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107 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 | Variant Type | Variant Effect | Source of Genetic Variant | Pathogenicity Classification* | Reference Sequence | Chr. | g. or m. | c. or n. | p. | Verbal Description | EVA ID | Year Published | PubMed ID(s) | Acknowledgements |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1001 | OMIA:001271-9796 | horse | Miniature Horse (Horse) | Dwarfism, ACAN-related | ACAN | D4 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | 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 | Not currently ISAG evaluated | 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 | 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 | Not currently ISAG evaluated | EquCab3.0 | 1 | g.95284530C>T | p.(V424M) | 2018 | 30058072 | |||||
| 999 | OMIA:001271-9796 | horse | Miniature Horse (Horse) | Dwarfism, ACAN-related | ACAN | D1 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | 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 | 2018 | 30058072 | ||
| 436 | OMIA:000991-9796 | horse | Quarter Horse (Horse) | Androgen insensitivity syndrome (AIS) | AR | regulatory | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | X | NC_009175.3:g.52728703A>G | NM_001163891.1:c.1A>G | mutation in start codon for NP_001157363.1; | 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 | Not currently ISAG evaluated | EquCab3.0 | X | NC_009175.3:g.52728885del | NM_001163891.1:c.183del | NP_001157363.1:p.(R63Gfs) | 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 | Not currently ISAG evaluated | EquCab3.0 | X | NC_009175.3:g.52808634_52808658del | NM_001163891.1:c.1630_1654del | 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 | Not currently ISAG evaluated | EquCab3.0 | X | NC_009175.3:g.52872393G>C | NM_001163891.1:c.2042G>C | NP_001157363.1:p.(W681S) | 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 | Not currently ISAG evaluated | EquCab3.0 | X | NC_009175.3:g.52878093C>T | NM_001163891.1:c.2132C>T | NP_001157363.1:p.(A711V) | 2020 | 31936796 | |||||
| 509 | OMIA:000201-9796 | horse | Coat colour, recessive black | ASIP | a | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 22 | NC_009165.3:g.26067463_26067473del | NM_001164017.1:c.187_197del | published as g.2174_2184del and c.191_201del - coordinates in the table updated to a recent reference genome | rs3091770233 | 2001 | 11353392 | Coordinates in EquCab3.0 kindly provided by Haley Rutstein, working under the guidance of Professor Ernie Bailey. | |||
| 348 | OMIA:000487-9796 | horse | Belgian Draft (Horse) Friesian (Horse) | Hydrocephalus | B3GALNT2 | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 1 | g.76887901C>T | c.1423C>T | p.(Q475*) | XM_001491545; XP_001491595; Ducro et al. (2015): "The nomenclature for the mutation is c.1423C>T [GenBank:XM_001491545] corresponding to p.Gln475* [GenBank:XP_001491595]". As at 25 April 2019, Ensembl's Variant Effect Predictor (VEP) gives the EquCab3 c. and p. coordinates as having not changed from the EquCab2 coordinates reported by Ducro et al. (2015). The Ensembl ref is ENSECAT00000049072 | rs3429464524 | 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 | ||
| 421 | OMIA:002068-9796 | horse | Friesian (Horse) | Dwarfism, Friesian | B4GALT7 | splicing | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 14 | g.3772591C>T | c.50G>A | p.(R17K) | 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. | ||||
| 161 | OMIA:000698-9796 | horse | New Forest Pony (Horse) | Myotonia | CLCN1 | missense | Naturally occurring variant | Not currently ISAG evaluated | 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 | |||
| 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 | Not currently ISAG evaluated | 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 | 2017 | 28425625 | The EquCab3 g. coordinates were provided by by Meredith O’Connell, working under the guidance of Professor Ernie Bailey, 5 March 2019 | ||
| 321 | OMIA:001715-9796 | horse | Gaitedness | DMRT3 | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 23 | g.22391254C>A | c.902C>A | p.(S301*) | ENSECAT00000025062.2; ENSECAP00000020841.2 | rs1150690013 | 2012 | 22932389 | ||||
| 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 | Not currently ISAG evaluated | EquCab3.0 | 17 | g.50503041_50503042delinsCT | c.353_354delinsAG | p.(I118K) | NM_001081837.2; NP_001075306.2 | 1998 | 9530628 | |||
