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1524 variant records found

[show instead phene records]

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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 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 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 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 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 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 Border Collie Collie German Shepherd Dog Longhaired whippet Miniature Australian shepherd Old English Sheepdog Shetland Sheepdog Silken windhound Waller White Swiss shepherd 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 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 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) 2015 25660379 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
572 OMIA:001524-9615 dog Shetland Sheepdog Gallbladder mucoceles ABCB4 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 14 g.13584928_13584929insC c.1660_1661insG p.(L554Rfs) XM_539403.6; XP_539403.3; published as c.1583_1584G, the association between this variant and disease was later disproven and this variant should not be used as a diagnostic marker for GBM (Cullen et al. 2014) 2010 20598156
1574 OMIA:002710-9615 dog Manchester Terrier 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 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 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
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
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
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 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 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 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 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 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:001271-9913 cattle 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 American Akita 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 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 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 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 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 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 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 Chinese Crested Dog German Hunting Terrier Jack Russell Terrier Lancashire heeler Miniature Bull Terrier Parson Russell Terrier Patterdale Terrier Rat Terrier Sealyham Terrier Tenterfield Terrier Tibetan Terrier Toy Fox Terrier Volpino Italiano Welsh Terrier Wirehaired Fox Terrier Yorkshire Terrier 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 Gould et al. (2011) 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 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 Vendéen 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 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 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 Pit Bull Terrier 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 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 dogs 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
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 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 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
1084 OMIA:001893-9615 dog Norwich Terrier Upper airway syndrome ADAMTS3 missense Naturally occurring variant yes CanFam3.1 13 g.61287796G>A c.2786G>A p.(R929H) 2019 31095560
60 OMIA:001509-9615 dog Beagle 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 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 cattle Brown Swiss (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 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 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 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)
1094 OMIA:002205-9615 dog Rough Collie 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 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. 2021 33639992
1021 OMIA:002162-9615 dog Karelian bear 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:001551-9685 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 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 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 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
1129 OMIA:001868-9615 dog Siberian Husky Blue eyes ALX4 duplication Naturally occurring variant no CanFam3.1 18 g.44791414_44890185dup Deane-Coe et al. (2018): "a 98.6-kb duplication directly upstream of the Homeobox gene ALX4" 2018 30286082 g. coordinates kindly provided by Anna Letko and Cord Drögemüller (7th Oct 2019)
280 OMIA:000791-9615 dog Miniature Schnauzer 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 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 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 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 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 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 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 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*) 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 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 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 Saint Bernard 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 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 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 Miniature Poodle 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 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 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 1996 8910299 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
67 OMIA:001503-9615 dog American Staffordshire Terrier 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
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
712 OMIA:000201-9913 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
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
1321 OMIA:002200-9915 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
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
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 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 No light points ASIP NLP missense Naturally occurring variant no c.349T>C p.(C117R) 2015 25887951
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 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 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 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 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]" 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 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
1270 OMIA:000213-89462 water buffalo White ASIP insertion, gross (>20) Naturally occurring variant no UOA_WB_1 14 "2,809-bp-long LINE-1 insertion in the ASIP (agouti signaling protein) gene" (Liang et al. (2020) 2021 33212507
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 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 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*) 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 Standard Poodle 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 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 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 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 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 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) 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 cattle Romagnola (Cattle) Pseudomyotonia, congenital ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25939141C>A c.857G>T p.(G286V) 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 cattle Romagnola (Cattle) Pseudomyotonia, congenital ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25939366C>A c.632G>T p.(G211V) 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 cattle Chianina (Cattle) Pseudomyotonia, congenital ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25940510C>T c.491G>A p.(R164H) 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 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 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 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 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 rs851958524 rs851958524 2016 26747866 30 Dec 2020: correct genomic location provided by Angelica K Kallenberg
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*) 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 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 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 Hungarian Puli 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 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 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 1990 2303405
200 OMIA:000627-9913 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 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 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 Gammelnorsk spaelsau, Norway (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 Lapponian Herder 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 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 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 Bull Mastiff English Mastiff Great Pyrenees 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 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
862 OMIA:001551-9615 dog Brachycephaly BMP3 missense Naturally occurring variant yes CanFam3.1 32 g.5231894C>A c.1344C>A p.(F448L) rs851217657 rs851217657 2012 22876193 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
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
