 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1368 OMIA:000439-9685 domestic cat Maine Coon (Cat) Long hair FGF5 l^MCC2 (M5) missense Naturally occurring variant unknown Felis_catus_9.0 B1 g.142165850C>T c.577G>A p.(A193T) NM_001114546.1; NP_001108018.1 2021 34599367
130 OMIA:000439-9685 domestic cat Long hair FGF5 l (M4) missense Naturally occurring variant no Felis_catus_9.0 B1 g.142165952T>G c.475A>C p.(T159P) NM_001114546.1; NP_001108018.1; published as c.474delT; variant can be in a haplotype with c.474del rs5334475161 2007 17433015 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
498 OMIA:000439-9685 domestic cat Maine Coon (Cat) Ragdoll (Cat) Long hair FGF5 l^MCC1 (M3) deletion, small (<=20) Naturally occurring variant no Felis_catus_9.0 B1 g.142165953del c.474del NM_001114546.1; NP_001108018.1; published as c.474delT; variant can be in a haplotype with c.475A>C resulting in two different predicted effects on the protein 2007 17433015 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
311 OMIA:000439-9685 domestic cat Norwegian Forest Cat (Cat) Long hair FGF5 l^NFC (M2) nonsense (stop-gain) Naturally occurring variant no Felis_catus_9.0 B1 g.142177919G>A c.406C>T p.(R136*) NM_001114546.1; NP_001108018.1 rs5334475123 2007 17767004 The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
595 OMIA:000439-9685 domestic cat Ragdoll (Cat) Long hair FGF5 l^Rag (M1) insertion, small (<=20) Naturally occurring variant no Felis_catus_9.0 B1 g.142185646_142185647insA c.356_357insT p.(M119Ifs) NM_001114546.1; NP_001108018.1; published as c.ins356T 2007 17767004 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1575 OMIA:000439-9986 rabbit Angora (Rabbit) Hair, long FGF5 missense Naturally occurring variant no OryCun2.0 15 g.70103616A>G c.571T>C p.(L191S) XM_008267686.2; XP_008265908.1; published as c.T19234C in exon 2; coordinates in this table are based on a recent reference genome 2023 37268908
787 OMIA:002090-9913 taurine cattle Holstein (black and white) (Cattle) Facial dysplasia syndrome FGFR2 missense Naturally occurring variant yes ARS-UCD1.2 26 g.41489034C>A c.927G>T p.(W309C) rs5334475009 2017 28768473 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1179 OMIA:001703-9913 taurine cattle Holstein (black and white) (Cattle) Chondrodysplasia, disproportionate FGFR3 extension (stop-lost) Naturally occurring variant yes ARS-UCD1.2 6 g.116767863C>A c.2408G>T p.(*803Lext*93) NM_174318.3: c.2408G>T; [XM_024992994.1: p.(Ter803Leuext*93) rs5334474953 2020 32239744
225 OMIA:001703-9940 sheep Suffolk (Sheep) Chondrodysplasia, Spider lamb FGFR3 missense Naturally occurring variant yes Oar_rambouillet_v1.0 6 g.128784747A>T c.1719T>A p.(V700E) 2006 16441300 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
77 OMIA:001335-9615 dog German Shepherd Dog (Dog) Renal cystadenocarcinoma and nodular dermatofibrosis FLCN missense Naturally occurring variant yes CanFam3.1 5 g.42186445A>G c.764A>G p.(H255R) rs1152388411 rs1152388411 2003 14532326 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
860 OMIA:001360-9031 chicken Beijing You, China (Chicken) Commercial strain- layer- ISA Brown (Chicken) Commercial strain- layer- Lohmann Brown (Chicken) Marans (Chicken) Rhode Island Red (Chicken) TETRA strain, United States of America (Chicken) Transylvanian Naked Neck (Chicken) Trimethylaminuria (fishy taint) FMO3 missense Naturally occurring variant yes 8 c.1034A>T p.(T329S) 2005 15916878
304 OMIA:001360-9913 taurine cattle Swedish Red and White (Cattle) Trimethylaminuria (fishy taint) FMO3 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 16 g.38666821C>T c.712C>T p.(R238*) rs797790546 rs797790546 2002 12466292 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; rsID gleaned from or confirmed by Table 1 of  Sharma et al. (2017) Animal Genetics 48(3):369-370
531 OMIA:000526-9615 dog Weimaraner (Dog) Hypomyelination of the central nervous system FNIP2 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 15 g.55928287del c.1078del p.(I360Lfs*3) XM_005629382.3; XP_005629439.1; published as CanFam2:58974928delA, XM_532705:c.880delA and p.(I294fs*296) - coordinates in the table have been updated to a recent reference genome and / or transcript and HGVS nomenclature 2014 24272703
571 OMIA:000323-9615 dog Chinese Crested (Dog) Peruvian Hairless Dog (Dog) Xoloitzcuintli (Dog) Ectodermal dysplasia FOXI3 insertion, small (<=20) Naturally occurring variant yes ROS_Cfam_1.0 17 g.38764875_38764881dup c.57_63dup p.(A23Rfs*219) NM_001135646.1; NP_001129118.1 2008 18787161
1319 OMIA:001949-9685 domestic cat Birman (Cat) Hypotrichosis, with short life expectancy FOXN1 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 E1 g.18255880_18255883del c.1030_1033del p.L344Gfs XM_019817475.2; XP_019673034.1; published as c.1030_1033delCTGT; predicted to cause a frameshift leading to a premature stop codon at position 547 2015 25781316 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
461 OMIA:000396-9615 dog English Springer Spaniel (Dog) Fucosidosis, alpha FUCA1 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 2 g.75665866_75665879del c.379_392del p.(A127Vfs*26) NM_001003250.1; NP_001003250.1; a 14-bp deletion at the 3' end of exon 1 1996 8730282
178 OMIA:000862-9823 pig Resistance to oedema disease (F18 receptor) FUT1 missense Naturally occurring variant no Sscrofa11.1 6 g.54079560T>C c.304A>G p.(T103A) The variant was initially described as c.307G>A and p.A103T by Vögeli et al. 1997. VEP analysis identified the variant as c.304A>G p.T102A in transcript ENSSSCT00000051297.2 rs335979375 rs335979375 2000 11132149
1436 OMIA:002536-9615 dog Wirehaired Pointing Griffon (Dog) Juvenile cataract FYCO1 deletion, small (<=20) Naturally occurring variant yes UU_Cfam_GSD_1.0 20 g.42952995del c.2024delG p.(S675Tfs*5) XM_038566669.1; XP_038422597.1 2022 35205377
1299 OMIA:002318-9913 taurine cattle Montbéliarde (Cattle) coat colour, dilution (milca) FZD7 missense Naturally occurring variant no ARS-UCD1.2 2 g.90572569G>C c.1241G>C p.(G414A) CDS position in transcript ENSBTAT00000002946.6 based on ENSEMBL Variant Effect Predictor rs5334475107 2021 33686687
1361 OMIA:000418-9615 dog German Pinscher (Dog) Glycogen storage disease Ia G6PC insertion, gross (>20) Naturally occurring variant yes CanFam3.1 9 g.20134857_20134858insN[76] c.634_635insN[76] XM_038676372.1; insertion of 60 consecutive adenines and an additional 16 bp duplication of the integration site (Christen et al., 2021) 2021 34610166
44 OMIA:000418-9615 dog Maltese (Dog) Glycogen storage disease Ia G6PC missense Naturally occurring variant yes CanFam3.1 9 g.20138777C>G c.363G>C p.(M121I) NM_001002993.2; NP_001002993.2; published as c.450G>C; coordinates in the table have been updated to a recent reference genome and / or transcript 1997 9259982 Genomic coordinates in CanFam3.1 provided by Robert Kuhn
488 OMIA:000419-9913 taurine cattle Shorthorn (Cattle) Glycogen storage disease II GAA E18 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.52484973_52484974del c.2454_2455del p.(T819R) 2000 10723725 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
294 OMIA:000419-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Brahman (Cattle) Glycogen storage disease II GAA E13 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 19 g.52488949G>A c1783C>T p.(R595*) UMD3.1 position is g.53105979C>T; variant initially identified in Brahman cattle and later reported in additional breeds:PMID:34779908. rs5334474904 2000 10723725 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
487 OMIA:000419-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Brahman (Cattle) Droughtmaster (Cattle) Glycogen storage disease II GAA E7 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.52492405_52492406del c.1057_1058del p.(Y353L) UMD3.1 position is g.53109436_53109437del; variant initially identified in Brahman cattle and later reported in additional breeds: PMID:28444756, PMID:34779908. 2000 10723725 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
270 OMIA:000419-9615 dog Finnish Lapphund (Dog) Swedish Lapphund (Dog) Glycogen storage disease II GAA nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 9 g.1603730C>T c.2237G>A p.(W746*) 2013 23457621 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1544 OMIA:000419-9685 domestic cat Domestic Shorthair Glycogen Storage Disease Type II (Pompe Disease) GAA missense Naturally occurring variant yes Felis_catus_9.0 E1 g.60946737G>A c.1799G>A p.(R600H) XM_006940651.4; XP_006940713.4 2023 37106898 The OMIA curators thank Osamu Yamato for providing the variant information not included in Rakib et al. (2023); 17 April 2023.
517 OMIA:000578-9544 Rhesus monkey Krabbe disease GALC deletion, small (<=20) Naturally occurring variant yes c.387delAC 1997 9192853
953 OMIA:000578-9615 dog Irish Setter (Dog) Krabbe disease GALC insertion, gross (>20) Naturally occurring variant yes CanFam3.1 8 g.59294611_59294612insN[78] c.790_791insN[78] NM_001003238.1; NP_001003238.1; the 78 bp insertion includes a 16-bp insertion site duplication and a 62 bp U4 snRNA-derived sequence; the downstream reading frame is preserved (for sequence details see McGraw et al., 2006) 2006 16490723
51 OMIA:000578-9615 dog Cairn Terrier (Dog) West Highland White Terrier (Dog) Krabbe disease GALC missense Naturally occurring variant yes CanFam3.1 8 g.59311801T>G c.473A>C p.(Y158S) NM_001003238.1; NP_001003238.1 1996 8661004 Genomic coordinates in CanFam3.1 provided by Robert Kuhn
1607 OMIA:000578-9615 dog Mixed Breed (Dog) Krabbe disease GALC missense Naturally occurring variant yes canFam6 8 g.58893972G>A c.149C>T p.(A50V) NM_001003238.1; NP_001003238.1; published as NC_006590.4:g.58893972G>A 2023 37593836
1327 OMIA:002375-9913 taurine cattle Holstein Friesian (Cattle) Jersey (Cattle) Congenital disorder of glycosylation GALNT2 splicing Naturally occurring variant yes ARS-UCD1.2 28 g.2281801G>A c.1561-1G>A Splice acceptor mutation based on NM_001193103.1. rs5334474933 2021 34045765
182 OMIA:001826-9913 taurine cattle Holstein (black and white) (Cattle) Abortion due to haplotype HH4 GART missense Naturally occurring variant yes ARS-UCD1.2 1 g.1997582A>C c.869A>C p.(N290T) rs465495560 rs465495560 2013 23762392 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1501 OMIA:002559-9913 taurine cattle Holstein Friesian (Cattle) Persistent truncus arteriosus GATA6 nonsense (stop-gain) Naturally occurring variant unknown ARS-UCD1.2 24 g.34187181T>A c.1249A>T p.K417X ENSBTAT00000007537.6 2022 36333145
231 OMIA:002621-9940 sheep South Down (Sheep) Gaucher disease, type GBA missense Naturally occurring variant yes Oar_rambouillet_v1.0 1 g.111561271C>T c.1142G>A p.(C381Y) Oar_v3.1 position is g.103978212C>T rs429928390 2017 29023809 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
322 OMIA:000420-9796 horse American Paint (Horse) Quarter Horse (Horse) Glycogen storage disease IV GBE1 nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 26 g.8667651C>A c.102C>A p.(Y34*) NM_001081940.2; NP_001075409.1 rs3437568674 rs3437568674 2004 15366377 The genomic position in EquCab3.0 was provided by Elizabeth Clark, working under the guidance of Professor Ernie Bailey in April 2022
742 OMIA:000420-9685 domestic cat Norwegian Forest Cat (Cat) Glycogen storage disease IV GBE1 delins, gross (>20) Naturally occurring variant yes Felis_catus_9.0 C2 g.34744479_34781895delinsN[334] published as "334 bp insertion at the site of a 6.2 kb deletion that extends from intron 11 to intron 12 (g. IVS11+1552_IVS12-1339 del6.2kb ins334 bp), removing exon 12" 2007 17257876 Genomic position in Felis_catus_9.0 is based on information provided by Leslie Lyons and Reuben Buckley.
744 OMIA:001245-9031 chicken Rhode Island Red (Chicken) Retinal degeneration I GC1 complex rearrangement Naturally occurring variant yes 26 This allele is characterised by an 81bp insertion adjacent to a 642bp deletion 1998 9448321
1494 OMIA:002579-9913 taurine cattle Irish Moiled (Cattle) Perinatal mortality syndrome, GCK-related GCK splicing Naturally occurring variant yes ARS-UCD1.2 4 g.77173487A>T 2022 36105082
721 OMIA:000701-9031 chicken Naked neck GDF7 insertion, gross (>20) Naturally occurring variant yes 3 a large insertion approximately 260kb downstream from the BMP12 gene (now known as GFD7), increasing the expression of this gene in embryonic skin 2011 21423653
1221 OMIA:002366-9685 domestic cat Toyger (Cat) Holoprosencephaly GDF7 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 A3 g.127002233_127002239del c.221_227del p.(R74Pfs*17) XM_023252074.1; XP_023107842.1; published as "a 7 bp deletion in the coding region of GDF7 (c.221_227delGCCGCGC [p.Arg74Profs*17]) at the position A3:127002233 (ENSFCAT00000063603)" (Yu et al., 2020) rs5334475136 2020 32575532
239 OMIA:002362-9940 sheep Wicklow Cheviot (Sheep) Fecundity, Thoka, FecG GDF9 FecG(T) missense Naturally occurring variant no Oar_rambouillet_v1.0 5 g.46545130T>G c.1279A>C p.(S427R) Oar_v3.1 position is g.41841117T>G; protein and cDNA positions are based on NP_001136360.2 and NM_001142888.2, respectively 2009 19713444 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
242 OMIA:002362-9940 sheep Belclare (Sheep) Cambridge (Sheep) Fecundity, High fertility, FecG GDF9 FecG(H) missense Naturally occurring variant no Oar_rambouillet_v1.0 5 g.46545225G>A c.1184C>T p.(S395F) Oar_v3.1 position is g.41841212G>A; protein and cDNA position based on NP_001136360.2 and NM_001142888.2 respectively 2004 14627550 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
243 OMIA:002362-9940 sheep Gammelnorsk spaelsau, Norway (Sheep) Fecundity, Norwegian White Sheep GDF9 FecG(F) missense Naturally occurring variant no Oar_rambouillet_v1.0 5 g.46545298C>T c.1111G>A p.(V371M) Oar_v3.1 position is g.41841285C>T, protein and cDNA positions based on NP_001136360.2 and NM_001142888.2, respectively rs403536877 2013 23280002 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
240 OMIA:002362-9940 sheep Pelibuey, Mexico (Sheep) Santa Ines, Brazil (Sheep) Fecundity, Embrapa, FecG GDF9 FecG(E) missense Naturally occurring variant no Oar_rambouillet_v1.0 5 g.46545375A>C c.1034T>G p.(F345C) Oar_v3.1 position is g.41841362T>G; protein and cDNA position based on NP_001136360.2 and NM_001142888.2, respectively rs1092755620 2011 20528846 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1407 OMIA:002362-9940 sheep Icelandic (Sheep) Fecundity, Loa, FecG GDF9 FecG(L) deletion, small (<=20) Naturally occurring variant no Oar_rambouillet_v1.0 5 g.46545396_46545399del p.(N337Rfs*26) Oar_v3.1 position is g.41841383_41841386del 2021 34967038
246 OMIA:002362-9940 sheep Ile-De-France (Sheep) Fecundity, Vacaria, FecG GDF9 FecG(V) missense Naturally occurring variant no Oar_rambouillet_v1.0 5 g.46545466G>A c.943C>T p.(R315C) Oar_v3.1 position is g.41841453G>A; protein and cDNA positions based on NP_001136360.2 and NM_001142888.2, respectively 2014 25039891 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
444 OMIA:001514-9615 dog English Pointer (Dog) English Springer Spaniel (Dog) French Spaniel (Dog) German Shorthaired Pointer (Dog) Acral mutilation syndrome GDNF regulatory Naturally occurring variant yes CanFam3.1 4 g.70875561C>T "This variant, located 90 kb upstream of the GDNF gene, a highly relevant neurotrophic factor candidate gene, lies in [the last exon of] a long intergenic non-coding RNAs (lincRNA), GDNF-AS." 2016 28033318
114 OMIA:001208-9615 dog Labrador Retriever (Dog) Alexander disease GFAP missense Naturally occurring variant yes CanFam3.1 9 g.18572769G>A c.719G>A p.(R240H) rs850986067 rs850986067 2016 26486469 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
293 OMIA:001442-9913 taurine cattle Japanese Black, Japan (Cattle) Forelimb-girdle muscular anomaly GFRA1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 26 g.36627244G>A c.430C>T p.(Q144*) rs5334475112 2013 Reference not in PubMed; see OMIA 001442-9913 for reference details Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
655 OMIA:001089-9823 pig Blood group system ABO GGTA1 O deletion, gross (>20) Naturally occurring variant no 1 "the 0 allele has a large deletion between exon 7 of the A0 blood group gene and the neighbouring SURF6". 2011 21554350
190 OMIA:001473-9915 indicine cattle (zebu) Brahman (Cattle) Dwarfism, growth-hormone deficiency GH1 missense Naturally occurring variant yes c.641C>T p.(T200M) Bos indicus cDNA position based on AF034386, protein position based on AAB92549 2009 19524387 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1232 OMIA:001473-9615 dog Chihuahua (Dog) Dwarfism, growth-hormone deficiency GH1 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 9 g.11832438_11832443del c.573_578del p.(K191_D193delinsN) NM_001003168.1; NP_001003168.1; variant initially identified in Chihuahuas and later reported in additional breeds: PMID: 37582787 2020 32646299 Genomic coordinates in CanFam3.1 provided by Robert Kuhn
660 OMIA:000309-9031 chicken Connecticut (CT) strain, United States of America (Chicken) S2 line, China (Chicken) Dwarfism, sex-linked GHR deletion, gross (>20) Naturally occurring variant yes Z deletion of 1773 bp in the 3' end of the coding region of the growth hormone receptor gene 1994 7964293
677 OMIA:001920-27706 largemouth bass Abortion due to deletion in GHRH GHRH deletion, gross (>20) Naturally occurring variant yes a 66bp deletion (c.-923_-858del) in the 5' flanking region of the GHRH gene in an autosomal recessive embryonic lethal 2014 24697798
1362 OMIA:001152-9031 chicken Feather colour, melanotic GJA5 delins, gross (>20) Naturally occurring variant no GRCg6a 1 g.95256761_95256801delinsAAACTACTGCTTATTAAACTACTACTACTATTTAAGAT cis-acting regulatory mutation 2021 34607956
794 OMIA:002119-9615 dog Leonberger (Dog) Polyneuropathy (LPN2) GJA9 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 15 g.3863524_3863525del c.1107_1108delAG p.(A370Nfs*12) 2017 28841859
41 OMIA:000402-9615 dog Portuguese Water Dog (Dog) Gangliosidosis, GM1 GLB1 missense Naturally occurring variant yes CanFam3.1 23 g.3754313G>A c.179G>A p.(R60H) NM_001037641.1; NP_001032730.1; published as c.200G>A; coordinates in the table have been updated to a recent reference genome and / or transcript 2000 11032334
462 OMIA:000402-9615 dog obsolete Shiba (Dog) Shiba Inu (Dog) Gangliosidosis, GM1 GLB1 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 23 g.3796317delC c.1649delC p.(P550Rfs*50) 2002 12555949 The variant coordinates are those reported by Pervin et al. (2022) Animals 12(10), 1242.