| 322 | OMIA:000420-9796 | horse | American Paint (Horse) Quarter Horse (Horse) | Glycogen storage disease IV | GBE1 | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 26 | g.8667651C>A | c.102C>A | p.(Y34*) | NM_001081940.2; NP_001075409.1 | rs3437568674 | 2004 | 15366377 | The genomic position in EquCab3.0 was provided by Elizabeth Clark, working under the guidance of Professor Ernie Bailey in April 2022 | ||
| 1552 | OMIA:002692-9796 | horse | American Saddle Horse (Horse) American Trotter (Horse) Miniature Horse (Horse) Missouri Fox Trotting Horse, United States of America (Horse) Morgan (Horse) Quarter Horse (Horse) Racking Horse (Horse) Rocky Mountain, United States of America (Horse) Spotted Saddle Horse (Horse) Tennessee Walking Horse (Horse) | Night blindness, congenital stationary, GRM6-related | GRM6 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 14 | g.2655618C>T | c.533C>T | p.(T178M) | XM_001916934.4; XP_001916969.3; variant initially reported in Tennessee Walking horse and later reported in other breeds [PMID:37815029] | rs1138010744 | 2021 | 32654228 | |||
| 163 | OMIA:001158-9796 | horse | American Paint (Horse) Appaloosa (Horse) Quarter Horse (Horse) | Polysaccharide storage myopathy/Exertional rhabdomyolysis | GYS1 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 10 | g.19203501C>T | c.926G>A | p.(R309H) | ENSECAT00000023453.3:c.926G>A ENSECAP00000019426.2:p.Arg309His | rs1150416011 | 2008 | 18358695 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| 691 | OMIA:000081-9796 | horse | Arab (Horse) | Atlanto occipital fusion | HOXD3 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | 18 | "a 2.7-kb deletion located 4.4 kb downstream of the end of HOXD4 and 8.2 kb upstream of the start of HOXD3." | 2017 | 28111759 | ||||||||
| 337 | OMIA:001899-9796 | horse | Quarter Horse (Horse) | Incontinentia pigmenti | IKBKG | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | X | g.126898409C>T | c.202C>T | p.(R68*) | 2013 | 24324710 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||||
| 164 | OMIA:001000-9796 | horse | Quarter Horse (Horse) Thoroughbred (Horse) | Thrombasthenia | ITGA2B | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 11 | g.19245752G>C | c.215G>C | p.(R72P) | NM_001081793.1; NP_001075262.1; originally published as p.(R41P) and listed by Leite et al. (2019) as c.122G>C; coordinates in this table have been updated to a recent reference genome and / or transcript | 2006 | 16407493 | ||||
| 512 | OMIA:001000-9796 | horse | Peruvian Paso (Horse) Quarter Horse (Horse) | Thrombasthenia | ITGA2B | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 11 | g.19247983_19247992del | g.19247983_19247992delCAGGTGAGGA | 2007 | 17338169 | g. coordinates obtained from Dahlgren et al. (2020) | |||||
| 1331 | OMIA:000209-9796 | horse | American Paint (Horse) Quarter Horse (Horse) | White spotting | KIT | W32 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79538738C>T | c.3214G>A | p.(A1072T) | cDNA position based on transcript ENSECAT00000014037.3 | rs1141982296 | 2021 | 34223905 | ||
| 882 | OMIA:000209-9796 | horse | Süddeutsches Kaltblut, Germany (Horse) | Coat colour, dominant white | KIT | W11 | splicing | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79540429C>T | c.2684+1G>A | 2009 | 19456317 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||||
| 939 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W26 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79540694del | c.2536del | p.(S846Vfs*15) | NM_001163866.1; NP_001157338.1; published as c.2536delA | 2018 | 29333746 | |||
| 873 | OMIA:000209-9796 | horse | Oldenburg (Horse) | Coat colour, dominant white | KIT | W16 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79540741T>A | c.2489A>T | p.(K830I) | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 883 | OMIA:000209-9796 | horse | Miniature Horse (Horse) Quarter Horse (Horse) Shetland Pony (Horse) | Coat colour, dominant white | KIT | W13 | splicing | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79544066C>G | c.2472+5G>C | NM_001163866.1 | rs3102773259 | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||
| 889 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W14 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79544098_79544151del | c.2392_2445del | p.(H798_N815del) | NM_001163866.1; NP_001157338.1 | 2011 | 21554354 | genomic coordinates updated from g.79544151_79544204del to g.79544098_79544151del in EquCab3.0 [17/09/2023] | ||
