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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:Â "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 |