573 OMIA:000402-9615 dog Alaskan Husky (Dog) Gangliosidosis, GM1 GLB1 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 23 g.3796356_3796374dup c.1688_1706dup p.(T570Pfs*22) NM_001037641.1; NP_001032730.1; 19 base pair duplication in exon 15. Two different aberrant mRNA transcripts are produced from the mutant allele. The protein variant designation refers to one of these transcripts that includes the mutant exon 15. In the other aberrant transcript, the mutant exon 15 is skipped and a different truncated protein is encoded. 2005 15944348
126 OMIA:000402-9685 domestic cat Korat (Cat) Siamese (Cat) Gangliosidosis, GM1 GLB1 missense Naturally occurring variant yes Felis_catus_9.0 C2 g.158932167C>G c.1448G>C p.(R483P) rs5334475143 2008 18353697 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
230 OMIA:000402-9940 sheep Romney Marsh (Sheep) Gangliosidosis, GM1 GLB1 missense Naturally occurring variant yes Oar_rambouillet_v1.0 19 g.8003247C>A c.686G>T p.(C299F) cDNA position based on ENSOART00020038844.1 2012 Reference not in PubMed; see OMIA 000402-9940 for reference details The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
302 OMIA:000689-9913 taurine cattle Polled Hereford (Cattle) Myoclonus GLRA1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 7 g.63070074G>T c.156C>A p.(Y52*) rs5334475027 2001 11178872 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1571 OMIA:000689-9615 dog Miniature Australian Shepherd Dog (Dog) Hyperekplexia GLRA1 deletion, gross (>20) Naturally occurring variant yes UU_Cfam_GSD_1.0 4 g.58338954_58338989del published as a 36-bp deletion encompassing part of the intron 1 and exon 2 (chr4:g.58,338,953); coordinates in the this table are in accordance with HGVS nomenclature 2023 37222814
496 OMIA:001427-9685 domestic cat Gangliosidosis, GM2, GM2A deficiency GM2A deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 A1 g.198114664_198114667del c.516_519del p.(V173Sfs*17) XM_003981379.5; XP_003981428.2; published as c.516_519delGGTC 2005 16200419 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
515 OMIA:001368-9031 chicken Retinopathy globe enlarged GNB3 deletion, small (<=20) Naturally occurring variant yes 1 c.D153del 2006 17065478
1035 OMIA:001248-9685 domestic cat Domestic Shorthair Mucolipidosis II GNPTAB nonsense (stop-gain) Naturally occurring variant yes Felis_catus_9.0 B4 g.124431151G>A c.2644C>T p.(Q882*) XM_003989173.5; XP_003989222.2 2018 30591066 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
265 OMIA:000665-9925 goat Mucopolysaccharidosis IIID GNS nonsense (stop-gain) Naturally occurring variant yes ARS1 5 g.48406875C>T c.304C>T p.(R102*) rs5334475114 1995 7623459 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries. Published as c.322C>T. Updated position based on ENSEMBL Variant Effect Predictor: transcript ENSCHIT00000018630.1
778 OMIA:001985-9913 taurine cattle Simmental (Cattle) Dwarfism, Fleckvieh GON4L deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 3 g.15024245del c.4286del p.(G1430Kfs*66) rs723240647 rs723240647 2016 27036302 Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 210909: to be consistent with HGVS, FN changed g.15079217delC to g.15079217del. An examination of the information for rs723240647 indicated that c.4285_4287delCCCinsCC should be changed to c.4286del
1097 OMIA:002207-9615 dog Cocker Spaniel (Dog) Bernard-Soulier syndrome, type C GP9 deletion, gross (>20) Naturally occurring variant yes CanFam3.1 20 g.3025814_3028273del c.127_*2052del XM_846924.3; Gentilini et al. (2019): "The [2460bp] deletion truncates 104 (71%) of the 146 codons of the wildtype canine reading frame." 2019 31484196
383 OMIA:000821-9685 domestic cat Primary hyperoxaluria type II (Oxalosis II) GRHPR splicing Naturally occurring variant yes Felis_catus_9.0 D4 g.60968927G>A p.(N169Kfs*46) "point mutation, G to A, . . . at the 3# splice acceptor site of intron 4" ; protein position based on XP_006939354.1 rs5334475152 2009 Reference not in PubMed; see OMIA 000821-9685 for reference details
693 OMIA:000078-9615 dog Coton de Tulear (Dog) Ataxia, cerebellar GRM1 insertion, gross (>20) Naturally occurring variant yes 1 "a 62-bp truncated retrotransposon insert in exon 8" 2011 21281350
1552 OMIA:002692-9796 horse American Saddle Horse (Horse) American Trotter (Horse) Miniature Horse (Horse) Missouri Fox Trotting Horse, United States of America (Horse) Morgan (Horse) Quarter Horse (Horse) Racking Horse (Horse) Rocky Mountain, United States of America (Horse) Spotted Saddle Horse (Horse) Tennessee Walking Horse (Horse) Night blindness, congenital stationary, GRM6-related GRM6 missense Naturally occurring variant yes EquCab3 14 g.2655618C>T c.533C>T p.(T178M) XM_001916934.4; XP_001916969.3; variant initially reported in Tennessee Walking horse and later reported in other breeds [PMID:37815029] rs1138010744 rs1138010744 2021 32654228
1536 OMIA:002646-9615 dog German Spitz (Dog) Progressive retinal atrophy GUCY2D insertion, small (<=20) Naturally occurring variant yes CanFam3.1 5 g.32849537_32849538insT c.1598_1599insT p.(S534Efs*20) NM_001003207.1; NP_001003207.1 2023 36872573
1195 OMIA:002268-9823 pig Danish Landrace (Pig) Vitamin C deficiency GULO od deletion, gross (>20) Naturally occurring variant yes 14 "This deletion includes 77 bp of exon VIII, 398 bp of intron 7 and 3.7 kbp of intron 8, which leads to a frame shift. The mutant protein is truncated to 356 amino acids, but only the first 236 amino acids are identical to the wild-type GULO protein." (Hasan et al., 2004) 2004 15112110
58 OMIA:000667-9615 dog Brazilian Terrier (Dog) Mucopolysaccharidosis VII GUSB missense Naturally occurring variant yes CanFam3.1 6 g.740428G>A c.866C>T p.(P289L) 2012 22815736 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
57 OMIA:000667-9615 dog German Shepherd Dog (Dog) Mucopolysaccharidosis VII GUSB missense Naturally occurring variant yes CanFam3.1 6 g.741429C>T c.497G>A p.(R166H) ROS_Cfam_1.0:g.546709C>T ENSCAFT00845023689.1:c.482G>A ENSCAFP00845018598.1:p.Arg161His rs1152388412 rs1152388412 1998 9521879 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
133 OMIA:000667-9685 domestic cat Mucopolysaccharidosis VII GUSB missense Naturally occurring variant yes Felis_catus_9.0 E3 g.16120173G>A c.1051G>A p.(E351K) NM_001009310.1; NP_001009310.1; published as "single G-to-A transition at nucleotide position 1074, predicting a glutamate-to-lysine substitution of amino acid residue 351 (E351K)" rs5334475137 1999 10366443 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
139 OMIA:000667-9685 domestic cat Mucopolysaccharidosis VII GUSB missense Naturally occurring variant yes Felis_catus_9.0 E3 g.[16123229T>G;16123232C>T] c.[1423T>G;1426C>T] p.(S475_R476delinsAW) NM_001009310.1; NP_001009310.1; published as c.1421T>G and c.1424C>T; coordinates in the table have been updated to a recent reference genome and / or transcript 2015 26118695 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
163 OMIA:001158-9796 horse American Paint (Horse) Appaloosa (Horse) Quarter Horse (Horse) Polysaccharide storage myopathy/Exertional rhabdomyolysis GYS1 missense Naturally occurring variant yes EquCab3.0 10 g.19203501C>T c.926G>A p.(R309H) ENSECAT00000023453.3:c.926G>A ENSECAP00000019426.2:p.Arg309His rs1150416011 rs1150416011 2008 18358695 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
924 OMIA:001374-9615 dog Labrador Retriever (Dog) Centronuclear myopathy, HACD1-related HACD1 insertion, gross (>20) Naturally occurring variant yes CanFam3.1 2 g.19371988_19371989ins[N[236];CACACAAAGGTTT] c.203_204ins[N[236];CACACAAAGGTTT] NM_001025269.1; published as insertion of a 236 bp antisense canine tRNA-like SINE (EMBL accession no. AJ876906), flanked on both sides by a 13 bp direct duplication of the insertion site; resulting in multiple splicing defects 2005 15829503
1421 OMIA:002522-9615 dog Norwegian Elkhound (Dog) Ataxia, HACE1-related HACE1 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 12 g.62282767del c.1001del p.(G334Vfs*34) ENSCAFT00000072236.1; ENSCAFP00000049888.1 2022 35061740
709 OMIA:001561-9615 dog Chinese Shar-Pei (Dog) Periodic Fever Syndrome HAS2 insertion, gross (>20) Naturally occurring variant yes 13 "several copies of a the "meatmouth" (CNV-E) duplication upstream of the HAS2 gene", variant is associated with the disease but may not be causal 2011 21437276
64 OMIA:000703-9615 dog Dachshund (Dog) Narcolepsy HCRTR2 missense Naturally occurring variant yes CanFam3.1 12 g.22517939G>A c.160G>A p.(E54K) NM_001002933.1; NP_001002933.1 2001 11282968 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
419 OMIA:000703-9615 dog Doberman Pinscher (Dog) Narcolepsy HCRTR2 splicing Naturally occurring variant yes CanFam3.1 12 g.22603767_22603768insN[226] c.647-36_647-35insN[226] NM_001002933.1; a 226 bp SINE insertion in intron 3 of the HCRTR2 gene leads to skipping of exon 4 1999 10458611
368 OMIA:000703-9615 dog Labrador Retriever (Dog) Narcolepsy HCRTR2 splicing Naturally occurring variant yes CanFam3.1 12 g.22620881G>A c.1105+5G>A NM_001002933.1; NP_001002933.1; experimentally confirmed splice defect; skipping of exon 6 in the HCRTR2 mRNA transcript due to a G to A transition at position +5 in the 5′-splice site of intron 6 rs1152388413 1999 10458611
296 OMIA:002230-9913 taurine cattle Belted Galloway (Cattle) Brown Swiss (Cattle) Hypotrichosis HEPHL1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 29 g.721234T>A c.1684A>T p.(K562*) NC_037356.1 (ARS-UCD1.2 assembly, chromosome 29): g.721234A>T; NM_001192511.2 c.1684A>T; NP_001179440.1: p.Lys562* (Kuca et al., 2021); Variant initially identified in Galloway cattle and later reported in additional breeds: PMID:30014197 rs5334475051 2021 33926013
535 OMIA:001944-9615 dog Miniature Schnauzer (Dog) Spondylocostal dysostosis, autosomal recessive HES7 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 5 g.32945846del c.126delG p.(T43Pfs*24) 2015 25659135
145 OMIA:001987-9685 domestic cat Japanese domestic Bobtail HES7 JBT missense Naturally occurring variant yes Felis_catus_9.0 E1 g.2918735A>G c.5A>G p.(V2A) XM_003996191.4:c.5T>C; Felis_catus_6.2: g.2819475A>G rs5334475119 2016 27030474 The genomic location on Felis_catus_9.0 and transcript information is based on Rodney et al. 2021 (PMID: 33785770)
1178 OMIA:001461-9217 American flamingo Tay-Sachs disease HEXA missense Naturally occurring variant yes c.1406C>T p.(P469L) 2008 18693054
26 OMIA:001461-9615 dog Japanese Chin (Dog) Gangliosidosis, GM2, type I HEXA missense Naturally occurring variant yes CanFam3.1 30 g.35841247C>T c.967G>A p.(E323K) 2013 23266199 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
387 OMIA:001461-9940 sheep Jacob (Sheep) Gangliosidosis, GM2, type I (B variant) HEXA splicing Naturally occurring variant yes Oar_rambouillet_v1.0 7 g.20584348C>G c.1330G>C The variant [c.1330G>C; G444R] at the end of exon 11 effects splicing and results in skipping of exon 11. 2010 20817517 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1318 OMIA:001461-9823 pig Wild boar Gangliosidosis, GM2, type I HEXA missense Naturally occurring variant yes Sscrofa11.1 7 g.60910365C>T c.1495C>T p.(R499C) cDNA positions based on NM_001123221.1 rs5334475169 2021 34119419
463 OMIA:001462-9615 dog Poodle, Toy (Dog) Gangliosidosis, GM2, type II (Sandhoff or variant 0) HEXB deletion, small (<=20) Naturally occurring variant yes CanFam3.1 2 g.57225684del c.391del p.(V131*) XM_022414769.1; XP_022270477.1; published as c.283delG and p.(V59fs); coordinates in the table have been updated to a recent reference genome and / or transcript 2012 22766310
798 OMIA:001462-9615 dog Shiba Inu (Dog) Gangliosidosis, GM2, type II (Sandhoff or variant 0) HEXB deletion, small (<=20) Naturally occurring variant yes CanFam3.1 2 g.57243656_57243658del c.849_851del p.(L284del) XM_022414769.1; XP_022270477.1; published by Kolicheski et al. (2017) as p.Leu317del and reported by Wang et al. (2018) as p.(L207del) 2017 28833537
497 OMIA:001462-9685 domestic cat Korat (Cat) Gangliosidosis, GM2, type II (Sandhoff or variant 0) HEXB deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 A1 g.141540010del c.39del p.(L14Sfs*82) NM_001009333.2; NP_001009333.2; published as c.39delC 1994 8178934 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
309 OMIA:001462-9685 domestic cat Japanese domestic Gangliosidosis, GM2, type II (Sandoff or variant 0) HEXB nonsense (stop-gain) Naturally occurring variant yes Felis_catus_9.0 A1 g.141565348C>T c.667C>T p.(R223*) NM_001009333.2; NP_001009333.2 2007 16872651 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
381 OMIA:001462-9685 domestic cat Burmese (Cat) Gangliosidosis, GM2, type II (Sandhoff or variant 0) HEXB splicing Naturally occurring variant yes Felis_catus_9.0 A1 g.141571030_141571044del c.1244-8_1250del NM_001009333.2 2009 19231264 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
741 OMIA:001462-9685 domestic cat Domestic Shorthair Gangliosidosis, GM2, type II (Sandhoff or variant 0) HEXB inversion Naturally occurring variant yes Felis_catus_9.0 A1 g.141571788_141571812inv c.1467_1491inv p.(F489Lfs*4) NM_001009333.2; NP_001009333.2 2004 15081585 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1584 OMIA:001243-9601 Sumatran orangutan Alkaptonuria HGD missense Naturally occurring variant yes Susiae_PABv2/ponAbe3 3 g.17314095G>A c.1081G>A p.(G361R) 2023 37354891
1170 OMIA:001311-9615 dog Miniature Schnauzer (Dog) Progressive retinal atrophy, Miniature Schnauzer, type 1 HIVEP3 probably not causal, can be used as linked marker for genetic testing not known Naturally occurring variant unknown CanFam3.1 15 g.1432293G>A "intronic variant in HIVEP3/ENSCAFG00000035604" (Kaukonen et al., 2020). The genetic evidence is unable to distinguish between the HIVEP3 and PPT1 variants as potential causes of PRA. ... functional considerations favor causality of the coding PPT1 structural variant over the intronic HIVEP3 SNV" (Aguirre et al. 2020). 2020 32150541
596 OMIA:001493-9685 domestic cat Siamese (Cat) Porphyria, acute intermittent HMBS insertion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 D1 16541468dup c.189dup p.(L64Sfs*2) NM_001177808.1; NP_001171279.1; published as c.189dupT 2010 19934113 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
530 OMIA:001493-9685 domestic cat Porphyria, acute intermittent HMBS deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 D1 g.16540928_16540931del c.107_110del p.(D36Vfs*6) NM_001177808.1; NP_001171279.1; published as c.107_110delACAG 2013 24239138 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
135 OMIA:001493-9685 domestic cat Porphyria, acute intermittent HMBS missense Naturally occurring variant yes Felis_catus_9.0 D1 g.16541614G>A c.250G>A p.(A84T) NM_001177808.1; NP_001171279.1 rs5334475139 2013 24239138 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
136 OMIA:001493-9685 domestic cat Porphyria, acute intermittent HMBS missense Naturally occurring variant yes Felis_catus_9.0 D1 g.16542541C>T c.445C>T p.(R149W) NM_001177808.1; NP_001171279.1 rs5334475165 2013 24239138 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
402 OMIA:001493-9685 domestic cat Porphyria, acute intermittent HMBS splicing Naturally occurring variant yes Felis_catus_9.0 D1 g.16544575G>A c.826-1G>A NM_001177808.1 rs5334475129 2013 24239138 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
501 OMIA:001493-9685 domestic cat Siamese (Cat) Porphyria, acute intermittent HMBS deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 D1 g.16544592_16544594del c.842_844del p.(G281del) NM_001177808.1; NP_001171279.1; published as c.842_844delGAG 2013 24239138 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
689 OMIA:000299-9986 rabbit Dwarf, long-haired Holland Lop (Rabbit) Netherland dwarf (Rabbit) Dwarfism HMGA2 dw deletion, gross (>20) Naturally occurring variant yes 4 "that the dwarf allele constitutes a ~12.1 kb deletion overlapping the promoter region and first three exons of the HMGA2 gene leading to inactivation of this gene." 2017 27986804