| 891 | OMIA:000209-9796 | horse | Iceland Pony (Horse) | White spotting | KIT | W21 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79544174del | c.2369delC | p.(A790Efs*20) | 2015 | 26059442 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 885 | OMIA:000209-9796 | horse | Appaloosa (Horse) Haflinger (Horse) Lipizzan horse (Horse) Noric (Horse) Quarter Horse (Horse) | Coat colour, dominant white | KIT | sabino 1 (SB1) | splicing | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79544206A>T | "SNP AX-103727726 (ECA3:77735520; SB1, SNP KI16+1037A)" (Druml et al., 2018) | 2005 | 16284805 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||||
| 893 | OMIA:000209-9796 | horse | Trottatore Italiano, Italy (Horse) | Coat colour, dominant white | KIT | W24 | splicing | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79545245C>T | 2017 | 28856698 | ||||||
| 1462 | OMIA:000209-9796 | horse | American Trotter (Horse) | Dominant white spotting | KIT | W33 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79545248T>A | c.2783A>T | p.(N895Y) | NC_009146.3; ENSECAT00000014037.3 | 2022 | 35641888 | |||
| 881 | OMIA:000209-9796 | horse | Iceland Pony (Horse) | Coat colour, dominant white | KIT | W8 | splicing | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79545374C>T | c.2222-1G>A | NM_001163866.1 | rs3434854925 | 2009 | 19456317 | |||
| 886 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W5 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79545900del | c.2193delG | p.(T732Qfs*9) | 2009 | 19456317 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 878 | OMIA:000209-9796 | horse | Freiberger (Horse) | Coat colour, dominant white | KIT | W1 | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79545942G>C | c.2151C>G | p.(Y717*) | 2007 | 17997609 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 877 | OMIA:000209-9796 | horse | American Paint (Horse) Appaloosa (Horse) German Riding Pony (Horse) Noric (Horse) Oldenburg (Horse) Quarter Horse (Horse) Thoroughbred (Horse) Tori hobune, Estonia (Horse) Traditional Gypsy Cob, United Kingdom of Great Britain and Northern Ireland (Horse) Welsh Pony (Horse) | Coat colour, dominant white | KIT | W20 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79548220C>T | c.2045G>A | p.(R682H) | ENSECAT00000014037.3:c.2381A>G ENSECAP00000011188.2:p.His794Arg | rs1143160924 | 2013 | 23659293 | Variant coordinates initially gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
| 875 | OMIA:000209-9796 | horse | Japanese Draft, Japan (Horse) | Coat colour, dominant white | KIT | W17b | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79548244A>G | c.2021T>C | p.(L674P) | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 1261 | OMIA:000209-9796 | horse | Berber, Germany (Horse) | Extensive coat white patterning | KIT | W30 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79548244A>T | c.2020T>A | p.(L674H) | g.79548244, c.2020T>A; p.L674H (Martin et al., 2020) | 2020 | 33111383 | |||
| 874 | OMIA:000209-9796 | horse | Japanese Draft, Japan (Horse) | Coat colour, dominant white | KIT | w17a | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79548265T>A | c.2001A>T | p.(E667D) | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 890 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | White spotting | KIT | W22 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79548925_79550822del | 1898bp deletion | 2017 | 28444912 | |||||
| 868 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W2 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79549540C>T | c.1960G>A | p.(G654R) | 2007 | 17997609 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 869 | OMIA:000209-9796 | horse | Camarillo White Horse, United States of America (Horse) | Coat colour, dominant white | KIT | W4 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79549780G>A | c.1805C>T | p.(A602V) | 2007 | 17997609 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 871 | OMIA:000209-9796 | horse | Holsteiner (Horse) | Coat colour, dominant white | KIT | W9 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79549797C>T | c.1789G>A | p.(G597R) | 2009 | 19456317 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 872 | OMIA:000209-9796 | horse | Arab (Horse) | Coat colour, dominant white | KIT | W15 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79550351A>G | c.1597T>C | p.(C533R) | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 940 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W27 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79551937A>C | c.1473T>G | p.(C491W) | NM_001163866.1; NP_001157338.1 | 2018 | 29333746 | |||