93 OMIA:001512-9615 dog Invasive transitional cell carcinoma of the bladder BRAF missense Naturally occurring variant yes CanFam3.1 16 g.8296284T>A c.1643T>A p.(V548E) XM_005629551.3; XP_005629608.1; published as somatic mutation p.(V594E) 2015 25767210
851 OMIA:002132-9615 dog German Shorthaired Pointer 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 rs852549625 2017 29053721
981 OMIA:001991-9913 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
583 OMIA:001575-9615 dog Gordon Setter Irish Setter Miniature Poodle Old Danish Pointing Dog (Dog) Polski Owczarek Nizinny Polski Owczarek Podhalanski Standard Poodle Tibetan Terrier Rod-cone dysplasia 4 C17H2orf71 insertion, small (<=20) Naturally occurring variant yes CanFam3.1 17 g.22907394_22907395insG c.3149_3150insC p.(C1051Vfs*90) NM_001284459.1; NP_001271388.1; genomic position adjusted based on HGVS 3' rule; EVA variant with equivalent alleles: rs397510935 rs1152388416 rs1152388416 2013 22686255
1047 OMIA:000303-9031 chicken White Leghorn (Chicken) Dwarfism, autosomal C1H12ORF23 nonsense (stop-gain) Naturally occurring variant yes GRCg6a 1 g.53638233C>T c.433G>A p.(W59*) Wu et al. (2018): "NM_001006244.1:c.433G > A . . . NP_001006244.1:p.(Trp59∗)" 2018 29930570
1085 OMIA:001040-9615 dog Rhodesian Ridgeback Ventricular arrhythmias and sudden death C20H19orf70 missense Naturally occurring variant yes CanFam3.1 20 g.54343438G>A c.325G>A p.(G109S) ENSCAFG00000018796: g.54343438 G>A. ENSCAFT00000029838.4:c.325G>A ENSCAFP00000027731.3:p.G109S) rs852200012 rs852200012 2019 30795627
455 OMIA:000155-9615 dog Brittany Spaniel 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
1087 OMIA:002201-9913 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 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 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 Beagle Hypocatalasia CAT missense Naturally occurring variant yes CanFam3.1 18 g.33397548C>T c.979G>A p.(A327T) 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 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." 2019 30975085
266 OMIA:001540-9615 dog Old English Sheepdog 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 Portugese water 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 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.
1008 OMIA:001752-9823 pig Resistance to PRRS virus CD163 deletion, gross (>20) Naturally occurring variant no 5 Burkhard et al (2018): "the deletion of exon 7 of CD163 using CRISPR/Cas9 editing" 2018 29925651
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 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 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 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 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*) 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 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 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*) 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:000685-9913 cattle 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 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 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 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
399 OMIA:000698-89462 water 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 1996 8855341
609 OMIA:000698-9615 dog Australian Cattle Dog Border Collie 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 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 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 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. 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) 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*) published as chrA2:15897085‐15 897 092, coordinates in this table have been verified in Felis_catus_9.0 2022 35815860 NP_001291956.1
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 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 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 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 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 Border Collie 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 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 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) 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 Alpenländische Dachsbracke 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 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 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 German Shorthaired Pointer 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) 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 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) 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 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 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 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) 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 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 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 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:000830-9615 dog Papillon Phalène 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 Miniature Australian shepherd 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 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 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 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 Leonberger Saint Bernard 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 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) 2000 11130976 The genomic and CDS position was determined by Stephanie Shields and the effect was confirmed with Ensembl VEP (27/05/2020)
78 OMIA:001772-9615 dog Labrador Retriever 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
1031 OMIA:002127-9913 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 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 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) 2021 33672767
959 OMIA:002126-9615 dog Golden Retriever 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 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 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 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 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) 2017 28904385 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1275 OMIA:001926-9913 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 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 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) 2017 28904385 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
414 OMIA:001926-9913 cattle Danish Holstein (Cattle) bulldog calf COL2A1 splicing Naturally occurring variant yes ARS-UCD1.2 5 g.32305226G>A c.2463+1G>A 2016 27296271 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
223 OMIA:001926-9913 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 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 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) 2019 30378686
278 OMIA:002618-9615 dog English Springer Spaniel 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 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) 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 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 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
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 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) 2020 33143196
1460 OMIA:002295-9615 dog Chihuahua 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 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 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. 2017 28904385
1208 OMIA:002274-9615 dog Labrador Retriever Muscular dystrophy, COL6A3-related COL6A3 splicing Naturally occurring variant yes CanFam3.1 25 g.48007994C>T c.6210+1G>A 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 Muscular dystrophy, COL6A3-related COL6A3 nonsense (stop-gain) Naturally occurring variant yes CanFam3.1 25 g.48014962G>A c.4726C>T p.(R1576*) 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 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 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 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 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 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 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 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 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 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 wb^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 wb^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 wb^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 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*) 2017 28683140
1418 OMIA:002519-9913 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 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 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. 2017 28904385
66 OMIA:001505-9615 dog American Bulldog 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
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 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 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 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 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 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 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 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 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; 2012 22553308 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1411 OMIA:002508-9913 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 2021 34944310