727 OMIA:000317-9913 taurine cattle Highland (Cattle) Ears, crop HMX1 insertion, gross (>20) Naturally occurring variant no 6 76bp duplication of 106,720058 to 106,720,133 on BTA6; UMD3 reference assembly 2013 24194898
1153 OMIA:001952-9940 sheep Altay Fat-Rumped, China (Sheep) Awassi (Sheep) Kazakh Fat-Rumped (Sheep) Microtia HMX1 duplication Naturally occurring variant yes Oar_v4.0 6 g.114173249_114173324dup He et al. (2020) identified a 76 bp duplication in an evolutionary conserved region downstream of HMX1 (duplication of 76bp segment 6:126893417-126893492) in Altay sheep, the variant was later identified in other breeds and validated (PMID:32481741; PMID:38395239). 2020 31691317
624 OMIA:001952-9823 pig Microtia HOXA1 delins, small (<=20) Naturally occurring variant yes Sscrofa11.1 18 g.45478109delinsTC c.451delinsTC p.(L151fs) 2015 26035869 The genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcript: XM_003134844.5 by Stephanie Shields (27/05/2020)
751 OMIA:000668-9031 chicken Huiyang Bearded, China (Chicken) Muffs and beard HOXB8 complex rearrangement Naturally occurring variant no 27 "The Mb allele differs from the wild-type mb allele by three duplications, one in tandem and two that are translocated to that of the tandem repeat around 1.70 Mb on GGA27 2016 27253709
1296 OMIA:000240-9031 chicken Crested (Chicken) Silkie (Chicken) Crest HOXC10 duplication Naturally occurring variant no GRCg6a 33 g.7587588_7587784dup "a 197 bp duplication of an evolutionarily conserved sequence located in the intron of HOXC10 on chromosome 33" (Li et al., 2021) 2021 33704432
1286 OMIA:000806-9925 goat Polyceraty HOXD1 delins, gross (>20) Naturally occurring variant no ARS1 2 g.115652290_116155699delins137kb 2021 33528505
1285 OMIA:000806-9940 sheep Polyceraty HOXD1 deletion, small (<=20) Naturally occurring variant no Oar_rambouillet_v1.0 2 g.144548739_144548742del "a four-nucleotide deletion located at position +4 to +7 bp after exon 1 of the HOXD1 gene ([Oar_v4.0] g.132,832,249_132,832,252del; . . . ), i.e. encompassing three nucleotides (+4, +5, +6) of the consensus splice donor site" (Allais-Bonnet et al., 2021) 2021 33528505
691 OMIA:000081-9796 horse Arab (Horse) Atlanto occipital fusion HOXD3 deletion, gross (>20) Naturally occurring variant yes 18 "a 2.7-kb deletion located 4.4 kb downstream of the end of HOXD4 and 8.2 kb upstream of the start of HOXD3." 2017 28111759
1215 OMIA:002275-9615 dog French Bulldog (Dog) Cocoa HPS3 HPS3^co nonsense (stop-gain) Naturally occurring variant no CanFam3.1 23 g.43969695G>A c.2420G>A p.(T807*) XM_542830.6:c.2420G>A; XP_542830.3:p.(Trp807*) 2020 32526956
789 OMIA:002116-69293 three-spined stickleback Coat colour, albinism, oculocutaneous, HPS5-related Hps5 casper insertion, small (<=20) Naturally occurring variant yes "casper mutants have an insertion of a single nucleotide in the 6th exon of Hsp5, predicted to generate an early frameshift" 2017 28739598
1423 OMIA:002116-9685 domestic cat Donskoy (Cat) Pink-eye HPS5 splicing Naturally occurring variant yes Felis_catus_9.0 D1 g.76211236C>T c.2571-1G>A XM_006937131.3 2020 32558164
1222 OMIA:002229-9685 domestic cat Lykoi (Cat) Hypotrichia and Roaning HR hr^TN duplication Naturally occurring variant yes Felis_catus_9.0 B1 g.36040784_36040785dup c.1255_1256dup p.(Q420Sfs*100) ENSFCAT00000012982.5; ENSFCAP00000012037.2; published as c.1255_1256dupGT 2020 32580512
1224 OMIA:002229-9685 domestic cat Lykoi (Cat) Hypotrichia and Roaning HR hr^Fr splicing Naturally occurring variant yes Felis_catus_9.0 B1 g.36040933delinsCAG c.1404+2delinsCAG ENSFCAT00000012982.5; ENSFCAP00000012037.2; published as c.1404+2delTinsCAG; changed to HGVS nomenclature in this table; "This variant should extend and change the reading frame, including an additional 24 amino acids in the aberrant protein before a stop codon is recognized. Alternatively, a cryptic splice site may be used from within intron 4." (Buckley et al., 2020) 2020 32580512
1225 OMIA:002229-9685 domestic cat Lykoi (Cat) Hypotrichia and Roaning HR hr^TX splicing Naturally occurring variant yes Felis_catus_9.0 B1 g.36045776G>A c.2112G>A ENSFCAT00000012982.5; ENSFCAP00000012037.2; "This variant likely disrupts the splice donor allowing read-through for an additional 12 amino acids until a stop codon is encountered .... Alternatively, a cryptic splice site may be used from within intron 8." (Buckley et al., 2020) rs5334475128 2020 32580512
1226 OMIA:002229-9685 domestic cat Lykoi (Cat) Hypotrichia and Roaning HR hr^NC nonsense (stop-gain) Naturally occurring variant yes Felis_catus_9.0 B1 g.36047047C>T c.2243C>T p.(R748*) rs5334475155 2020 32580512
1227 OMIA:002229-9685 domestic cat Lykoi (Cat) Hypotrichia and Roaning HR hr^Ca nonsense (stop-gain) Naturally occurring variant yes Felis_catus_9.0 B1 g.36047518C>T c.2593C>T p.(Q865*) ENSFCAT00000012982.5; ENSFCAP00000012037.2 rs5334475120 2020 32580512
1223 OMIA:002229-9685 domestic cat Lykoi (Cat) Hypotrichia and Roaning HR hr^VA insertion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 B1 g.36051555_36051556insGACA c.3389_3390insGACA p.(S1130Rfs*29) ENSFCAT00000012982.5; ENSFCAP00000012037.2; published as g.36051555insGACA and c.3389insGACA; changed to HGVS nomenclature in this table 2020 32580512
331 OMIA:001348-9544 Rhesus monkey Atrichia with papular lesions HR nonsense (stop-gain) Naturally occurring variant yes MMUL_1 8 g.22046679C>T c.1831C>T p.(R611*) 2002 11831740 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
319 OMIA:002229-9940 sheep Valle del Belice, Italy (Sheep) Hypotrichosis HR nonsense (stop-gain) Naturally occurring variant yes Oar_rambouillet_v1.0 2 g.45703202C>T c.1312C>T p.(Q438*) Oar_v3.1 position is g.43224867C>T rs423413166 2003 12927087 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1095 OMIA:002777-9615 dog Dachshund (Dog) Disorder of sexual development, HSD17B3-related HSD17B3 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 1 g.70554301_70554302del c.159_160del p.(T54Wfs*13) XM_003638870.2; XP_003638918.1; deletion CA 2019 31476086
456 OMIA:001758-9615 dog Australian Shepherd (Dog) Cataract, early onset HSF4 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 5 g.82198114del c.971del p.(P324Hfs*87) NM_001048121.1; NP_001041586.1; published as g.85286582delC 2006 16939467
568 OMIA:001758-9615 dog Boston Terrier (Dog) Staffordshire Bull Terrier (Dog) Cataract, early onset HSF4 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 5 g.82198114_82198115insG c.971_972insC p.(L325Tfs*28) NM_001048121.1; NP_001041586.1; published as g.85286582_85286583insC 2006 16939467
919 OMIA:001319-9913 taurine cattle Holstein Friesian (Cattle) Myopathy of the diaphragmatic muscles HSPA1A deletion, gross (>20) Naturally occurring variant yes 23 Deletion of one of two HSP70 (heat-shock protein) genes in the bovine major histocompatibility complex 2003 12755819
204 OMIA:001817-9913 taurine cattle Japanese Black, Japan (Cattle) Perinatal weak calf syndrome IARS missense Naturally occurring variant yes ARS-UCD1.2 8 g.83909754C>G c.235G>C p.(V79L) rs5334475110 2013 23700453 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1604 OMIA:000706-9615 dog Nederlandse Kooikerhondje (Dog) Necrotising myelopathy IBA57 missense Naturally occurring variant yes CanFam3.1 14 g.801179G>A c.439C>T p.(R147W) XM_038686047.1; XP_038541975.1 2023 37588046
1237 OMIA:000664-9615 dog Golden Retriever (Dog) Mucopolysaccharidosis I IDUA deletion, gross (>20) Naturally occurring variant yes CanFam3.1 3 g.91523238_91523524del c.1400-76_1521+89del p.(G467_E507del) NM_001313883.1; NP_001300812.1 2020 32785987
911 OMIA:000664-9615 dog Plott Hound (Dog) Mucopolysaccharidosis I IDUA splicing Naturally occurring variant yes CanFam3.1 3 g.91534420C>T c.155+1G>A NM_001313883.1 rs1152388407 rs1152388407 1992 1339393
1190 OMIA:000664-9615 dog Boston Terrier (Dog) Mucopolysaccharidosis I IDUA insertion, small (<=20) Naturally occurring variant yes CanFam3.1 3 g.91534556_91534557insGGGGGCCG c.19_20insCGGCCCCC p.(R7Pfs) NM_001313883.1; NP_001300812.1 2020 32300136
500 OMIA:000664-9685 domestic cat Mucopolysaccharidosis I IDUA deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 B1 g.207800586_207800588del c.1042_1044del p.(D348del) NM_001305032.1; NP_001291961.1; a 3 bp deletion in the IDUA gene; HGVS 3'-rule applied to variant coordinates in this table 1999 10356309 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1301 OMIA:002320-9615 dog Lapponian Herder (Dog) Progressive retinal atrophy IFT122 missense Naturally occurring variant yes CanFam3.1 20 g.5648046C>T c.3176G>A p.(R1059H) Protein and CDS positions based on XP_533734.2 and XM_533734.6 2021 33606121
1396 OMIA:001823-9913 taurine cattle Holstein Friesian (Cattle) Haplotype with homozygous deficiency-HH2 IFT80 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 1 g.107172616delT c.1140del p.(L381Ffs*3) g.107172616delT rs523422030 rs523422030 2021 34873723 ENSBTAT00000044761.4:c.1140del ENSBTAP00000042227.4:p.Leu381PhefsTer3
687 OMIA:000006-9031 chicken Chinese Xingyi bantam, China (Chicken) Achondroplasia, creeper IHH deletion, gross (>20) Naturally occurring variant yes Gallus_gallus-4.0 7 g.21798705_21810600del "a 11,896bp large deletion region (chr7: 21,798,705-21,810,600) covering the entire Indian hedgehog (IHH) gene" 2016 27439785
337 OMIA:001899-9796 horse Quarter Horse (Horse) Incontinentia pigmenti IKBKG nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 X g.126898409C>T c.202C>T p.(R68*) rs3433281055 2013 24324710 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1202 OMIA:002271-9913 taurine cattle Holstein (black and white) (Cattle) Immunodeficiency, IL17Ra-related IL17RA deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 5 g.108813251del c.180del p.(C61Afs*62) XM_015460734.2: c.180delC; XP_015316220.2: p.(Cys61AlafsTer62) (Häfliger et al., 2020) rs5334474974 2020 32448141
584 OMIA:000899-9615 dog Cardigan Welsh Corgi (Dog) Severe combined immunodeficiency disease, X-linked IL2RG insertion, small (<=20) Naturally occurring variant yes CanFam3.1 X g.55483461_55483462insG c.583_584insC p.(R195Pfs*5) NM_001003201.1; NP_001003201.1; "a single nucleotide insertion causing a frameshift". The variant could also be described as a duplication of a cytosine (c.583dup). 1995 8571541
476 OMIA:000899-9615 dog Basset Hound (Dog) Severe combined immunodeficiency disease, X-linked IL2RG deletion, small (<=20) Naturally occurring variant yes CanFam3.1 X g.55484657_55484660del c.30_33del p.(L11Yfs) NM_001003201.1; NP_001003201.1; c.30_33delCCTC 1994 7829104
1622 OMIA:002763-9541 crab-eating macaque Severe combined immunodeficiency disease IL2RG nonsense (stop-gain) Base-editing yes Macaca_fascicularis_5.0 X g.68110639G>A c.391C>T p.(Q131*) XM_005593892.2; XP_005593949.1 2023 37661226
1253 OMIA:002289-9615 dog Lhasa Apso (Dog) Progressive retinal atrophy 4 (PRA4) IMPG2 insertion, gross (>20) Naturally occurring variant yes CanFam3.1 33 " LINE-1 insertion was identified within the critical region in this PRA-affected LA, situated within 200 bp upstream of the interphotoreceptor matrix proteoglycan 2 (IMPG2) gene within the following coordinates: CANFA33: 7,785,475-7,785,491" (Hitti-Malin et al., 2020) 2020 32894063
1034 OMIA:002173-9615 dog Norwich Terrier (Dog) Diffuse cystic renal dysplasia and hepatic fibrosis INPP5E splicing Naturally occurring variant yes CanFam3.1 9 g.49069064G>A c.1572+5G>A Dillard et al. (2018): "the identified variant introduces a novel splice site in INPP5E causing a frameshift and formation of a premature stop codon." 2018 30235266
962 OMIA:001675-61379 black-footed cat Cone-rod dystrophy 2 IQCB1 deletion, small (<=20) Naturally occurring variant yes c.1282delCT p.(L428*) 2017 28322220
606 OMIA:001675-9615 dog American Pit Bull Terrier (Dog) Cone-rod dystrophy 2 IQCB1 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 33 g.25078909_25078910insC c.952_53insC p.(S319Ifs*12) 2013 24045995
805 OMIA:001528-9940 sheep INRA 401, France (Sheep) Fleece variation, woolly IRF2BP2 insertion, gross (>20) Naturally occurring variant no Oar_rambouillet_v1.0 25 insertion of an antisense EIF2S2 retrogene (called asEIF2S2) into the 3' UTR of the IRF2BP2 gene 2017 28379502
336 OMIA:001886-9615 dog Karelian Bear Dog (Dog) Norwegian Elkhound (Dog) Chondrodysplasia, disproportionate short-limbed ITGA10 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 17 g.58703935G>A c.2083C>T p.(R695*) XM_845262.4; XP_850355.1 2013 24086591 Genomic coordinates in CanFam3.1 provided by Robert Kuhn
1569 OMIA:001000-9615 dog Golden Retriever (Dog) Thrombastenia ITGA2B deletion, small (<=20) Naturally occurring variant yes 9 Published in a conference proceeding as (1924delC) 2017 Reference not in PubMed; see OMIA 001000-9615 for reference details
80 OMIA:001000-9615 dog Otterhound (Dog) Thrombasthenia ITGA2B missense Naturally occurring variant yes CanFam3.1 9 g.19054488G>C c.1192G>C p.(D398H) NM_001003163.2; NP_001003163.1; published as c.1193G>C / c.1100G>C; substitution of histidine for aspartic acid at position 398 (367). Coordinates in the table have been updated to a recent reference genome and or transcripts. 2001 11703027 Breed was incorrectly listed as Scottish Deerhound. Changed to Otterhound [19/5/2023]
1568 OMIA:001000-9615 dog Mixed Breed (Dog) Thrombasthenia ITGA2B nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 9 g.19057141C>T 1357C>T p.(R453*) NM_001003163.2; NP_001003163.1; published as (C1264T) and (R422X), coordinates in this table have been updated to a recent reference genome 2016 26764135
369 OMIA:001000-9615 dog Great Pyrenees (Dog) Thrombasthenia ITGA2B splicing Naturally occurring variant yes CanFam3.1 9 g.19057144_19057157dup c.1360_1373dup NM_001003163.2; NP_001003163.1; experimentally confirmed splice defect; a 14-base duplication in exon 13 and defective splicing of intron 13 2000 11105947
164 OMIA:001000-9796 horse Quarter Horse (Horse) Thoroughbred (Horse) Thrombasthenia ITGA2B missense Naturally occurring variant yes EquCab3.0 11 g.19245752G>C c.215G>C p.(R72P) NM_001081793.1; NP_001075262.1; originally published as p.(R41P) and listed by Leite et al. (2019) as c.122G>C; coordinates in this table have been updated to a recent reference genome and / or transcript 2006 16407493
512 OMIA:001000-9796 horse Peruvian Paso (Horse) Quarter Horse (Horse) Thrombasthenia ITGA2B deletion, small (<=20) Naturally occurring variant yes EquCab3.0 11 g.19247983_19247992del g.19247983_19247992delCAGGTGAGGA 2007 17338169 g. coordinates obtained from Dahlgren et al. (2020)
1245 OMIA:001000-9685 domestic cat Domestic Shorthair Glanzmann's thrombasthenia ITGA2B deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 E1 g.44416063del c.1986delC p.(P662fs) ENSFCAT00000003056.6:c.1986delC; p.Pro662fs (Li et al., 2020) rs5334475153 2020 32935881
1185 OMIA:002261-9913 taurine cattle Holstein (black and white) (Cattle) de novo mutation in an AI sire ITGA3 missense Naturally occurring variant yes ARS-UCD1.2 19 g.36586185G>A p.(T252M) Bourneuf et al. (2017) detected ITGA3 g.37219021G>A; p.T252M as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Holstein AI bull. No information was provided on the descendants of this bull. rs5334475090 2017 28904385
1577 OMIA:002718-9913 taurine cattle Charolais (Cattle) Epidermolysis bullosa, junctional, ITGA6-related ITGA6 splicing Naturally occurring variant yes ARS-UCD1.2 2 g.24112740C>A c.2160+1G>T p.(I657Mfs) NM_001109981.1 2023 37308849
197 OMIA:000595-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Holstein Friesian (Cattle) Jersey (Cattle) Simmental (Cattle) Leukocyte adhesion deficiency, type I ITGB2 BLAD missense Naturally occurring variant yes ARS-UCD1.2 1 g.144770078T>C c.383A>G p.(D128G) Variant initially identified in Holstein Friesian cattle and later reported in additional breeds. rs445709131 rs445709131 1992 1384046 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager & Shernae Woolley, EMAI, NSW Department of Primary Industries.