| 884 | OMIA:000209-9796 | horse | CH-Warmblut, Switzerland (Horse) | Coat colour, dominant white | KIT | W18 | splicing | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79553751C>T | c.1346+1G>A | 2013 | 23659293 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||||
| 876 | OMIA:000209-9796 | horse | Arab (Horse) | Coat colour, dominant white | KIT | W19 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79553776T>C | c.1322A>G | p.(Y441C) | 2013 | 23659293 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 1476 | OMIA:000209-9796 | horse | American Paint (Horse) Appaloosa (Horse) Arab (Horse) Mangalarga (Horse) Morgan (Horse) Mustang (Horse) Quarter Horse (Horse) Rocky Mountain, United States of America (Bighorn sheep) Warmblood breeds | Increased white spotting | KIT | W34 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79566881T>C | c.1495A>G | p.(T499A) | ENSECAT00000014037.3; ENSECAP00000011188.2 | rs1140732842 | 2022 | 35953947 | ||
| 887 | OMIA:000209-9796 | horse | Quarter Horse (Horse) | Coat colour, dominant white | KIT | W10 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79566923_79566926del | c.1126_1129del | p.(E376Ffs*3) | NM_001163866.1; NP_001157338.1; published as c.1126_1129delGAAC | 2009 | 19456317 | Genomic coordinates updated in this table from g.79566926_79566929del in EquCab3.0 after feedback from Micaela Vierra identified that these coordinates were incorrect [27/09/2023]. | ||
| 870 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W6 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79573754C>T | c.856G>A | p.(G286R) | 2009 | 19456317 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 892 | OMIA:000209-9796 | horse | Arab (Horse) | White spotting | KIT | W23 | splicing | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79578484C>G | c.756+1G>C | rs1095048836 | 2017 | 28378922 | ||||
| 879 | OMIA:000209-9796 | horse | Arab (Horse) | Coat colour, dominant white | KIT | W3 | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79578535T>A | c.706A>T | p.(K236*) | 2007 | 17997609 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 938 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W25 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79578573A>G | c.668T>C | p.(L223P) | NM_001163866.1; NP_001157338.1 | 2018 | 29333746 | |||
| 888 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W12 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79579774_79579778del | c.559_563del | p.(S187Rfs*10) | NM_001163866.1; NP_001157338.1; published as c.559_563delTCTGC | 2010 | Reference not in PubMed; see OMIA 000209-9796 for reference details | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||
| 1091 | OMIA:000209-9796 | horse | German Riding Pony (Horse) | White spotting | KIT | W28 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79579925_79581197del | 2019 | 31463981 | ||||||
| 880 | OMIA:000209-9796 | horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W7 | splicing | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79580000C>G | c.338-1G>C | 2009 | 19456317 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||||
| 1330 | OMIA:000209-9796 | horse | Quarter Horse (Horse) | White spotting | KIT | W31 | insertion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.79618532_79618533insA | c.30_31insT | p.(L11Sfs*115) | 2021 | 34223905 | ||||
| 856 | OMIA:000245-9796 | horse | Bashkir Curly (Horse) Curly Horse (Horse) | Curly coat | KRT25 | Crd | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 11 | g.21962991G>A | c.266G>A | p.(R89H) | rs1095048844 | 2017 | 29686323 29141579 | Variant coordinates obtained from and/or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| 658 | OMIA:001677-9796 | horse | American Saddle Horse (Horse) | Epidermolysis bullosa, junctionalis, LAMA3-related | LAMA3 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 8 | NC_009151.3:g.48678342_48684920del | "6589-bp deletion spanning exons 24-27 . . . in the LAMA3 gene in American Saddlebred foals" | 2009 | 19016681 | Coordinates in EquCab3.0 kindly provided by Haley Rutstein, working under the guidance of Professor Ernie Bailey. | |||||