52 OMIA:002684-9615 dog Australian Cattle Dog Shetland Sheepdog 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 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*) 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
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 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 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) 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 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 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 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
957 OMIA:001081-9615 dog Rottweiler 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
536 OMIA:001081-9615 dog Cocker Spaniel 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
680 OMIA:001081-9615 dog German Shorthaired Pointer Muscular dystrophy, Duchenne type DMD deletion, gross (>20) Naturally occurring variant yes X a "deletion encompassing the entire dystrophin [DMD] gene" 1999 10407848
681 OMIA:001081-9615 dog Tibetan Terrier Muscular dystrophy, Duchenne type DMD deletion, gross (>20) Naturally occurring variant yes X "a large deletion of exons 8-29" 2012 22218699
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
989 OMIA:001081-9615 dog Miniature Poodle 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
729 OMIA:001081-9615 dog Labrador Retriever 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
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
367 OMIA:001081-9615 dog Cavalier King Charles Spaniel 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 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 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 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 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 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 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 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 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 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 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
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 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
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" 2021 33724408
39 OMIA:001466-9615 dog Chesapeake Bay Retriever Curly-coated retriever Labrador Retriever 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 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 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 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 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) 2019 30651277
1056 OMIA:002186-9615 dog Boston Terrier Bulldog French Bulldog 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 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 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 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 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 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 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 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) 2011 21740563 Allele id and c. information were copied from Table 1 of Capuzzello et al. (2022)
1294 OMIA:000543-9913 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*) 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 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 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) 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 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." 2011 21410470 Allele id and p. information were copied from Table 1 of Capuzzello et al. (2022)
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 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 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 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 2023 37137429
1474 OMIA:002560-9913 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
1562 OMIA:002701-51751 ball python Skin colour, EDNRB1-related EDNRB1 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, EDNRB1-related EDNRB1 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, EDNRB1-related EDNRB1 specter missense Naturally occurring variant unknown c.2601G>C p.(R315P) OP589186.1 2023 37191439
1567 OMIA:002701-51751 ball python Skin colour, EDNRB1-related EDNRB1 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, EDNRB1-related EDNRB1 spark missense Naturally occurring variant unknown c.481G>C p.(L152F) OP589186.1 2023 37191439
1566 OMIA:002701-51751 ball python Skin colour, EDNRB1-related EDNRB1 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
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 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 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 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 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 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 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) 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 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. 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 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 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 cattle Tirolean gray cattle (Cattle) Chondrodysplasia EVC2 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 6 g.103651709_103651710del c.2993_2994del p.(D998Efs*13) 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 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 Mixed breed (dog) 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 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 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 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) 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 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 2017 28392508 Genomic position in Felis_catus_9.0 provided by Leslie Lyons and Reuben Buckley.
1532 OMIA:001818-9913 cattle Japanese Black, 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 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 Beagle 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
363 OMIA:000437-9615 dog Irish Setter Miniature Schnauzer 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 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 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) 2009 19456318 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
350 OMIA:000437-9615 dog Old English Sheepdog 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 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 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 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
1284 OMIA:000437-9615 dog Rhodesian Ridgeback Haemophilia A F8 insertion, gross (>20) Naturally occurring variant yes CanFam3.1 X g.1240738676_1240738677insN[221] c.4824_4825insN[221] NM_001003212.1; published as c.4824_25ins221 2021 33494213
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.
636 OMIA:000438-9615 dog Labrador Retriever Haemophilia B F9 deletion, gross (>20) Naturally occurring variant yes X a deletion of the entire gene 1997 9394892
637 OMIA:000438-9615 dog Pit Bull Terrier 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 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 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 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 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 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 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 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 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 Mixed breed (duplicate) 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 (duplicate) 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 Tibetan Terrier 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 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. 2017 28904385
102 OMIA:002015-9615 dog Border Collie 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 Kromfohrländer 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 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 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 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 cattle Limousin (Cattle) Marfan syndrome FBN1 missense Naturally occurring variant yes ARS-UCD1.2 10 g.61831200G>A c.3598G>A p.(E1200K) 2005 15776436 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
377 OMIA:000628-9913 cattle Japanese Black, Japan (Cattle) Marfan syndrome FBN1 splicing Naturally occurring variant yes ARS-UCD1.2 10 g.61917867G>A c.8227-1G>A 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 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) 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 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 Miniature Wirehaired Dachshund 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 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 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 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 Thai Ridgeback 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 Cairn Terrier Cardigan Welsh Corgi Dachshund Dandie Dinmont Terrier Lancashire heeler Norwich Terrier Pekingese Pembroke Welsh Corgi Petit Basset Griffon Vendéen Shih-Tzu Skye Terrier Swedish Vallhund Tibetan Spaniel West Highland Terrier 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 Basset Hound Beagle Cardigan Welsh Corgi Chesapeake Bay Retriever Chihuahua Coton de Tulear Dachshund English Springer Spaniel French Bulldog Nova Scotia Duck Tolling retriever 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 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