53 OMIA:000595-9615 dog Irish Setter (Dog) Leukocyte adhesion deficiency, type I ITGB2 missense Naturally occurring variant yes CanFam3.1 31 g.38537012C>G c.107G>C p.(C36S) ROS_Cfam_1.0: g.38142116C>G ENSCAFT00845038113.1:c.107G>C ENSCAFP00845029856.1:p.Cys36Ser rs1152388503 rs1152388503 1999 10512685 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
775 OMIA:000595-9685 domestic cat Leukocyte adhesion deficiency, type I ITGB2 ITGB-2 missing exon 2 deletion, gross (>20) Naturally occurring variant yes Felis_catus_9.0 C2 g.1772101_1772124del c.46_58+11del XM_011285804.3; Bauer et al. (2017) "24 bp deletion at the exon 2 to intron 2 boundary (c.46_58 + 11del), predicting premature translational termination due to abnormal splicing of exon 1 to exon 3 or 4." 2017 28750142 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
684 OMIA:001948-9913 taurine cattle Charolais (Cattle) Epidermolysis bullosa, junctionalis, ITGB4 ITGB4 deletion, gross (>20) Naturally occurring variant yes 19 "a 4.4 kb deletion involving exons 17 to 22" of the ITGB4 gene 2015 25890340
1272 OMIA:001948-9940 sheep Mouton vendéen, France (Sheep) Epidermolysis bullosa, junctionalis, ITGB4 ITGB4 nonsense (stop-gain) Naturally occurring variant yes Oar_rambouillet_v1.0 11 g.7412626C>T c.2653C>T p.(R885*) c.2653C>T position is based on mRNA XM_015098951.1; Oar_v4.0 position is g.54799925 2020 33225458
543 OMIA:001948-9940 sheep Spanish Churro (Sheep) Epidermolysis bullosa, junctionalis, ITGB4 ITGB4 deletion, small (<=20) Naturally occurring variant yes Oar_rambouillet_v1.0 11 g.7425460_7425463del c.4412_4415del Oar_v3.1: g.54849767_54849770del 2015 25955497 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
754 OMIA:002097-9615 dog Italian Spinone (Dog) Ataxia, spinocerebellar ITPR1 complex rearrangement Naturally occurring variant yes 20 Forman et al. (2015) identified an expanded GAA-repeat in intron 35 of the ITPR1 gene in affected dogs. The wildtype sequence contains 8 GAA repeats. The expanded disease-associated alleles carry an estimated 318-651 GAA repeats. 2015 25354648
739 OMIA:000809-9615 dog Polycythemia JAK2 delins, small (<=20) Naturally occurring variant yes CanFam3.1 1 g.93416506_93416510delinsTTCCT c.1849_1853delinsTTCCT p.(V617_C618delinsFL) XM_022421838.1; XP_022277546.1; published as a three-base change in codons 617 and 618 of JAK2 giving rise to V617F and C618L, SOMATIC MUTATION/MOSAICISM 2011 21320566
1390 OMIA:002483-9913 taurine cattle Neuromuscular channelopathy KCNG1 missense Naturally occurring variant yes ARS-UCD1.2 13 g.78918850C>A c.1248G>T p.(W416C) NM_001205719.1; NP_001192648.1 rs3423356335 2021 34828398
1154 OMIA:002240-9615 dog Norwegian Buhund (Dog) Ataxia, cerebellar, KCNIP4-related KCNIP4 missense Naturally occurring variant yes CanFam3.1 3 g.88890674T>C c.436T>C p.(T146R) XM_005618660.3; XP_005618717.1 2020 31999692
945 OMIA:002089-9615 dog Dachshund (Dog) Jack Russell Terrier (Dog) Parson Russell Terrier (Dog) Smooth Fox Terrier (Dog) Ataxia, cerebellar, KCNJ10-related KCNJ10 missense Naturally occurring variant yes CanFam3.1 38 g.22140300C>G c.627C>G p.(I209M) XM_545752.6; XP_545752.3; reference for Dachshund is PMID:37905444 rs1152388456 rs1152388456 2014 24708069 Genomic coordinates in CanFam3.1 and EVA ID provided by Zoe Shmidt and Robert Kuhn.
947 OMIA:002089-9615 dog Belgian Shepherd Dog, Malinois (Dog) Spongy degeneration with cerebellar ataxia 1 (SDCA1) KCNJ10 missense Naturally occurring variant yes CanFam3.1 38 g.22140659T>C c.986T>C p.(L329P) XM_545752.6; XP_545752.3 2017 27966545 28007838 Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
612 OMIA:002089-9615 dog Jack Russell Terrier (Dog) Ataxia, cerebellar, KCNJ10-related KCNJ10 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 38 g.22141027insC c.*214_*215insC XM_005640901.1; Gast et al. (2016) "Bioinformatic analysis using RegRNA indicated the KCNJ10:g.22141027insC affecting regulation of gene expression via a regulatory RNA motif or miRNA target site." rs1152388457 2016 27724896
1596 OMIA:002332-9615 dog English Springer Spaniel (Dog) Long QT syndrome KCNQ1 missense Naturally occurring variant yes CanFam3.1 18 g.46604412C>A c.770C>A p.(T257K) XM_022405121.1; XP_022260829.1; published as "Genbank KF439050, KCNQ1_T377K" - coordinates in this table are updated to a recent reference genome. 2015 25779927
196 OMIA:001722-9913 taurine cattle Marchigiana (Cattle) Romagnola (Cattle) Lethal multi-organ developmental dysplasia KDM2B missense Naturally occurring variant yes ARS-UCD1.2 17 g.53761149G>A c.2503G>A p.(D835N) rs5334475109 2012 23029151 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
207 OMIA:002390-9913 taurine cattle Brown Swiss (Cattle) Spinal muscular atrophy KDSR missense Naturally occurring variant yes ARS-UCD1.2 24 g.61620302C>T c.562G>A p.(A188T) rs5334475102 2007 17420465 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
604 OMIA:000979-9031 chicken Talpid-3 KIAA0586 insertion, small (<=20) Naturally occurring variant yes 5 insT 2006 16702409
1005 OMIA:000527-9913 taurine cattle Angus (Cattle) Charolais (Cattle) Uckermärker, Germany (Cattle) Progressive ataxia KIF1C missense Naturally occurring variant yes ARS-UCD1.2 19 g.26407668C>T c.608G>A p.(R203Q); p.(R203_T204delinsQ*) ENSBTAT00000081136.1:c.608G>A ENSBTAP00000062635.1:p.Arg203Gln Duchesne et al. (2018): "This substitution has two effects: firstly, it modifies a conserved amino acid (p.R203Q). Secondly, it causes an alternative splicing event, resulting in exon 5 skipping in most of the transcripts (p.RT203-204QStop) associated with a drastic reduction of overall mRNA expression and leading to the absence of detectable KIF1C protein in brain extracts from affected cattle." The variant was initially reported in Charolais cattle and later reported in additional breeds (see PMIDs 38338009 and 32281115). rs800926237 rs800926237 2018 30067756
1231 OMIA:002283-9823 pig Large White (Pig) Arthrogryposis multiplex congenita, KIF21A-related KIF21A insertion, gross (>20) Naturally occurring variant yes Sscrofa11.1 5 g.70964237_70964238insAAGATAGAGGTTCTTTCCTCTAGACTTGAGGTTCTCCTGGTGTGACAGATGGTTCTTTCCTCT p.(V41_F42ins*) (NC_010447.5:g70964237_ g70964238insAAGATAGAGGTTCTTTCCTCTAGACTTGAGGTTCTCCTGGTGTGACAGATGGTTCTTTCCTCT; p.Val41_Phe42insTer) (Fang et al., 2020) rs5334475173 2020 32686171
1191 OMIA:002267-9685 domestic cat Bengal (Cat) Progressive retinal atrophy KIF3B missense Naturally occurring variant yes Felis_catus_9.0 A3 g.26784019C>T c.1000G>A p.(A334T) ENSFCAT00000022266; c.1000G>A (p.Ala334Thr) rs5334475117 2020 32386558 The genomic location on Felis_catus_9.0 is based on Rodney et al. 2021 (PMID: 33785770)
1440 OMIA:001836-9913 taurine cattle Holstein-Friesian, Switzerland (Cattle) Abortion due to haplotype HH13 KIR2DS1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 18 g.62758881G>A c.475C>T p.(Q159*) NM_001097567.1; NP_001091036.1 rs437566778 2022 35361830
715 OMIA:001743-9823 pig Coat colour, patch KIT duplication Naturally occurring variant no 8 the patch allele comprises a 450kb duplication that includes KIT (roughly in the middle) 1998 9724328
743 OMIA:001745-9823 pig Essex, United Kingdom of Great Britain and Northern Ireland (Pig) Hampshire Down (Sheep) Schwäbisch Hällisches Schwein, Germany (Pig) Wessex Saddleback (Pig) White belt KIT complex rearrangement Naturally occurring variant no 8 Hampshire pigs (belted phenotype) have "a 4.3-kb duplication (DUP2) located ~¼100 kb upstream of KIT and a 23-kb duplication (DUP3) ~100 kb downstream of KIT, which in turn contained a fourth ~4.3-kb duplication (DUP4) not present on wild-type chromosomes". Across four breeds, belted pigs always had DUP2 and DUP4, but some lacked DUP3. 2012 23151514
1525 OMIA:001652-9627 red fox Platinum coat colour KIT splicing Naturally occurring variant yes G>A variant in the first nucleotide of KIT intron 17 causes skipping of exon 17 2015 25662789
748 OMIA:000426-9913 taurine cattle Fjällnära boskap, Sweden (Cattle) Pohjoissuomenkarja, Finland (Cattle) Gonadal hypoplasia KIT cs(29) complex rearrangement Naturally occurring variant yes 6 "gonadal hypoplasia in Northern Finncattle and Swedish Mountain cattle is associated with a complex chromosomal rearrangement including a ~500kb duplicated segment from BTA6 which is translocated to BTA29. This duplicated segment includes the entire coding sequence of the KIT gene" 2013 24086604
391 OMIA:001216-9823 pig Coat colour, roan KIT splicing Naturally occurring variant no 8 a U(26) repeat in intron 5 of the KIT gene, which is likely to mediate skipping of exon 5 of the gene in some tissues including skin 2011 21749430
749 OMIA:001576-9913 taurine cattle Belgian Blue (Cattle) Brown Swiss (Cattle) Galloway (Cattle) White Park, United Kingdom of Great Britain and Northern Ireland (Cattle) Coat colour, colour-sided KIT Cs(29) complex rearrangement Naturally occurring variant no 29 Durkin et al. (2012): "colour sidedness is determined by a first allele on chromosome 29 (Cs(29)), which results from the translocation of a 492-kilobase chromosome 6 segment encompassing KIT to chromosome 29, and a second allele on chromosome 6 (Cs(6)), derived from the first by repatriation of fused 575-kilobase chromosome 6 and 29 sequences to the KIT locus. We provide evidence that both translocation events involved circular intermediates. This is the first example, to our knowledge, of a phenotype determined by homologous yet non-syntenic alleles that result from a novel copy-number-variant-generating mechanism." 2012 22297974
1133 OMIA:001576-9913 taurine cattle Belgian Blue (Cattle) Brown Swiss (Cattle) Coat colour, colour-sided KIT Cs(6) complex rearrangement Naturally occurring variant no 6 Durkin et al. (2012): "colour sidedness is determined by a first allele on chromosome 29 (Cs(29)), which results from the translocation of a 492-kilobase chromosome 6 segment encompassing KIT to chromosome 29, and a second allele on chromosome 6 (Cs(6)), derived from the first by repatriation of fused 575-kilobase chromosome 6 and 29 sequences to the KIT locus. We provide evidence that both translocation events involved circular intermediates. This is the first example, to our knowledge, of a phenotype determined by homologous yet non-syntenic alleles that result from a novel copy-number-variant-generating mechanism." 2012 22297974
1116 OMIA:001576-9913 OMIA:001737-9913 taurine cattle Berrenda en Negro, Spain (Cattle) Cikasto govedo, Slovenia (Cattle) Evolèner, Switzerland (Cattle) Gloucester, United Kingdom of Great Britain and Northern Ireland (Cattle) Herens (Cattle) Pinzgau (Cattle) Tux-Zillertaler, Austria (Cattle) Pinzgauer spotting KIT KIT^PINZ complex rearrangement Naturally occurring variant no 6 Briefly: the KIT^PINZ variant is "characterized by the fusion of a duplicated chromosome 4 segment into a deleted part of chromosome 6." (Küttel et al., 2019) In more detail: "a complex structural variant characterized by a ~9.4-kb deletion . . . and in silico evidence for a duplication of ~1.5 kb about 34 kb farther downstream . . . . Apparently, the duplicated copy of the ~1.5-kb segment appears inversely inserted at the upstream breakpoint of the ~9.4-kb deletion . . . . Furthermore, we noticed at the upstream breakpoint of the inversely inserted segment chimeric read pairs in which both ends mapped to chromosome 6 and 4 . . . . The inspection of the sequence coverage of the involved genome region on chromosome 4 indicated a ~310-kb duplication from 84 864 544 to ~85 174 000 bp". (Küttel et al., 2019) 2019 31294880
979 OMIA:000209-9823 pig Dominant white KIT I complex rearrangement Naturally occurring variant no 8 This dominant white allele carries at least three causal polymorphisms, namely a 450 kb duplication (originally reported by Johansson Moller (1996); also present in Patch - see OMIA 001743-9825), the splice mutation reported by Marklund et al. (1998) (unique to Dominant white) and smaller duplication(s) (that occur within the 450kb duplication) causing Belt (see OMIA 001745-9825).(with thanks to Leif Andersson). To emphasise the original discovery of the duplication, the ref cited here is Johansson Moller (1996) 1996 8875890
566 OMIA:001737-9838 Arabian camel Coat colour, white spotting, KIT-related KIT deletion, small (<=20) Naturally occurring variant no c.1842delG p.(M614Ifs*5) 2017 28282952
403 OMIA:000209-494514 Arctic fox Coat colour, dominant white KIT splicing Naturally occurring variant no c.1867+1G>T 2013 24308634
405 OMIA:001737-9793 ass (donkey) Coat colour, white spotting, due to KIT KIT Ws splicing Naturally occurring variant no c.1978+2T>A 2015 25818843
1102 OMIA:000209-30538 alpaca Classic grey coat colour KIT missense Naturally occurring variant no c.376G>A p.(G126R) 2019 31297861
150 OMIA:000209-9793 ass (donkey) Coat colour, dominant white KIT W missense Naturally occurring variant no c.662A>C p.(Y221S) 2015 25818843
1165 OMIA:001737-9913 taurine cattle Brown Swiss (Cattle) White spotting KIT deletion, gross (>20) Naturally occurring variant no ARS-UCD1.2 6 g.70239551_70239590del c.1390_1429del p.(N464Afs*50) "NC_037333.1:g.70239551_70239590del; NM_001166484.1:c.1390_1429del; NP_001159956.1:p.(Asn464AlafsTer50)" (Häfliger et al., 2020) rs5411005071 2020 32065668
1201 OMIA:001737-9925 goat Bezoar (Goat) Wild type or Bezoar KIT reference sequence allele Naturally occurring variant no ARS1 6 "The coverage plot of bezoars (BEZ) does not show any copy number variation and represents the wildtype allele." (Henkel et al., 2019) 2019 31841508
1187 OMIA:001737-9925 goat Barbari (Goat) White-spotted KIT KIT^BAR repeat variation Naturally occurring variant no ARS1 6 g.70859258_70959918 (2 copies) The CNV "started ~63 kb downstream of KIT and covered ~100 kb of the genome reference sequence without known coding DNA. The short read-aligments of read-pairs spanning the amplification breakpoints confirmed that the individual copies of the CNV were arranged in tandem in a head to tail orientation" (Henkel et al., 2019) "70'911'301-70'927'581: deleted; 89'210'545-89'233'246: 3 copies of which 2 are inserted at 70'911'302" (Table S5; Henkel et al., 2019) 2019 31841508
1188 OMIA:000209-9925 goat Pak Angora, Pakistan (Goat) White KIT KIT^ANG repeat variation Naturally occurring variant no ARS1 6 g.70859258_70959918 (3 copies) This CNV "started ~63 kb downstream of KIT and covered ~100 kb of the genome reference sequence without known coding DNA. The short read-aligments of read-pairs spanning the amplification breakpoints confirmed that the individual copies of the CNV were arranged in tandem in a head to tail orientation" (Henkel et al.,2019) 2019 31841508
570 OMIA:001737-9615 dog Coat colour, white spotting, KIT-related KIT insertion, small (<=20) Naturally occurring variant no CanFam3.1 13 g.47144513_47144514insA c.140_141insA p.(L48Vfs*10) NM_001003181.1; NP_001003181.1; "a 1-bp insertion of an adenine 70 bases downstream of the beginning of exon 2." The variant represents a duplication of an adenine and could also be described as c.140dup. 2013 23134432
464 OMIA:001516-9615 dog Gastrointestinal stromal tumor KIT deletion, small (<=20) Naturally occurring variant yes CanFam3.1 13 g.47178531_47178536del c.1664_1669del NM_001003181.1; deletion of AGTGGA; SOMATIC MUTATION 2010 20950418
465 OMIA:001516-9615 dog Gastrointestinal stromal tumor KIT deletion, small (<=20) Naturally occurring variant yes CanFam3.1 13 g.47178534_47178539del c.1667_1672del NM_001003181.1; deletion of GGAAGG; SOMATIC MUTATION 2010 20950418
459 OMIA:001737-9615 dog Coat colour, white spotting, KIT-related KIT deletion, small (<=20) Naturally occurring variant no CanFam3.1 13 g.47179174_47179176del c.1936_1938del p.(L646del) NM_001003181.1; NP_001003181.1; published as c.1960_1962delCTC; p.(L654del); coordinates in the table have been updated to a recent reference genome and / or transcript 2013 23659249 Dr. Wanda M. Gerding provided additional sequence information to facilitate identification of the genomic position in CanFam3.1
1331 OMIA:000209-9796 horse American Paint (Horse) Quarter Horse (Horse) White spotting KIT W32 missense Naturally occurring variant unknown EquCab3.0 3 g.79538738C>T c.3214G>A p.(A1072T) cDNA position based on transcript ENSECAT00000014037.3 rs1141982296 rs1141982296 2021 34223905
882 OMIA:000209-9796 horse Süddeutsches Kaltblut, Germany (Horse) Coat colour, dominant white KIT W11 splicing Naturally occurring variant no EquCab3.0 3 g.79540429C>T c.2684+1G>A rs5334475183 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