| 599 | OMIA:001678-9796 | horse | Belgian Draft (Horse) Breton, France (Horse) Cavallo Agricolo Italiano da Tiro Pesante Rapido, Italy (Horse) Comtois (Horse) | Epidermolysis bullosa, junctionalis, LAMC2-related | LAMC2 | insertion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 5 | g.17498175dup | c.1372dup | p.(R458Pfs) | NM_001081768.1; NP_001075237.1; published as c.1368insC; coordinates in the table have been updated to HGVS nomenclature (3'-rule) and recent reference genome and / or transcript inforamtion 1,372 Protein position: 458 | 2002 | 12230513 | The genomic position in EquCab3.0 was provided by Margaret Higgins, working under the guidance of Professor Ernie Bailey [April 2022] | |||
| 413 | OMIA:002021-9796 | horse | Quarter Horse (Horse) | Coat colour, brindle 1 | MBTPS2 | splicing | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | X | g.17286855T>C | c.1437+4T>C | 2016 | 27449517 | ||||||
| 154 | OMIA:001199-9796 | horse | Coat colour, chesnut | MC1R | e | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.36979560C>T | c.248C>T | p.(S83F) | ENSECAT00000129995.1; ENSECAP00000088247.1 | rs68458866 | 1996 | 8995760 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| 155 | OMIA:001199-9796 | horse | Coat colour, chesnut | MC1R | e^a | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 3 | g.36979562G>A | c.250G>A | p.(D84N) | ENSECAT00000129995.1; ENSECAP00000088247.1 | rs3443929753 | 2000 | 11086549 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| 1426 | OMIA:002197-9796 | horse | Shetland Pony (Horse) | Coat colour, dilution (mushroom) | MFSD12 | Mu | duplication | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 7 | g.2544518dup | c.600dup | p.(D201fs) | XM_023646425.1; XP_023502193.1; published as NC_009150.3: g.2544512dup (XM_023646425.1:c.600dupC, p.Asp201fs); coordinates in the table have been updated to reflect HGVS nomenclature | 2019 | 31635058 | |||
| 1023 | OMIA:000214-9796 | horse | American Paint (Horse) | White spotting, blue eyes and deafness | MITF | SW5 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 16 | g.21503211_21566617del | "~63-kb deletion spanning exons 6-9 of the MITF gene" | 2019 | 30644113 | |||||
| 1180 | OMIA:000214-9796 | horse | American Paint (Horse) | Splashed white | MITF | SW6 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 16 | g.21551060_21559770del | NC_009159.3:g.21551060-21559770del (Magdesian et al., 2020) | 2020 | 32242630 | |||||
| 1626 | OMIA:000214-9796 | horse | Thoroughbred (Horse) | Splashed white | MITF | SW8 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 16 | g.21555811_21558139delinsAAAT | 2023 | 37697831 | ||||||
| 166 | OMIA:000214-9796 | horse | American Trotter (Horse) | White | MITF | MITF^244Glu | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 16 | g.21556522C>T | c.731G>A | p.(G244E) | 2017 | 27592871 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 1606 | OMIA:000214-9796 | horse | Purebred Spanish (Horse) | Splashed white | MITF | SW9 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 16 | g.21559940T>A | c.961A>T | p.(N321Y) | NM_001163874.1; NP_001157346.1; published as c.993A>T, variant associated with increased depigmentation | 2023 | 37406837 | |||
| 1488 | OMIA:000214-9796 | horse | American Paint (Horse) Quarter Horse (Horse) | Splashed white | MITF | SW7 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 16 | g.21559953_21559955del | c.949_951del | p.R317del | NM_001163874.1; NP_001157346.1; published as c.949_951delTCT | 2022 | 35672910 | |||
| 156 | OMIA:000214-9796 | horse | Freiberger (Horse) | Macchiato | MITF | macchiato | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 16 | g.21564980T>C | c.629A>G | p.(N210S) | 2012 | 22511888 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 793 | OMIA:000214-9796 | horse | Quarter Horse (Horse) | Splashed white | MITF | SW3 | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 16 | g.21567245_21567249del | c.837_841del | p.(C280Sfs*20) | NM_001163874.1; NP_001157346.1; published as c.837_841delGTGTC | 2012 | 22511888 | |||
| 792 | OMIA:000214-9796 | horse | American Miniature Horse (Horse) American Paint (Horse) Appaloosa (Horse) Iceland Pony (Horse) Morgan (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Tori hobune, Estonia (Horse) Trakehner (Horse) | Splashed white | MITF | SW1 | delins, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 16 | g.21579201delinsATAATAACCTA | g.20117302Tdelins11 | 2012 | 22511888 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||||
| 806 | OMIA:000214-9796 | horse | Cavall Menorquí, Spain (Horse) | White splashing | MITF | regulatory | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 16 | g.21608936C>T | Published as g.20147039C>T (EquCab2.0) | 2017 | 28084638 | ||||||
| 443 | OMIA:001538-9796 | horse | Racing distance | MSTN | insertion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | 18 | A "227 bp SINE insertion positioned upstream of exon 1" | 2018 | 30379863 | |||||||||
| 437 | OMIA:000175-9796 | horse | Arab (Horse) Bashkir Curly (Horse) Trakehner (Horse) Welsh Pony (Horse) | Cerebellar abiotrophy | MUTYH | not known | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 2 | g.13122415C>T | c.541-13539C>T | ENSECAT00000009202.3:c.541-13539C>T ENSECAT00000024892.2:c.284G>A ENSECAP00000020698.1:p.Arg95His A SNP "located in exon 4 of TOE1 and approximately 1200 base pairs upstream of MUTYH, adjacent to a possible binding site for the transcription factor GATA2" (Brault et al., 2011). EquCab3.1 coordinate provided by Meredith O’Connell, working under the supervision of Professor E. Bailey. | rs397160943 | 2011 | 21126570 | ||||
| 973 | OMIA:002141-9796 | horse | Quarter Horse (Horse) | Immune-mediated myositis | MYH1 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 11 | g.53345548T>C | p.(E321G) | The location of this likely causal variant was given as chr11:52,993,878T>C by Finno et al. (2018) in relation to the EquCab2.0 assembly. Applying NCBI's remap gives the EquCab3.0 coordinate as chr11:53,345,548 | 2018 | 29510741 | |||||
| 510 | OMIA:001501-9796 | horse | Arab (Horse) | Lavender foal syndrome | MYO5A | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 1 | g.139290592del | c.4249del | p.(R1417Afs*13) | XM_023617258.1; XP_023473026.1; published as g.138235715delC; coordinates in the table have been updated to a recent reference genome | 2010 | 20419149 | The genomic position in EquCab3.0 was provided by Gracie Zinsmeister, working under the guidance of Professor Ernie Bailey in April 2022 | |||
| 1605 | OMIA:001688-9796 | horse | Purebred Spanish (Horse) | Splashed white | PAX3 | SW10 | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 6 | g.11196181G>A | c.583C>T | p.(R195*) | XM_005610643.3; XP_005610700.1; association with increased depigmentation, published as c.927C>T | 2023 | 37406837 | |||
| 791 | OMIA:001688-9796 | horse | Lipizzan horse (Horse) Noric (Horse) Quarter Horse (Horse) | Splashed white | PAX3 | SW2 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 6 | g.11199026C>T | c.209G>A | p.(C70Y) | 2012 | 22511888 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |||
| 978 | OMIA:001688-9796 | horse | Appaloosa (Horse) | Splashed white | PAX3 | SW4 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 6 | g.11199140G>C | c.95C>G | p.(P32R) | 2013 | 23659293 | ||||
| 165 | OMIA:001982-9796 | horse | Thoroughbred (Horse) Warmblood breeds | Fragile Foal Syndrome | PLOD1 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 2 | g.39927817C>T | c.2032G>A | p.(G678R) | rs1136065234 | 2015 | 25637337 | rsID and Variant coordinates obtained from Zhang et al. (2020): "g.39927817C>T (rs1136065234; NC_009145.3, Equ-Cab3.0)" c. and p. coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| 903 | OMIA:001438-9796 OMIA:000733-9796 | horse | American Miniature Horse (Horse) Ardennes (Horse) Comtois (Horse) Iceland Pony (Horse) Missouri Fox Trotter, Germany (Horse) Morgan (Horse) Rocky Mountain, United States of America (Bighorn sheep) | Coat colour, silver AND Multiple congenital ocular anomalies | PMEL | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 6 | g.74569773G>A | c.1849C>T | p.(R617C) | NM_001163889.1; NP_001157361.1; previously listed in OMIA as g.73665304 and published a C (wild type) to T (Silver) transition, p.Arg618Cys, as well as p.(R625C); coordinates in this table have been updated to a recent reference genome and / or transcript | rs3448111155 | 2006 | 17029645 | The genomic position in EquCab3.0 was provided by Mary Katherine Easterwood, working under the guidance of Professor Ernie Bailey in April 2022 | ||