939 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W26 deletion, small (<=20) Naturally occurring variant unknown EquCab3.0 3 g.79540694del c.2536del p.(S846Vfs*15) NM_001163866.1; NP_001157338.1; published as c.2536delA rs3101685403 2018 29333746
873 OMIA:000209-9796 horse Oldenburg (Horse) Coat colour, dominant white KIT W16 missense Naturally occurring variant no EquCab3.0 3 g.79540741T>A c.2489A>T p.(K830I) rs5334475213 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
883 OMIA:000209-9796 horse Miniature Horse (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Coat colour, dominant white KIT W13 splicing Naturally occurring variant no EquCab3.0 3 g.79544066C>G c.2472+5G>C NM_001163866.1 rs3102773259 rs3102773259 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
889 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W14 deletion, gross (>20) Naturally occurring variant no EquCab3.0 3 g.79544098_79544151del c.2392_2445del p.(H798_N815del) NM_001163866.1; NP_001157338.1 2011 21554354 genomic coordinates updated from g.79544151_79544204del to g.79544098_79544151del in EquCab3.0 [17/09/2023]
891 OMIA:000209-9796 horse Iceland Pony (Horse) White spotting KIT W21 deletion, small (<=20) Naturally occurring variant no EquCab3.0 3 g.79544174del c.2369delC p.(A790Efs*20) rs5334475210 2015 26059442 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
885 OMIA:000209-9796 horse Appaloosa (Horse) Haflinger (Horse) Lipizzan horse (Horse) Noric (Horse) Quarter Horse (Horse) Coat colour, dominant white KIT sabino 1 (SB1) splicing Naturally occurring variant no EquCab3.0 3 g.79544206A>T "SNP AX-103727726 (ECA3:77735520; SB1, SNP KI16+1037A)" (Druml et al., 2018) rs5334475211 2005 16284805 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
893 OMIA:000209-9796 horse Trottatore Italiano, Italy (Horse) Coat colour, dominant white KIT W24 splicing Naturally occurring variant no EquCab3.0 3 g.79545245C>T rs3443588955 2017 28856698
1462 OMIA:000209-9796 horse American Trotter (Horse) Dominant white spotting KIT W33 missense Naturally occurring variant no EquCab3.0 3 g.79545248T>A c.2783A>T p.(N895Y) NC_009146.3; ENSECAT00000014037.3 2022 35641888
881 OMIA:000209-9796 horse Iceland Pony (Horse) Coat colour, dominant white KIT W8 splicing Naturally occurring variant no EquCab3.0 3 g.79545374C>T c.2222-1G>A NM_001163866.1 rs3434854925 rs3434854925 2009 19456317
886 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W5 deletion, small (<=20) Naturally occurring variant no EquCab3.0 3 g.79545900del c.2193delG p.(T732Qfs*9) rs5334475194 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
878 OMIA:000209-9796 horse Freiberger (Horse) Coat colour, dominant white KIT W1 nonsense (stop-gain) Naturally occurring variant no EquCab3.0 3 g.79545942G>C c.2151C>G p.(Y717*) rs5334475201 2007 17997609 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
877 OMIA:000209-9796 horse American Paint (Horse) Appaloosa (Horse) German Riding Pony (Horse) Noric (Horse) Oldenburg (Horse) Quarter Horse (Horse) Thoroughbred (Horse) Tori hobune, Estonia (Horse) Traditional Gypsy Cob, United Kingdom of Great Britain and Northern Ireland (Horse) Welsh Pony (Horse) Coat colour, dominant white KIT W20 missense Naturally occurring variant unknown EquCab3.0 3 g.79548220C>T c.2045G>A p.(R682H) ENSECAT00000014037.3:c.2381A>G ENSECAP00000011188.2:p.His794Arg rs1143160924 rs1143160924 2013 23659293 Variant coordinates initially gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
875 OMIA:000209-9796 horse Japanese Draft, Japan (Horse) Coat colour, dominant white KIT W17b missense Naturally occurring variant no EquCab3.0 3 g.79548244A>G c.2021T>C p.(L674P) rs5334475224 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
1261 OMIA:000209-9796 horse Berber, Germany (Horse) Extensive coat white patterning KIT W30 missense Naturally occurring variant no EquCab3.0 3 g.79548244A>T c.2020T>A p.(L674H) g.79548244, c.2020T>A; p.L674H (Martin et al., 2020) rs5334475224 2020 33111383
874 OMIA:000209-9796 horse Japanese Draft, Japan (Horse) Coat colour, dominant white KIT w17a missense Naturally occurring variant no EquCab3.0 3 g.79548265T>A c.2001A>T p.(E667D) rs5334475222 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
890 OMIA:000209-9796 horse Thoroughbred (Horse) White spotting KIT W22 deletion, gross (>20) Naturally occurring variant no EquCab3.0 3 g.79548925_79550822del 1898bp deletion 2017 28444912
868 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W2 missense Naturally occurring variant no EquCab3.0 3 g.79549540C>T c.1960G>A p.(G654R) rs5334475198 2007 17997609 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
869 OMIA:000209-9796 horse Camarillo White Horse, United States of America (Horse) Coat colour, dominant white KIT W4 missense Naturally occurring variant no EquCab3.0 3 g.79549780G>A c.1805C>T p.(A602V) rs5334475223 2007 17997609 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
871 OMIA:000209-9796 horse Holsteiner (Horse) Coat colour, dominant white KIT W9 missense Naturally occurring variant no EquCab3.0 3 g.79549797C>T c.1789G>A p.(G597R) rs5334475209 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
872 OMIA:000209-9796 horse Arab (Horse) Coat colour, dominant white KIT W15 missense Naturally occurring variant no EquCab3.0 3 g.79550351A>G c.1597T>C p.(C533R) rs5334475202 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
940 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W27 missense Naturally occurring variant unknown EquCab3.0 3 g.79551937A>C c.1473T>G p.(C491W) NM_001163866.1; NP_001157338.1 rs3110307743 2018 29333746
884 OMIA:000209-9796 horse CH-Warmblut, Switzerland (Horse) Coat colour, dominant white KIT W18 splicing Naturally occurring variant no EquCab3.0 3 g.79553751C>T c.1346+1G>A rs5334475221 2013 23659293 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
876 OMIA:000209-9796 horse Arab (Horse) Coat colour, dominant white KIT W19 missense Naturally occurring variant no EquCab3.0 3 g.79553776T>C c.1322A>G p.(Y441C) rs5334475217 2013 23659293 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
1476 OMIA:000209-9796 horse American Paint (Horse) Appaloosa (Horse) Arab (Horse) Mangalarga (Horse) Morgan (Horse) Mustang (Horse) Quarter Horse (Horse) Rocky Mountain, United States of America (Bighorn sheep) Warmblood breeds Increased white spotting KIT W34 missense Naturally occurring variant no EquCab3.0 3 g.79566881T>C c.1495A>G p.(T499A) ENSECAT00000014037.3; ENSECAP00000011188.2 rs1140732842 rs1140732842 2022 35953947
887 OMIA:000209-9796 horse Quarter Horse (Horse) Coat colour, dominant white KIT W10 deletion, small (<=20) Naturally occurring variant no EquCab3.0 3 g.79566923_79566926del c.1126_1129del p.(E376Ffs*3) NM_001163866.1; NP_001157338.1; published as c.1126_1129delGAAC 2009 19456317 Genomic coordinates updated in this table from g.79566926_79566929del in EquCab3.0 after feedback from Micaela Vierra identified that these coordinates were incorrect [27/09/2023].
870 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W6 missense Naturally occurring variant no EquCab3.0 3 g.79573754C>T c.856G>A p.(G286R) rs5334475167 2009 19456317 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
892 OMIA:000209-9796 horse Arab (Horse) White spotting KIT W23 splicing Naturally occurring variant unknown EquCab3.0 3 g.79578484C>G c.756+1G>C rs1095048836 rs1095048836 2017 28378922
879 OMIA:000209-9796 horse Arab (Horse) Coat colour, dominant white KIT W3 nonsense (stop-gain) Naturally occurring variant no EquCab3.0 3 g.79578535T>A c.706A>T p.(K236*) rs5334475200 2007 17997609 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
938 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W25 missense Naturally occurring variant unknown EquCab3.0 3 g.79578573A>G c.668T>C p.(L223P) NM_001163866.1; NP_001157338.1 rs3103992630 2018 29333746
888 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W12 deletion, small (<=20) Naturally occurring variant unknown EquCab3.0 3 g.79579774_79579778del c.559_563del p.(S187Rfs*10) NM_001163866.1; NP_001157338.1; published as c.559_563delTCTGC rs5334475188 2010 Reference not in PubMed; see OMIA 000209-9796 for reference details Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
880 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W7 splicing Naturally occurring variant no EquCab3.0 3 g.79580000C>G c.338-1G>C rs5334475216 2009 19456317 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
1330 OMIA:000209-9796 horse Quarter Horse (Horse) White spotting KIT W31 insertion, small (<=20) Naturally occurring variant unknown EquCab3.0 3 g.79618532_79618533insA c.30_31insT p.(L11Sfs*115) 2021 34223905
620 OMIA:001580-9685 domestic cat Birman (Cat) Feet white (gloving) KIT g delins, small (<=20) Naturally occurring variant no Felis_catus_9.0 B1 g.163986474_163986475delinsTG c.1035_1036delinsCA p.(E345_H346delinsDN) NM_001009837.3; NP_001009837.3; Montague et al. (2014) describe this variant as "two adjacent missense mutations". 2010 21147473 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
994 OMIA:000209-9685 domestic cat Domestic Longhair Coat colour, dominant white KIT W insertion, gross (>20) Naturally occurring variant yes Felis_catus_9.0 B1 g.164038110_164038111insN[617] published as "a FERV1 long terminal repeat (LTR) is associated with all Dominant White individuals" 2014 25085922 Genomic position in Felis_catus_9.0 is based on information provided by Leslie Lyons and Reuben Buckley.
732 OMIA:001737-9685 domestic cat Coat colour, white spotting, KIT-related KIT S insertion, gross (>20) Naturally occurring variant no Felis_catus_9.0 B1 g.164038110_164038111insN[7125] "an insertion of an entire feline endogenous retrovirus (FERV1) into intron 1 of the KIT gene." 2014 25085922 Genomic position in Felis_catus_9.0 is based on information provided by Leslie Lyons and Reuben Buckley.
1505 OMIA:000449-452646 American mink Shadow coat colour KIT S^h missense Naturally occurring variant unknown NNQGG.v01 NWR01000037.1 g.6253028G>T c.2374G>T p.(D792Y) 2022 35481560
1248 OMIA:002287-9823 pig Bama Xiang Zhu, China (Pig) Hypopigmentation (piebald) and deafness KIT missense Naturally occurring variant yes Sscrofa11.1 8 g.41485957T>A c.2418T>A p.(D806E) ENU mutagenesis was used to create these pigs, NM_001044525.1; c.2418T>A; NP_001037990.1; p.(D806E) (Xu et al., 2020) 2020 33042408
1135 OMIA:001745-9823 pig Cinta Senese, Italy (Pig) White belt KIT not known Naturally occurring variant no Sscrofa11.1 8 g.41488472C>T c.2499C>T p.(P833P) ENSSSCT00000009679.4:c.2499C>T ENSSSCP00000009430.3:p.Pro833= ENSSSCT00000062378.2:c.*1559C>T Sscrofa10.2 g.43,597,545C>T; Ensembl VEP analysis suggests that this can be a synonymous or 3_prime_UTR_variant depending on the transcript analysed rs328592739 rs328592739 2016 Reference not in PubMed; see OMIA 001745-9823 for reference details Ogorevc et al. (2017) reported the EVA ID of this variant as rs328592739
186 OMIA:001216-9913 taurine cattle Belgian Blue (Cattle) Shorthorn (Cattle) Roan KITLG missense Naturally occurring variant no ARS-UCD1.3 5 18262908G>T c.653C>A p.(A218D) 1999 10384045 NM_174375.2; NP_776800.1; published as c.654 variant, p.Ala193Asp. Variant information in this table were originally based on information listed in Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The coordinates were corrected after Cord Drögemüller notified OMIA curators that the previously listed variant was not present in roan cattle [17/11/2022]
1145 OMIA:002228-9615 dog Nova Scotia Duck Tolling Retriever (Dog) Poodle (Dog) Pigment intensity KITLG repeat variation Naturally occurring variant no CanFam3.1 15 Weich et al. (2020): "the reference genome shows two tandem copies of the CNV spanning a region of approximately 12 kb. The CNV is located in an intergenic region about 152 kb upstream from the closest gene, KITLG." 200922: g. info moved here (g.29821450_29832950) until it can be standardised 2020 31936656
1152 OMIA:002237-8090 Japanese medaka Few melanophore kitlga insertion, gross (>20) Naturally occurring variant no Otsuki et al. (2020): "the phenotype of fm medaka is attributable to insertion of a Tcb1-like transposon at the kitlga locus" 2020 31757930
74 OMIA:000819-9615 dog Shih Tzu (Dog) Prekallikrein deficiency KLKB1 missense Naturally occurring variant yes CanFam3.1 16 g.44501415A>T c.988T>A p.(F330I) 2011 20736516 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1495 OMIA:002425-9615 dog Chinese Shar-Pei (Dog) Ichthyosis, KRT1-related KRT1 deletion, small (<=20) Naturally occurring variant yes UU_Cfam_GSD_1.0 27 g.44229728_44229730del c.567_569del p.(N190del) NM_001003392.1; NP_001003392.1 2022 36251712
364 OMIA:001415-9615 dog Norfolk Terrier (Dog) Hyperkeratosis, epidermolytic KRT10 splicing Naturally occurring variant yes CanFam3.1 9 g.21866234G>T c.1125+1G>T XM_038676544.1; XP_038532472.1; experimentally confirmed splice defect; a single base GT>TT change in the consensus 5'-splice site of intron 5 2005 16029326
1579 OMIA:001415-9615 dog Chihuahua (Dog) Ichthyosis, epidermolytic KRT10 missense Naturally occurring variant yes UU_Cfam_GSD_1.0 9 g.21814695G>A c.437G>A p.(R146H) XM_038547368.1; XP_038403296 2023 37332248
1229 OMIA:002281-9685 domestic cat Domestic Shorthair Epidermolysis bullosa, simplex, KRT14-related KRT14 nonsense (stop-gain) Naturally occurring variant yes Felis_catus_9.0 E1 g.42361726G>A c.979C>T p.(Q327*) XM_003996860.5; XP_003996909.2 2020 32657488 Genomic position in Felis_catus_9.0 provided by Joshua Khamis.
936 OMIA:002088-9615 dog Dogue de Bordeaux (Dog) Palmoplantar keratoderma, nonepidermolytic, focal 1 KRT16 delins, small (<=20) Naturally occurring variant yes CanFam3.1 9 g.[21170012_21170013delinsCGGA;21170030del] c.[1147_1148delinsCGGA;1165del] p.(V383Rfs) XM_548101.4; XP_548101.2; published as p.(E392*) - protein coordinates updated to HGVS nomenclature 2015 25521457
856 OMIA:000245-9796 horse Bashkir Curly (Horse) Curly Horse (Horse) Curly coat KRT25 Crd missense Naturally occurring variant no EquCab3.0 11 g.21962991G>A c.266G>A p.(R89H) rs1095048844 rs1095048844 2018 29686323 29141579 Variant coordinates obtained from and/or confirmed by EBI's Some Effect Predictor (VEP) tool
777 OMIA:000246-9913 taurine cattle Aberdeen-Angus (Cattle) Ayrshire (Cattle) Montbéliarde (Cattle) Simmental (Cattle) Curly hair, karakul-type KRT27 missense Naturally occurring variant no ARS-UCD1.2 19 g.40982250G>C c.276C>G p.(N92K) rs384881761 rs384881761 2014 25017103 Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
1265 OMIA:002081-9913 taurine cattle Epidermolysis bullosa, simplex, KRT5-related` KRT5 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 5 g.27367604_27367606del c.534_536del p.(N178del) "27367604delCAA (NM_001008663.1:c.534_536delCAA), leading to a loss of an asparagine amino acid at residue 178 of the encoded KRT5 protein (NP_001008663.1:p.Asn178del)" (Jacinto et al., 2020). rs5334475014 2020 33135329 In an email dated 5 November 2020, Cord Drögemüller confirmed that the genomic specification for this variant is g.27367604_27367606delCAA
192 OMIA:002081-9913 taurine cattle Friesian cross (Cattle) Jersey cross Epidermolysis bullosa KRT5 missense Naturally occurring variant yes ARS-UCD1.2 5 g.27371128G>A c.1432G>A p.(E478K) rs5334474982 2005 15955091 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1480 OMIA:002081-9615 dog Cardigan Welsh Corgi (Dog) Epidermolysis bullosa, simplex, KRT5-related KRT5 missense Naturally occurring variant yes UU_Cfam_GSD_1.0 27 g.44080887C>T c.1426G>A p.(E476K) NM_001346035.1; NP_001332964.1 2022 36004757
662 OMIA:000394-9031 chicken Frizzle KRT6A deletion, gross (>20) Naturally occurring variant no GRCg6a 33 g.5251413_5251496del p.(V311_K333del) NM_001001313.2; NP_001001313.2; published as a 84bp deletion that covers positions −24 of exon 5 to +59 of intron 5 of KRT6A (called KRT75 in an earlier genome assembly); the deletion activates a cryptic splice site resulting in a 69 bp in-frame deletion in mRNA after splicing and a deletion of 23-amino acids (position 311–333) 2012 22829773
1337 OMIA:002114-9913 taurine cattle Hereford (Cattle) Hypotrichosis, KRT71-related KRT71 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 5 g.27331221_27331228del c.281_288del p.(M94Nfs*14) cDNA and protein positions based on NM_001075970.1 and NP_001069438.1, respectively 2021 34356054 210909: FN checked the ARS-UCD1.2 assembly, and discovered that the deletion spans 27331221 to 27331228. Thus g.27331221delTGTGCCCA was changed to g.27331221_27331228del. From NCBI's genome browser, worked out that the c. notation needs to be changed from c.281delTGTGCCCA to c.281_288del.
35 OMIA:000245-9615 dog Portuguese Water Dog (Dog) Curly coat KRT71 c^1 missense Naturally occurring variant no CanFam3.1 27 g.2539211C>T c.451C>T p.(R151W) NM_001197029.1; NP_001183958.1 rs23373415 rs23373415 2009 19713490 Genomic coordinates in CanFam3.1 and EVA ID provided by Robert Kuhn
1043 OMIA:000245-9615 dog Bichon Frise (Dog) Chesapeake Bay Retriever (Dog) Curly Coated Retriever (Dog) Irish Terrier (Dog) Lagotto Romagnolo (Dog) Spanish Water Dog (Dog) Curly coat KRT71 c^2 delins, small (<=20) Naturally occurring variant no CanFam3.1 27 g.2543230_2543237delinsACA c.1266_1273delinsACA p.(S422Rfs) NM_001197029.1; NP_001183958.1 2019 30444027 30456859 Genomic position in CanFam3.1 provided by Mateo Etcheveste and Robert Kuhn.
382 OMIA:001583-9685 domestic cat Sphynx (Cat) Sphynx hairless KRT71 Re^HR splicing Naturally occurring variant yes Felis_catus_9.0 B4 g.81048680C>T c.816+1G>A rs5334475135 2010 20953787 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
394 OMIA:001712-9685 domestic cat Selkirk Rex (Cat) Curly coat, Selkirk rex KRT71 Re^S splicing Naturally occurring variant no Felis_catus_9.0 B4 g.81050264C>G c.445-1G>C NM_001195239.1 2013 23770706 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
380 OMIA:001581-9685 domestic cat Devon Rex (Cat) Curly coat, Devon rex KRT71 re complex rearrangement Naturally occurring variant no Felis_catus_9.0 B4 g.[81046358_81046359insA;81046370_81046371insCTCCAACT;81046371_81046451del] c.[1108-4_1184del;1184_1185insAGTTGGAG;1196_1197insT] NM_001195239.1; published as c.1108-4_1184del;c.1184_1185insAGTTGGAG;c.1196insT; variant causes a splicing variation 2010 20953787 Genomic position in Felis_catus_9.0 is based on information provided by Leslie Lyons and Reuben Buckley.
1549 OMIA:002687-9940 sheep Fleece variation, fine wool KRT74 missense Naturally occurring variant no Oar_v4.0 3 g.133486008C>A c.367C>A p.(H123N) XM_004006324.3; XP_004006373.1; the C allele is associated with wool fineness rs427563779 rs427563779 2023 37137429
1398 OMIA:002486-9031 chicken Kirin (Chicken) Xiushui Yellow (Chicken) Frizzle KRT75L4 deletion, small (<=20) Naturally occurring variant no GRCg6a 33 g.5285437_5285451del g.5285437-5285451delGATGCCGGCAGGACG 2018 30572816
735 OMIA:001371-9615 dog Staffordshire Bull Terrier (Dog) L-2-hydroxyglutaricacidemia L2HGDH delins, small (<=20) Naturally occurring variant yes CanFam3.1 8 g.26723470_26723472delinsAAG c.1298_1300delinsCTT p.(L433_H434delinsPY) XM_858437.5; XP_863530.2; published as ENSCAFG00000014237; CanFam1.0: (c[1297T→C; 1299c→t]; p[Leu433Pro; His434Tyr]; coordinates in the table have been updated to a recent reference genome and / or transcript 2007 17475916
427 OMIA:001371-9615 dog Yorkshire Terrier (Dog) L-2-hydroxyglutaricacidemia L2HGDH missense Naturally occurring variant yes CanFam3.1 8 g.26760351T>C c.1A>G p.(M1?) XM_858437.5; published as p.(Met1?) 2012 22843824 Genomic coordinates in CanFam3.1 provided by Robert Kuhn
1535 OMIA:001371-9685 domestic cat Domestic Shorthair L-2-hydroxyglutaricacidemia L2HGDH nonsense (stop-gain) Naturally occurring variant yes F.catus_Fca126_mat1.0 B3 g.97881395G>A c.397C>T p.(Q133*) XM_023255678.2; XP_023111446.2 2023 36880414
1317 OMIA:001371-9685 domestic cat Domestic Longhair L-2-hydroxyglutaric aciduria L2HGDH missense Naturally occurring variant yes Felis_catus_9.0 B3 g.100207200T>C c.1301A>G p.(H434R) XM_023255678.1; XP_023111446.1 rs5334475154 2021 34062805
1399 OMIA:002459-9615 dog Staffordshire Bull Terrier (Dog) Congenital muscular dystrophy LAMA2 deletion, gross (>20) Naturally occurring variant yes CanFam3.1 1 g.67734331_67736575del c.610-1412_789+653del XM_003432522.2; 2022 34854126
1389 OMIA:002459-9615 dog Italian Greyhound (Dog) Congenital muscular dystrophy LAMA2 CMD nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 1 g.67883271G>A c.3285G>A p.(W1095*) XM_022419950.1; XP_022275658.1 2021 34828429
701 OMIA:001677-9615 dog German Pointer (Dog) Epidermolysis bullosa, junctionalis, LAMA3 LAMA3 insertion, gross (>20) Naturally occurring variant yes 7 "insertion (4818+207ins6.5 kb) of repetitive satellite DNA within intron 35 of the gene (LAMA3)" 2005 15737193
658 OMIA:001677-9796 horse American Saddle Horse (Horse) Epidermolysis bullosa, junctionalis, LAMA3-related LAMA3 deletion, gross (>20) Naturally occurring variant yes 8 "6589-bp deletion spanning exons 24-27 . . . in the LAMA3 gene in American Saddlebred foals" 2009 19016681
909 OMIA:001677-9913 taurine cattle Belgian Blue (Cattle) Epidermolysis bullosa, junctionalis, LAMA3-related LAMA3 nonsense (stop-gain) Naturally occurring variant unknown ARS-UCD1.2 24 g.32749369G>A c.7549C>T p.(R2517*) rs5334475046 2015 26370913 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1324 OMIA:001677-9615 dog Australian Cattle Dog X Epidermolysis bullosa, junctionalis, LAMA3 LAMA3 missense Naturally occurring variant yes CanFam3.1 7 g.64427161T>A c.8615T>A p.(D2867V) cDNA and protein positions based on XM_537297.6 and XP_537297.2, respectively 2021 34250689
1387 OMIA:002479-9913 taurine cattle Romagnola (Cattle) Hemifacial microsomia LAMB1 HFM missense Naturally occurring variant unknown ARS-UCD1.2 4 g.49019693G>A c.2002C>T p.(R668C) NM_001206519.1; NP_001193448.1; 2022 34796979
1239 OMIA:002269-9615 dog Australian Shepherd (Dog) Epidermolysis bullosa, junctionalis, LAMB3-related LAMB3 JEB missense Naturally occurring variant yes CanFam3.1 7 g.8286613A>G c.1174T>C p.(C392R) NC_006589.3:g.8286613A>G; XM_014115071.2:c.1174T>C; XP_013970546.1:p.Cys392Arg 2020 32906717
682 OMIA:001678-9913 taurine cattle Hereford (Cattle) Epidermolysis bullosa, junctionalis, LAMC2 LAMC2 deletion, gross (>20) Naturally occurring variant yes 16 "2.4 kb deletion encompassing the first exon of the LAMC2 gene" 2015 25888738
599 OMIA:001678-9796 horse Belgian Draft (Horse) Breton, France (Horse) Cavallo Agricolo Italiano da Tiro Pesante Rapido, Italy (Horse) Comtois (Horse) Epidermolysis bullosa, junctionalis, LAMC2-related LAMC2 insertion, small (<=20) Naturally occurring variant yes EquCab3.0 5 g.17498175dup c.1372dup p.(R458Pfs) NM_001081768.1; NP_001075237.1; published as c.1368insC; coordinates in the table have been updated to HGVS nomenclature (3'-rule) and recent reference genome and / or transcript inforamtion 1,372 Protein position: 458 2002 12230513 The genomic position in EquCab3.0 was provided by Margaret Higgins, working under the guidance of Professor Ernie Bailey [April 2022]
507 OMIA:001678-9940 sheep German Blackheaded Mutton (Sheep) Epidermolysis bullosa, junctionalis, LAMC2-related LAMC2 deletion, small (<=20) Naturally occurring variant yes Oar_rambouillet_v1.0 12 g.68856318_68856319del c.2746_2747del p.(A928*) FM872310 c.2746delCA 2011 21573221 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1168 OMIA:002251-9615 dog Airedale Terrier (Dog) Surfactant metabolism dysfunction, pulmonary LAMP3 missense Naturally occurring variant yes CanFam3.1 34 g.16092728C>T c.1159G>A p.(E387K) 2020 32150563
1371 OMIA:002460-9615 dog Labrador Retriever (Dog) Muscular dystrophy-dystroglycanopathy LARGE nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 10 g.30357716C>T c.1363C>T p.(R455*) 2021 34654610
449 OMIA:001160-9986 rabbit Hyperlipidaemia LDLR deletion, small (<=20) Naturally occurring variant yes "an in-frame deletion of 12 nucleotides that eliminates four amino acids from the cysteine-rich ligand binding domain of the LDL receptor" 1986 3010466
1556 OMIA:000499-9544 Rhesus monkey Hypercholesterolaemia LDLR nonsense (stop-gain) Naturally occurring variant yes 19 p.(W284*) G>A in exon 6 in position 914 of the human cDNA resulting in p.(W284*) 1990 2326270
1557 OMIA:000499-9544 Rhesus monkey Hypercholesterolaemia LDLR missense Naturally occurring variant yes 19 c.245G>A p.(C82Y) 2023 37186395
987 OMIA:000499-9823 pig Hypercholesterolaemia LDLR missense Naturally occurring variant yes Sscrofa11.1 2 g.69841413C>T c.250C>T p.(R84C) rs701604154 rs701604154 1998 9556295 The genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcripts: XM_021080444.1, XM_021080449.1, XM_021080452.1, XM_021080457.1 by Stephanie Shields (27/05/2020)
269 OMIA:001596-9615 dog Lagotto Romagnolo (Dog) Epilepsy, benign familial juvenile LGI2 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 3 g.85210442A>T c.1558A>T p.(K520*) XM_022416405.1; XP_022272113.1; published as c.1552A>T & p.(K518*); coordinates in the table have been updated to a recent reference genome and / or transcript 2011 21829378
362 OMIA:002314-9615 dog Czechoslovakian Wolfdog (Dog) German Shepherd Dog (Dog) Saarloos Wolfhond (Dog) Tibetan Terrier (Dog) Pituitary dwarfism LHX3 splicing Naturally occurring variant yes 9 "a deletion of one of six 7 bp [GTGTTTT] repeats in intron 5 of LHX3" 2011 22132174
608 OMIA:002314-9615 dog German Shepherd Dog (Dog) Pituitary dwarfism LHX3 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 9 g.49252491_49252493dup c.545_547dup p.(N182dup) NM_001197187.1; NP_001184116.1; published as c.545_547dupACA 2011 22132174 Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
1415 OMIA:002516-9913 taurine cattle Brown Swiss (Cattle) Haplotype with homozygous deficiency OH4 LIG3 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.15080336_15080341del c.2483_2484+4delAGGTG p.K828fs NM_001038107.2 rs5381613636 2021 34915862
450 OMIA:001566-9986 rabbit Rex coat LIPH deletion, small (<=20) Naturally occurring variant no 14 c.1362delA 2011 21552526
1203 OMIA:002273-9685 domestic cat Ural Rex (Cat) Curly coat, Ural Rex LIPH urx delins, small (<=20) Naturally occurring variant no Felis_catus_9.0 C2 g.84136341_84136347delinsC c.477_483delinsC p.(S160_G161del) XM_023260327.1; XP_023116095.1; changed from c.478_483del to c.477_483delinsC in accordance with HGVS nomenclature [17/2/2022] 2020 32463158
649 OMIA:002389-9685 domestic cat Maine Coon (Cat) Spinal muscular atrophy LIX1 deletion, gross (>20) Naturally occurring variant yes Felis_catus_9.0 A1 g.161036890_161176706del published as "a ~140 kb deletion removing exons 4-6 of LIX1 and all except exon 1 of LNPEP" 2006 16899656 Genomic position in Felis_catus_9.0 is based on information provided by Leslie Lyons and Reuben Buckley.
663 OMIA:001612-9031 chicken Silkie (Chicken) Oligozeugodactyly LMBR1 deletion, gross (>20) Naturally occurring variant yes 2 "a large deletion in LMBR1-intron 5, eliminating most of the limb-specific enhancer conserved sequence." 2011 21509895
434 OMIA:000810-9685 domestic cat Polydactyly LMBR1 Pd^UK2 regulatory Naturally occurring variant yes Felis_catus_9.0 A2 g.169532842T>A regulatory variant in the ZPA regulatory sequence (ZRS); published as AGACACAG[A/T]AATGAG 2008 18156157 Genomic position in Felis_catus_9.0 provided by Joshua Khamis.
432 OMIA:000810-9685 domestic cat Maine Coon (Cat) Polydactyly LMBR1 Pd^Hw regulatory Naturally occurring variant yes Felis_catus_9.0 A2 g.169532844T>C regulatory variant in the ZPA regulatory sequence (ZRS); published as AGACAC[A/G]GAAATGAG 2008 18156157 Genomic position in Felis_catus_9.0 provided by Joshua Khamis, Leslie Lyons and Reuben Buckley.
433 OMIA:000810-9685 domestic cat Polydactyly LMBR1 Pd^UK1 regulatory Naturally occurring variant yes Felis_catus_9.0 A2 g.169533066C>G regulatory variant in the ZPA regulatory sequence (ZRS); published as CC[G/C]GTG 2008 18156157 Genomic position in Felis_catus_9.0 provided by Joshua Khamis, Leslie Lyons and Reuben Buckley.
1583 OMIA:002700-9615 dog Australian Shepherd (Dog) Hyposegmentation of granulocytes LMBR1L splicing Naturally occurring variant unknown UU_Cfam_GSD_1.0 27 g.41169674C>T c.191+1G>A XM_038577534.1 2023 37347778
1521 OMIA:001213-9986 rabbit Emery-Dreifuss muscular dystrophy LMNA missense Base-editing yes p.(L530P) 2022 35282412
1401 OMIA:001213-9823 pig Yucatan Miniature, United States of America (Pig) Hutchinson-Gilford progeria syndrome LMNA splicing Genome-editing (CRISPR-Cas9) yes Sscrofa11.1 4 g.93900345G>A c.1824C>T 2019 30911407
1638 OMIA:002796-9615 dog Nova Scotia Duck Tolling Retriever (Dog) Cardiomyopathy, dilated, LMNA-related LMNA deletion, small (<=20) Naturally occurring variant yes UU_Cfam_GSD_1.0 7 g.41688530del c.1726del p.(D576Tfs*124) NM_001287151.1; NP_001274080 2023 37925523
1046 OMIA:001701-13146 budgerigar Feater colour, blue LOC101880715 missense Naturally occurring variant no 1 p.(R644W) 2017 28985565
393 OMIA:000344-9031 chicken Fayoumi (Chicken) Epilepsy LOC430486 splicing Naturally occurring variant yes 25 c581-4CC>TG 2011 22046416
108 OMIA:002071-9615 dog Labrador Retriever (Dog) Macular corneal dystrophy LOC489707 missense Naturally occurring variant yes CanFam3.1 5 g.75279699C>A c.814C>A p.(R272S) 2016 26585178 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1151 OMIA:001928-9615 dog Golden Retriever (Dog) Myasthenic syndrome, congenital, COLQ-related LOC608697 missense Naturally occurring variant yes CanFam3.1 23 g.27175559G>A c.880G>A p.(G294R) 2020 31769119
900 OMIA:001928-9615 dog Labrador Retriever (Dog) Myasthenic syndrome, congenital LOC608697 missense Naturally occurring variant yes CanFam3.1 23 g.27176737T>C c.1010T>C p.(I337T) XM_858278.5; XP_863371.1 2014 25166616 Genomic position in CanFam3.1 provided by Robert Kuhn
1314 OMIA:002336-9615 dog Rottweiler (Dog) Nonsyndromic hearing loss LOXHD1 missense Naturally occurring variant yes CanFam3.1 7 g.44806821G>C c.5747G>C p.(G1914A) XM_022421426.1, c.5747G>C; J9PAE4, p.(G1914A) (Hytönen et al., 2021) 2021 33983508
522 OMIA:001684-9685 domestic cat Cornish Rex (Cat) German Rex (Cat) Curly/woolly coat, Cornish Rex and German Rex LPAR6 r deletion, small (<=20) Naturally occurring variant no Felis_catus_9.0 A1 g.22919307_22919310del c.250_253del p.(F84Efs*9) NM_001309049.1; NP_001295978.1; c.250_253delTTTG 2013 23826204 The genomic location on Felis_catus_9.0 and transcript information is based on Rodney et al. 2021 (PMID: 33785770)
131 OMIA:001210-9685 domestic cat Hyperlipoproteinaemia LPL missense Naturally occurring variant yes Felis_catus_9.0 B1 g.38078551C>T c.1315G>A p.(G439R) NM_001042567.1; NP_001036032.1; published as c.1234G>A and p.(G412R); coordinates in the table have been updated to a recent reference genome and / or transcript 1996 8636438 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1260 OMIA:001486-9615 dog Beagle (Dog) Night blindness, congenital stationary, LRIT3-related LRIT3 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 32 g.30038863del c.763del p.(K245Nfs*5) c.763delG 2019 31578364
378 OMIA:000963-9913 taurine cattle Angus (Cattle) Syndactyly (mule foot) LRP4 splicing Naturally occurring variant yes ARS-UCD1.2 15 g.76792588C>T c.5385+1G>A "a G to A transition at the first nucleotide in the splice donor site of intron 37" rs5334475003 2006 16963222 Variant information was initially kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4
627 OMIA:000963-9913 taurine cattle Holstein Friesian (Cattle) Syndactyly (mule foot) LRP4 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 15 g.76800972_76800973delinsAT c.4863_4864delinsAT p.(N1621_G1622delinsKC) Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4 2006 16859890
769 OMIA:000963-9913 taurine cattle Simmental (Cattle) Syndactyly (mule foot) LRP4 missense Naturally occurring variant yes ARS-UCD1.2 15 g.76807508C>T c.3595G>A p.(G1199S) rs3423411024 2007 17319939 Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4
768 OMIA:000963-9913 taurine cattle Simmental Charolais Cross Syndactyly (mule foot) LRP4 missense Naturally occurring variant yes ARS-UCD1.2 15 g.76812187C>T c.2719G>A p.(G907R) rs5334474664 2007 17319939 Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4
610 OMIA:002017-9685 domestic cat Siamese (Cat) Glaucoma 3, primary congenita LTBP2 duplication Naturally occurring variant yes Felis_catus_9.0 B3 g.121929604_121929607dup c.1449_1452dup p.(A485Gfs) ENSFCAT00000064963.2; ENSFCAP00000046761.2; published as "a 4-bp insertion in exon 8 located at chrB3: 120995236"[felCat5] 2016 27149523 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1394 OMIA:002485-9685 domestic cat British Shorthair (Cat) Skeletal dysplasia, LTBP3-related LTBP3 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 D1 g.110690432del c.158del p.(G53Afs*16) XM_023240055.1; XP_023095823.1 2021 34946872
605 OMIA:001721-32536 cheetah Coat colour, king LVRN insertion, small (<=20) Naturally occurring variant no p.(N977Kfs*110) 2012 22997338
1429 OMIA:001429-9685 domestic cat Tabby, atypical swirl LVRN Ta^as missense Naturally occurring variant no Felis_catus_9.0 A1 p.(T139N) DNA coordinates not published; associated with an atypical swirled pattern but is incompletely penetrant 2012 22997338
307 OMIA:001429-9685 domestic cat Blotched tabby LVRN Ta^b2 nonsense (stop-gain) Naturally occurring variant no Felis_catus_9.0 A1 g.96753652C>A c.176C>A p.(S59*) XM_023254329.1; XP_023110097.1 2012 22997338 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
124 OMIA:001429-9685 domestic cat Blotched tabby LVRN Ta^b1 missense Naturally occurring variant no Felis_catus_9.0 A1 g.96754158G>A c.682G>A p.(D228N) XM_023254329.1; XP_023110097.1 2012 22997338 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
308 OMIA:001429-9685 domestic cat Blotched tabby LVRN Ta^b3 nonsense (stop-gain) Naturally occurring variant no Felis_catus_9.0 A1 g.96813484G>A c.2522G>A p.(W841*) XM_023254329.1; XP_023110097.1; Felis_catus_9.0 represents g.96813484A 2012 22997338 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1348 OMIA:002431-9694 tiger Pseudomelamism LVRN missense Naturally occurring variant no PanTig1.0 A1 c.1360C>T p.H454Y Sagar et al. (2021): "[Assembly PanTig1.0(GCF_000464555.1)]. . . . (Taqpep c.1360C > T); XP_007086933.1) of the protein (Taqpep p.H454Y)" 2021 34518374
518 OMIA:000185-452646 American mink Chediak-Higashi syndrome LYST deletion, small (<=20) Naturally occurring variant yes c.9468delC 2013 22762706
1359 OMIA:002449-94885 corn snake Skin colour, lavender LYST nonsense (stop-gain) Naturally occurring variant no c.9508C>T p.(Q3169*) 2020 33020272
183 OMIA:000185-9913 taurine cattle Japanese Black, Japan (Cattle) Chediak-Higashi syndrome LYST missense Naturally occurring variant yes ARS-UCD1.2 28 g.8464077T>C c.6044A>G p.(H2015R) rs481318527 1999 10594238 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1147 OMIA:000185-9685 domestic cat Persian (Cat) Chediak-Higashi disease LYST repeat variation Naturally occurring variant yes Felis_catus_9.0 D2 g.13289500_13308861dup c.8347-2422_9548+1749dup Buckley et al. (2020): "a tandem segmental duplication encompassing exons 30 through to 38 (NM_001290242.1:c.8347-2422_9548 + 1749dup) (NC_018733.3:g.13289500_13308861dup)" 2020 31919397
249 OMIA:000625-10141 domestic guinea pig Mannosidosis, alpha Man2b1 missense Naturally occurring variant yes c.679C>T p.(R227W) 2002 11959458
199 OMIA:000625-9913 taurine cattle Galloway (Cattle) Mannosidosis, alpha MAN2B1 missense Naturally occurring variant yes ARS-UCD1.2 7 g.12840983G>A c.662G>A p.(R221H) rs5334474945 1997 9208932 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
198 OMIA:000625-9913 taurine cattle Angus (Cattle) Murray Grey (Cattle) Mannosidosis, alpha MAN2B1 missense Naturally occurring variant yes ARS-UCD1.2 7 g.12842292T>C c.961T>C p.(F321L) rs5334474873 1997 9208932 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1628 OMIA:000625-9615 dog Doberman Pinscher (Dog) Mannosidosis, alpha MAN2B1 missense Naturally occurring variant unknown Dog10K_Boxer_Tasha 20 g.49320989A>G c.311A>G p.(D104G) XM_005632833.4; XP_005632890.1 2023 37761886
499 OMIA:000625-9685 domestic cat Persian (Cat) Mannosidosis, alpha MAN2B1 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 A2 g.9011118_9011121del c.1749_1752del p.(Q584Afs) NM_001009222.1; NP_001009222.1 1997 9396732 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
297 OMIA:000626-9913 taurine cattle Salers (Cattle) Mannosidosis, beta MANBA nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 6 g.22188765G>A c.2574G>A p.(W858*) rs5334475094 1999 10594236 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
451 OMIA:000626-9925 goat Mannosidosis, beta MANBA deletion, small (<=20) Naturally occurring variant yes ARS1 6 g.22409150del c.1398del 1996 8921369 The genomic location on ARS1 was determined by Katie Eager, EMAI, NSW Department of Primary Industries
1093 OMIA:000626-9615 dog Mixed Breed (Dog) Beta mannosidosis MANBA duplication Naturally occurring variant yes CanFam3.1 32 g.24057654_24057658dup c.2377_2381dup p.(H794Hfs) XM_005639236.3; XP_005639293.1; published as c.2377_2381dupTATCA 2019 31439511 Genomic and protein coordinates in CanFam3.1 provided by Robert Kuhn
1072 OMIA:000626-9615 dog German Shepherd Dog (Dog) Beta mannosidosis MANBA missense Naturally occurring variant yes CanFam3.1 32 g.24147500A>T c.560T>A p.(I187N) 2019 30983534
1636 OMIA:000626-9685 domestic cat Domestic Shorthair Mannosidosis, beta MANBA missense Naturally occurring variant yes Felis_catus_9.0 B1 g.121800342G>A c.2506G>A p.(G836R) ENSFCAT00000007560, variant was reported in a single affected cat 2023 37913889
1473 OMIA:002381-9913 taurine cattle Romagnola (Cattle) Skeletal-cardio-enteric dysplasia MAP2K2 missense Naturally occurring variant yes ARS-UCD1.2 7 g.19923991C>T c.535G>A p.(R179W) NM_001038071.2; NP_001033160.2; possible de-novo causal variant 2021 34209498
943 OMIA:001432-9615 dog Dachshund, Miniature Long-Haired (Dog) Cone-rod dystrophy 4 MAP9 deletion, gross (>20) Naturally occurring variant yes CanFam3.1 15 g.52905336_52927296del c.75+181_1378-215del XM_005629374.1; An approximately 22kb deletion "approximately 30 Mb upstream of RPGRIP1 . . . The deletion breakpoints were identified in MAP9 intron 10 and in a downstream partial MAP9 pseudogene." … " The size of the deletion based on genome build CanFam3.1 MAP9_corrected is 21,961 bp, with deletion breakpoints in intron 10 of MAP9 and MAP9." 2016 27017229
1416 OMIA:002517-9913 taurine cattle Brown Swiss (Cattle) Haplotype with homozygous deficiency BH6 MARS2 BH6 missense Naturally occurring variant yes ARS-UCD1.2 2 g.86191230G>A c.1553G>A p.(R518Q) NM_001098971.1 rs434672528 2021 34915862
1646 OMIA:002804-9544 Rhesus monkey Germline mutation rate MBD4 deletion, small (<=20) Naturally occurring variant unknown MMul10 2 g.147059371del c.984del p.I330Sfs*2 ENSMMUG00000012723 2023 37984997
413 OMIA:002021-9796 horse Quarter Horse (Horse) Coat colour, brindle 1 MBTPS2 splicing Naturally occurring variant no EquCab3.0 X g.17286855T>C c.1437+4T>C rs3434246715 2016 27449517
1007 OMIA:001199-10141 domestic guinea pig Brown coat colour MC1R e (MC1R*4) deletion, gross (>20) Naturally occurring variant no Vidal (2018): "a deletion of 2760 bp, including the entire MC1R coding region" 2018 30101449
674 OMIA:001199-30640 gray squirrel Melanism (black) MC1R E^B deletion, gross (>20) Naturally occurring variant no MC1RΔ24 allele E^B ["at amino acid positions 87-94"] 2009 19643815
250 OMIA:001199-46844 Geoffroy's cat Melanism (black coat) MC1R missense Naturally occurring variant no p.(C125R) 2015 25695801
1002 OMIA:002156-46218 Chinese painted quail Feather colour, Blue Face MC1R missense Naturally occurring variant no p.(E92K) 2018 29974967
1328 OMIA:000374-495946 Eleonora's falcon Feather colour, extended black MC1R deletion, small (<=20) Naturally occurring variant no p.(M114_V117del) 2011 21696477
1100 OMIA:000374-57662 red-footed booby White plumage MC1R haplotype Naturally occurring variant no p.(M85V) + p.(R207H) 2007 17602182
1003 OMIA:002155-46218 Chinese painted quail Feather colour, Red Breasted MC1R missense Naturally occurring variant no p.(P292L) 2018 29974967
1173 OMIA:001199-37349 woolly mammoth Light hair colour MC1R missense Naturally occurring variant no p.(R67C) 2006 16825562
1101 OMIA:000374-70340 Lesser snow goose Blue plumage MC1R missense Naturally occurring variant no p.(V85M) 2004 15031505
262 OMIA:001199-494514 Arctic fox Blue coat colour MC1R Ed missense Naturally occurring variant no p.[(G5C);(F280C)] The blue (Ed) allele is a haplotype comprising two missense variants (p.Gly5Cys and p.Phe280Cys) (Våge et al., 2005) 2005 15982782
1271 OMIA:001199-30532 fallow deer White coat colour MC1R missense Naturally occurring variant no c.143T>C p.(L48P) NM_174108.2:c.143T>C; NP_776533.1:p.(L48P) 2020 33213385
180 OMIA:001199-9870 reindeer Coat colour, extension MC1R missense Naturally occurring variant no c.218T>C p.(M73T) 2014 25039753
448 OMIA:001199-9986 rabbit California (Rabbit) Champagne-Silberkaninchen, Germany (Rabbit) Checkered Giant Checkered Small Dutch (Rabbit) New Zealand White (Rabbit) White Giant (Rabbit) Dominant black or Steel MC1R E(D) or E(S) deletion, small (<=20) Naturally occurring variant no c.280_285del 2006 16978179
630 OMIA:001199-9986 rabbit Coloured dwarf Dutch (Rabbit) English Lop English Spot (Rabbit) Fauve de Borgogne (Rabbit) Lop Lop dwarf New Zealand Red (Rabbit) Saxon Gold Thüringer (Rabbit) Red/fawn/yellow MC1R e deletion, gross (>20) Naturally occurring variant no c.304_333del30 2006 16978179
18 OMIA:001494-9103 turkey Feather colour, dominant black MC1R missense Naturally occurring variant no c.364A>T p.(I122F) 2010 20634512
1329 OMIA:000374-120794 gyrfalcon Feather colour, extended black MC1R missense Naturally occurring variant no c.376A>G p.(I126V) 2012 22497627
996 OMIA:001199-9793 ass (donkey) Âne normand, France (Ass) Miniature, United States of America (Ass) Red coat colour MC1R e missense Naturally occurring variant no c.629T>C p.(M210T) 2014 25155046
1006 OMIA:001199-10141 domestic guinea pig Brown coat colour MC1R e (MC1R*2) missense Naturally occurring variant no c.749T>C p.(L250Q) 2018 30101449
181 OMIA:001199-9870 reindeer Coat colour, extension MC1R missense Naturally occurring variant no c.839T>G p.(F280C) 2014 25039753
1346 OMIA:001199-37190 antarctic fur seal Hypopigmentation (blond) MC1R missense Naturally occurring variant unknown c.872C>T p.(S291F) 2016 27547348
19 OMIA:001494-9103 turkey Feather colour, black-wing bronze MC1R missense Naturally occurring variant no c.887C>T p.(A296V) 2010 20634512
1009 OMIA:001199-9838 Arabian camel White coat colour MC1R missense Naturally occurring variant no c.901C>T p.(R301C) KU179867; c.901C>T; p.R301C 2018 29893870
328 OMIA:001494-9103 turkey Bronze feathers MC1R nonsense (stop-gain) Naturally occurring variant no c.96G>A 2010 20634512
256 OMIA:001435-93934 Japanese quail Feather colour, extended brown MC1R missense Naturally occurring variant no c.?G>A p.(E92K) 2006 16734695
1160 OMIA:001199-9986 rabbit Angora (Rabbit) Checkered Giant Dutch (Rabbit) Giant Grey Japanese (Rabbit) Rheinische Schecken (Rabbit) Japanese brindling MC1R eJ complex rearrangement Naturally occurring variant no c.[124G>A;125_130del6] "6 bp-in frame deletion flanked by a G > A transition in 5' (c.[124G>A;125_130del6]) that was present in all animals with Japanese brindling coat colour and pattern." (Fontanesi et al., 2010) 2010 20594318
1509 OMIA:001199-9913 taurine cattle Abondance (Cattle) Brown Swiss (Cattle) Evolèner, Switzerland (Cattle) Herens (Cattle) Holstein Friesian (Cattle) Itäsuomenkarja, Finland (Cattle) Original Schweizer Braunvieh, Switzerland (Cattle) Rotes Höhenvieh, Germany (Cattle) Simmental (Cattle) Recessive red MC1R e^v2 missense Naturally occurring variant no ARS-UCD1.2 18 g.14705638G>A c.263G>A p.(S88N) NM_174108; NP_776533 rs5412784355 2022 35451516
185 OMIA:001199-9913 taurine cattle Angus (Cattle) Holstein Friesian (Cattle) Iceland Pony (Horse) Dominant black MC1R E^D missense Naturally occurring variant no ARS-UCD1.2 18 g.14705671T>C c.296T>C p.(L99P) NM_174108; NP_776533 rs109688013 rs109688013 1995 8535072 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1167 OMIA:001544-9913 taurine cattle Rat-tail syndrome MC1R E^D missense Naturally occurring variant no ARS-UCD1.2 18 g.14705671T>C c.296T>C p.(L99P) rs109688013 rs109688013 2016 27037038
485 OMIA:001199-9913 taurine cattle Angus (Cattle) Fries Roodbont, Netherlands (Cattle) Simmental (Cattle) Recessive red MC1R e deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 18 g.14705685del c.310del p.(G104Vfs*53) NM_174108; NP_776533 rs110710422 rs110710422 1995 8535072 Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1508 OMIA:001199-9913 taurine cattle Angus (Cattle) Brown Swiss (Cattle) Evolèner, Switzerland (Cattle) Herens (Cattle) Holstein Friesian (Cattle) Limousin (Cattle) Normande (Cattle) Original Schweizer Braunvieh, Switzerland (Cattle) Witrood Ras van Belgie, Belgium (Cattle) recessive red MC1R e^v1 missense Naturally occurring variant no ARS-UCD1.2 18 g.14705799C>T c.424C>T p.(R142C) NM_174108; NP_776533 rs3423445958 2022 35451516
1332 OMIA:001199-9925 goat Murcia-Granada (Goat) Black coat colour MC1R missense Naturally occurring variant no ARS1 18 g.16105786C>G c.801C>G p.(C267W) cDNA position based on transcript ENSCHIT00000014455.1 rs669694251 2009 19706191
343 OMIA:001199-9615 dog Irish Setter (Dog) Labrador Retriever (Dog) Red/yellow coat MC1R e^1 nonsense (stop-gain) Naturally occurring variant no CanFam3.1 5 g.63694334G>A c.916C>T p.(R306*) NM_001014282.2; NP_001014304.2; ROS_Cfam_1.0:g.63922309A>G rs851563576 rs851563576 2000 10602988 Genomic location provided by Professor Claire Wade
1645 OMIA:001199-9615 dog Alaskan Klee Kai (Dog) Alaskan Malamute (Dog) Basenji (Dog) Basset Fauve de Bretagne (Dog) Beagle (Dog) Chesapeake Bay Retriever (Dog) Chihuahua (Dog) Chinese Crested (Dog) Chinook (Dog) English Foxhound (Dog) Finnish Hound (Dog) Finnish Lapphund (Dog) Finnish Spitz (Dog) Karelian Bear Dog (Dog) Lapponian Herder (Dog) Peruvian Hairless Dog (Dog) Phalène (Dog) Plott Hound (Dog) Saarloos Wolfhond (Dog) Siberian Husky (Dog) Tamaskan Dog (Dog) Coat colour, reduced expression of eumelanin MC1R e^A missense Naturally occurring variant no CanFam3.1 5 g.63694349G>A c.901C>T p.(R301C) NM_001014282.2; NP_001014304.2; variant was initially identified in ancient canids and later reported in additional breeds PMID:33292722 2013 24098367
997 OMIA:001199-9615 dog Alaskan Husky (Dog) Siberian Husky (Dog) White coat colour MC1R e^3 deletion, small (<=20) Naturally occurring variant no CanFam3.1 5 g.63694433_63694434del c.816_817del p.(I272Mfs*22) NM_001014282.2; NP_001014304.2; published as c.816_817delCT 2018 29932470 Genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
34 OMIA:001590-9615 dog Belgian Shepherd Dog, Malinois (Dog) Leonberger (Dog) Black melanistic mask MC1R E^M missense Naturally occurring variant no CanFam3.1 5 g.63694460C>T c.790A>G p.(M264V) rs24201590 rs24201590 2003 12692165 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. Correction to genomic details provided by Professor Claire Wade.
32 OMIA:001495-9615 dog Afghan Hound (Dog) Saluki (Dog) Grizzle MC1R E^G missense Naturally occurring variant no CanFam3.1 5 g.63695017C>A c.233G>T p.(G78V) NM_001014282.2; NP_001014304.2 2010 20525767 Genomic coordinates in CanFam3.1 provided by Robert Kuhn
998 OMIA:001199-9615 dog Australian Cattle Dog (Dog) Cream coat colour MC1R e^2 regulatory Naturally occurring variant no CanFam3.1 5 g.63695679C>G c.-432G>C NM_001014282.1 2018 29932470
154 OMIA:001199-9796 horse Coat colour, chesnut MC1R e missense Naturally occurring variant no EquCab3.0 3 g.36979560C>T c.248C>T p.(S83F) ENSECAT00000129995.1; ENSECAP00000088247.1 rs68458866 rs68458866 1996 8995760 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
155 OMIA:001199-9796 horse Coat colour, chesnut MC1R e^a missense Naturally occurring variant no EquCab3.0 3 g.36979562G>A c.250G>A p.(D84N) ENSECAT00000129995.1; ENSECAP00000088247.1 rs3443929753 rs3443929753 2000 11086549 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
123 OMIA:001199-9685 domestic cat Norwegian Forest Cat (Cat) Coat colour, amber MC1R e missense Naturally occurring variant no Felis_catus_9.0 E2 g.63829934G>A c.250G>A p.(D84N) NM_001009324.1; NP_001009324.1 rs5334475156 2009 19422360 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
561 OMIA:001199-9685 domestic cat Burmese (Cat) Coat colour, russet MC1R e^r deletion, small (<=20) Naturally occurring variant no Felis_catus_9.0 E2 g.63830124_63830126del c.440_442del p.(F147del) NM_001009324.1; NP_001009324.1; published as c.439_441del and p.(F146del); coordinates in the table have been updated to a recent reference genome and / or transcript 2017 27671997 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1090 OMIA:001199-9685 domestic cat Kurilian Bobtail (Cat) Coat colour, copal MC1R e^c deletion, small (<=20) Naturally occurring variant no Felis_catus_9.0 E2 g.63830324_63830353del c.640_669del p.(A214_R223del) NM_001009324.1; NP_001009324.1 2019 31361350
817 OMIA:000374-9031 chicken Feather colour, extended black MC1R regulatory Naturally occurring variant no GRCg6a 11 g.18840609C>T c.-37C>T 5 prime UTR variant rs733919322 rs733919322 2017 28699279 ENSGALT00000096195.1:c.-37C>T
818 OMIA:000374-9031 chicken Feather colour, extended black MC1R E missense Naturally occurring variant no GRCg6a 11 g.18840857T>C c.212T>C p.(M71T) ENSGALT00000096195.1:c.212T>C ENSGALP00000071620.1:p.Met71Thr rs312264213 rs312264213 2017 28699279
6 OMIA:000374-9031 chicken Feather colour, extended black MC1R E missense Naturally occurring variant no GRCg6a 11 g.18840919G>A c.274G>A p.(E92K) ENSGALT00000096195.1:c.274G>A ENSGALP00000071620.1:p.Glu92Lys rs314881228 rs314881228 2003 12873211
1306 OMIA:002108-9031 chicken Fayoumi (Chicken) Barring, autosomal MC1R E*R(Fay), Pg missense Naturally occurring variant no GRCg6a 11 g.18841043T>A c.398T>A p.(L133Q) rs737523889 rs737523889 2021 33793042
7 OMIA:000374-9031 chicken Feather colour, buttercup MC1R missense Naturally occurring variant no GRCg6a 11 g.18841289A>C c.644A>C p.(H215P) ENSGALT00000096195.1:c.644A>C ENSGALP00000071620.1:p.His215Pro rs735789743 rs735789743 2003 12873211
1142 OMIA:000374-9031 chicken Mie-Jidori, Japan (Chicken) Feather colour, wheaten-like MC1R e^m missense Naturally occurring variant no GRCg6a 11 g.18841289A>C c.644A>C p.(H215P) ENSGALT00000096195.1:c.644A>C ENSGALP00000071620.1:p.His215Pro rs735789743 rs735789743 2020 31977074
1110 OMIA:001199-9940 sheep Valle del Belice, Italy (Sheep) Recessive pheomelanism MC1R e missense Naturally occurring variant no Oar_rambouillet_v1.0 14 g.15487353C>T c.199C>T p.(R67C) 2010 Reference not in PubMed; see OMIA 001199-9940 for reference details The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
229 OMIA:001199-9940 sheep Corriedale (Sheep) Dala (Sheep) Damara (Sheep) Merino (Sheep) Dominant black MC1R E^D missense Naturally occurring variant no Oar_rambouillet_v1.0 14 g.15487372T>A c.218T>A p.(M73K) 1999 9892731 c.218T>A obtained from Fontanesi et al. (2010); breeds obtained from Rochus et al. (2019); the genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
228 OMIA:001199-9940 sheep Massese, Italy (Sheep) Dominant black MC1R E^D missense Naturally occurring variant no Oar_rambouillet_v1.0 14 g.15487515G>A c.361G>A p.(D121N) 1999 9892731 c.361G>A obtained from Fontanesi et al. (2010); breed obtained from Ruchus et al. (2019); the genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
1108 OMIA:001199-9940 sheep Gute (Sheep) Swedish Fur (Sheep) Värmlandsfår, Sweden (Sheep) Dominant black MC1R missense Naturally occurring variant no Oar_rambouillet_v1.0 14 g.15487606G>A c.452G>A p.(R151Q) 2019 31475378 The genomic location on Oar_rambouillet_v1.0 was determined by Katie Eager, EMAI, NSW Department of Primary Industries.
170 OMIA:001199-9823 pig Duroc (Pig) Red MC1R e missense Naturally occurring variant no Sscrofa11.1 6 g.181461C>T c.727G>A p.(A243T) Variant is called p.(A240T) in original paper (Kijas et al., 1998). Two substitutions were found in recessive red (e/e) animals p.(A161V) and p.(A240T) - the p.(A240T) was considered as causative (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2 rs321432333 1998 9799269
171 OMIA:001199-9823 pig Duroc (Pig) Red MC1R e missense Naturally occurring variant no Sscrofa11.1 6 g.181697G>A c.491C>T p.(A164V) Variant is called p.(A161V) in original paper (Kijas et al., 1998). Two substitutions were found in recessive red (e/e) animals p.(A161V) and p.(A240T) - the p.(A240T) was considered as causative (Kijas et al., 1998). cDNA and protein location based in this table are based on transcript ENSSSCT00000022534.2 rs45435032 1998 9799269
169 OMIA:001199-9823 pig Hampshire Down (Sheep) Dominant black MC1R E^D2 missense Naturally occurring variant no Sscrofa11.1 6 g.181818C>T c.370G>A p.(D124N) Variant is called p.(D121N) in original paper (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. rs326921593 rs326921593 2016 27703696 9799269
168 OMIA:001199-9823 pig Large Black (Pig) Meishan (Pig) Dominant black MC1R E^D1 missense Naturally occurring variant no Sscrofa11.1 6 g.181883A>G c.305T>C p.(L102P) Variant is called p.(L99P) in original paper (Kijas et al., 1998). Two silent (p.(A240A), p.(N118N)) and two missense substitutions p.(V92M) and p.(L99P) were found in dominant black Asian pigs (E^D1/E^D1) (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. rs45434630 rs45434630 1998 9799269
1290 OMIA:001199-9823 pig Large Black (Pig) Meishan (Pig) Dominant black MC1R E^D1 missense Naturally occurring variant no Sscrofa11.1 6 g.181905C>T c.283G>A p.(V95M) Variant is called p.(V92M) in original paper (Kijas et al., 1998). Two silent (p.(A240A), p.(N118N)) and two missense substitutions p.(V92M) and p.(L99P) were found in dominant black Asian pigs (E^D1/E^D1) (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. rs45434629 rs45434629 1998 9799269
597 OMIA:001199-9823 pig Bama Xiang Zhu, China (Pig) Pietrain (Pig) Coat colour, black spotting on red or white background MC1R E^P, E^qy insertion, small (<=20) Naturally occurring variant no Sscrofa11.1 6 g.182126_182127insGG c.67_68insCC p.(R23Pfs*33) Variant was published as nt67insCC (Kijas et al., 2001), g.462-463CC (Wu et al., 2017), c.67_68insCC (Jia et al. 2017) rs1113295336 rs1113295336 2017 28002929 28411032 11404341
115 OMIA:001199-9627 red fox Coat colour, extension MC1R E^A missense Naturally occurring variant no VulVul2.2 NW_020356486.1 g.6101019T>C c.373T>C p.(C125R) XM_026005028.1; XP_025860813.1 1997 9054949
1603 OMIA:002750-9615 dog reduced hair shedding MC5R missense Naturally occurring variant unknown UU_Cfam_GSD_1.0 1 g.24541931C>T c.709G>A p.(A237T) XM_038525579.1; XP_038381507.1; the variant is reported to be associated with reduced hair shedding and shorter hair length and may not be causal 2016 26795439
1437 OMIA:002716-9615 dog German Shepherd Dog (Dog) Congenital idiopathic megaesophagus MCHR2 repeat variation Naturally occurring variant yes CanFam3.1 12 Bell et al. (2022): "Within the first intron of MCHR2, we identified a 33 bp variable number tandem repeat (VNTR) containing a consensus binding sequence for the T-box family of transcription factors. Across dogs and wolves, the major allele includes two copies of the repeat, whereas the predominant alleles in GSDs have one or three copies. The single-copy allele is strongly associated with CIM (P-val = 1.32x10-17), with homozygosity for this allele posing the most significant risk". 2022 35271580
1658 OMIA:002814-9615 dog Eurasier (Dog) Polioencephalopathy MECR missense Naturally occurring variant yes UU_Cfam_GSD_1.0 2 g.70793040A>G c.823A>G p.(M275V) XM_038531348.1; XP_038387276.1, variant reported in 3 affected dogs 2023 38041431
558 OMIA:002043-9913 taurine cattle Belgian Blue (Cattle) Abortion (embryonic lethality), MED22-related MED22 deletion, small (<=20) Naturally occurring variant yes 11 p.(L38Rfs*25) 2016 27646536
819 OMIA:001932-9615 dog Swedish Vallhund (Dog) Progressive retinal atrophy, MERTK-related MERTK insertion, gross (>20) Naturally occurring variant yes CanFam3.1 17 An insertion of "a full-length [6.401 kb] LINE-1 element comprising the 15 bp target site duplication [indicated by 'ins' in the g. notation], a 5’UTR, 900 bp 5’ ORF1, a 49 bp intergenic spacer, a 3,828 bp 3’ ORF2, a 3’UTR and poly(A) tail. The LINE-1 element has been inserted in the same orientation as the MERTK gene.". 200922: g. info has been moved to here (g.36338043-36338057ins) until it can be standardised 2017 28813472 Genomic location provided by Sally Ricketts
1489 OMIA:002551-9615 dog Bull Mastiff (Dog) Mitochondrial fission encephalopathy MFF delins, small (<=20) Naturally occurring variant yes UU_Cfam_GSD_1.0 25 g.40322999_40323003delinsCGCTCT c.471_475delinsCGCTCT p.(E158Afs*14) XM_038574000.1; XP_038429928.1 2022 36085405
374 OMIA:001106-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Tiroler Grauvieh (Cattle) Axonopathy MFN2 splicing Naturally occurring variant yes ARS-UCD1.2 16 g.41686003G>A c.2229C>T "This SNP is located within a putative exonic splice enhancer (ESE) and the variant allele leads to partial retention of the entire intron 19 and a premature stop codon in the aberrant MFN2 transcript". Variant initially identified in Tiroler Grauvieh and later reported in additional breeds: PMID:34779908 rs5334475057 2011 21526202 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
472 OMIA:002153-9615 dog Schnauzer-Beagle Cross (Dog) Neuroaxonal dystrophy MFN2 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 2 g.84289962_84289964del c.1617_1619del p.(E539del) NM_001284441.1; NP_001271370.1; published as c.1617_1619delGGA; genomic position considers 3' rule of the HGVS 2011 21643798 Genomic position in CanFam3.1 provided by Robert Kuhn.
1081 OMIA:002197-9615 dog Coat colour, white or cream MFSD12 missense Naturally occurring variant no CanFam3.1 20 g.55850145C>T c.151C>T p.(R51C) ROS_Cfam_1.0:g.34222854T>A ENSCAFT00845015439.1:c.121T>A ENSCAFP00845011991.1:p.Cys41Ser rs22915955 rs22915955 2019 31117290 The cDNA coordinate kindly provided by Tosso Leeb 190523; alternate cDNA and protein coordinates in verbal description based on EVA ID.
1426 OMIA:002197-9796 horse Shetland Pony (Horse) Coat colour, dilution (mushroom) MFSD12 Mu duplication Naturally occurring variant no EquCab3.0 7 g.2544518dup c.600dup p.(D201fs) XM_023646425.1; XP_023502193.1; published as NC_009150.3: g.2544512dup (XM_023646425.1:c.600dupC, p.Asp201fs); coordinates in the table have been updated to reflect HGVS nomenclature 2019 31635058
1637 OMIA:002371-9940 sheep Kerry Hill (Sheep) Microcephaly, MFSD2A-related MFSD2A duplication Naturally occurring variant yes ARS-UI_Ramb_v2.0 1 g.14577421dup c.285dup p.(D96Rfs*9) XM_004001833.5; XP_004001882.2 2023 37921236
551 OMIA:001962-9615 dog Chihuahua (Dog) Chinese Crested (Dog) Neuronal ceroid lipofuscinosis, 7 MFSD8 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 19 g.13010761del c.846del p.(F282Lfs*13) XM_014121438.2;XP_013976913.1; published as c.843delT; coordinates in the table have been updated to a recent reference genome and / or transcript 2015 25551667 Breed and p. information obtained from Katz et al. (2017) Neurobiol Dis. doi: 10.1016/j.nbd.2017.08.017; genomic coordinates in CanFam3.1 provided by Zoe Shmidt and Robert Kuhn.
1148 OMIA:001962-9685 domestic cat Domestic Shorthair Neuronal ceroid lipofuscinosis, 7 MFSD8 deletion, small (<=20) Naturally occurring variant yes Felis_catus_9.0 B1 g.98935076del c.780del p.(Q262Kfs*33) XM_019828986.2; XP_019684545.1; published as c.780delT 2020 31860737
1374 OMIA:002465-9615 dog Italian Cane Corso (Dog) Dental-skeletal-retinal anomaly MIA3 deletion, small (<=20) Naturally occurring variant yes CanFam3.1 38 g.16920529_16920530del c.3822+3_3822+4del p.(V1238_K1274del) XM_005640835.3; XP_005640892.1; published as g.16920529_16920530delAT, leads to skipping of two exons: XM_005640835.3:r.3712_3822del 2021 34680893
644 OMIA:001565-9913 taurine cattle Ayrshire (Cattle) Abortion and stillbirth due to mutation in MIMT1 MIMT1 deletion, gross (>20) Naturally occurring variant yes 18 a 110 kb deletion in the MIMT1 gene 2010 21152099
1287 OMIA:002309-9646 giant panda Cataract MIP missense Naturally occurring variant yes c.686G>A p.(S229N) 2021 33530927
503 OMIA:000915-93934 Japanese quail Feather colour, silver MITF deletion, small (<=20) Naturally occurring variant no "a two-base deletion resulting in premature termination of the polypeptide in the region following the zipper region" = 2 bp deletion in exon 11 1998 9576828
505 OMIA:000755-93934 Japanese quail Osteopetrosis MITF deletion, small (<=20) Naturally occurring variant yes same MITF variant as for silver, as reported in 1998 2001 11169846
385 OMIA:001401-10036 golden hamster Waardenburg syndrome, type 2A MITF splicing Naturally occurring variant yes A T>A base substitution in intron 6 of MITF leads to the skipping of exon 7 and a premature termination. 2003 12871913
678 OMIA:001931-9913 taurine cattle Holstein (black and white) (Cattle) Depigmentation associated with microphthalmia MITF deletion, gross (>20) Naturally occurring variant yes 22 a de novo deletion of a 19.1 Mb region of BTA22 from 28 835 247-47 983 179 2014 25199536
341 OMIA:000214-89462 water buffalo Swamp buffalo (Buffalo) White spotting MITF nonsense (stop-gain) Naturally occurring variant no c.328C>T p.(R110*) 2015 26417640
1378 OMIA:001401-9823 pig Bama Xiang Zhu, China (Pig) Waardenburg syndrome, type 2A MITF missense Chemical mutagenesis (ENU) yes 13 c.740T>C p.(L247S) 2017 29094203
409 OMIA:000214-89462 water buffalo Swamp buffalo (Buffalo) White spotting MITF splicing Naturally occurring variant no c.840+2T>A 2015 26417640
837 OMIA:001680-9913 taurine cattle Holstein (black and white) (Cattle) Glass-eyed albino MITF deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 22 g.31628127_31628129del p.(R211del) UMD3.1 position g.31746506_31746508del rs5334474965 2017 28904385 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
189 OMIA:001680-9913 taurine cattle Fleckvieh-Simmental, Germany (Cattle) Dominant white with bilateral deafness MITF missense Naturally occurring variant yes ARS-UCD1.2 22 g.31628131C>A c.629G>T p.(R210I) UMD3.1 position is g.31746502 rs5334474903 2011 22174915 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1547 OMIA:001401-9913 taurine cattle Angus (Cattle) White coat colour MITF deletion, small (<=20) Naturally occurring variant unknown ARS-UCD1.2 22 g.31628133_31628135del c.668_670del p.(R224del) ENSBTAT00000080989.1; ENSBTAP00000059022.1; published as chr22.g.31628127_31628128del and delR217 - coordinates have been changed to HGVS nomenclature in this table 2023 37062854
424 OMIA:000214-9615 dog Coat colour, white spotting MITF regulatory Naturally occurring variant no CanFam3.1 20 g.21836232_21836427delinsN[198] This 198bp SINEC-Cf insertion is the first of three possible regulatory variants described by Karlsson et al. (2007). 2007 17906626 The genomic location was kindly provided by Professor Claire Wade in August 2018.
1023 OMIA:000214-9796 horse American Paint (Horse) White spotting, blue eyes and deafness MITF SW5 deletion, gross (>20) Naturally occurring variant yes EquCab3.0 16 g.21503211_21566617del "~63-kb deletion spanning exons 6-9 of the MITF gene" 2019 30644113
1180 OMIA:000214-9796 horse American Paint (Horse) Splashed white MITF SW6 deletion, gross (>20) Naturally occurring variant no EquCab3.0 16 g.21551060_21559770del NC_009159.3:g.21551060-21559770del (Magdesian et al., 2020) 2020 32242630
1626 OMIA:000214-9796 horse Thoroughbred (Horse) Splashed white MITF SW8 deletion, gross (>20) Naturally occurring variant yes EquCab3.0 16 g.21555811_21558139delinsAAAT 2023