| 157 | OMIA:000327-9796 | horse | Quarter Horse (Horse) | Ehlers-Danlos syndrome | PPIB | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 1 | g.129307092G>A | c.115G>A | p.(G39R) | rs396329681 | 2007 | 17498917 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| 511 | OMIA:000220-9796 | horse | Arab (Horse) | Severe combined immunodeficiency disease, autosomal | PRKDC | deletion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 9 | g.36395752_36395759del | c.9478_9482del | p.(N3160fs*3) | A 5bp deletion giving rise to a frameshift in PRKDC The following details (from which the coordinate fields were populated) were provided by Meredith O’Connell, Tanya German, Isabella Pisani and Karalie Andrews, under the supervision of Professor Ernie Bailey. 20 Feb 2019 NC_009152.3 g.36395752-36395976del; NM_001163858 c.9478_9482del; NP_001157330 p.N3160fs*3 | 1997 | 9103416 | ||||
| 1369 | OMIA:002458-9796 | horse | Thoroughbred (Horse) | Hypoparathyroidism | RAPGEF5 | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 4 | g.54108297G>T | c.2624C>A | p.(S875*) | 2020 | 32986719 | |||||
| 159 | OMIA:000621-9796 | horse | Quarter Horse (Horse) | Malignant hyperthermia | RYR1 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 10 | g.9678680C>G | c.7363C>G | p.(R2455G) | XM_023649662.1; XP_023505430.1; published as c.7360C>G and p.(R2454G); coordinates in the table have been updated to a recent reference genome and / or transcript | 2004 | 15318347 | The genomic position in EquCab3.0 was provided by Hailey Anderson, working under the guidance of Professor Ernie Bailey in April 2022 | |||
| 162 | OMIA:000785-9796 | horse | Quarter Horse (Horse) | HYPP | SCN4A | H | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 11 | g.15474228C>G | c.4248C>G | p.(F1416L) | NM_001081761.1; NP_001075230.1; ECA11 (NC_009154.3) g.15474228C>G; NM_001081761.1: c.4248C>G; NP_001075230.1: F1416L; Sift Score 0.01. The above information (from which the coordinate fields were populated) was provided by Tatyana German and Meredith O’Connell, working under the supervision of Professor Ernie Bailey. | rs1148998534 | 1992 | 1338908 | ||
| 965 | OMIA:001897-9796 | horse | Connemara Pony (Horse) | Hoof wall separation syndrome | SERPINB11 | insertion, small (<=20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 8 | g.83600643_83600644insC | c.504_505insC | p.(T169Hfs*3) | 2015 | 25875171 | FN thanks Daniel J. Schmidt, working under the supervision of Professor Ernie Bailey, for updating the coordinates to EquCab3.0. | ||||
| 686 | OMIA:002013-9796 | horse | Shetland Pony (Horse) | Skeletal atavism | SHOX | Del-1 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | PAR | 160−180 kb deletion in the pseudoautosomal region (PAR) of chromosome X/Y; removing the entire coding region of the short stature homeobox (SHOX) gene and parts of the cytokine receptor-like factor 2 (CRLF2) gene located downstream of SHOX | 2016 | 27207956 | |||||||
| 1455 | OMIA:002013-9796 | horse | Shetland Pony (Horse) | Skeletal atavism | SHOX | Del-2 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | PAR | 60−80 kb deletion in the pseudoautosomal region (PAR) of chromosome X/Y; removing parts of the cytokine receptor-like factor 2 (CRLF2) gene located downstream of SHOX | 2016 | 27207956 | |||||||
| 811 | OMIA:002124-9796 | horse | Paso Fino (Horse) | Tiger eye | SLC24A5 | Tiger-eye 2 | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 1 | g.143129074_143129702del | c.875-340_1081+82del | 2017 | 28655738 | |||||
| 810 | OMIA:002124-9796 | horse | Paso Fino (Horse) | Tiger eye | SLC24A5 | Tiger-eye 1 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 1 | g.143145865A>T | c.272A>T | p.(F91Y) | 2017 | 28655738 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| 152 | OMIA:001263-9796 | horse | Coat colour, champagne | SLC36A1 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 14 | g.26012449G>C | c.188C>G | p.(T63R) | 2008 | 18802473 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||||
| 1140 | OMIA:001344-9796 | horse | Traditional Gypsy Cob, United Kingdom of Great Britain and Northern Ireland (Horse) | Coat colour, snowdrop | SLC45A2 | C^sno | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 21 | g.31688649G>A | c.305G>A | p.(R102Q) | Bisbee et al. (2020): transcript ENSECAT00000026240.1 in the Ensembl EquCab2.0 assembly | 2020 | 31961951 | |||
| 153 | OMIA:001344-9796 | horse | Coat colour, cream dilution | SLC45A2 | C^Cr | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 21 | g.31690653G>A | c.457G>A | p.(D153N) | ENSECAT00000066600.2; ENSECAP00000054416.1 | rs1140980396 | 2003 | 12605854 | EquCab3 coordinates obtained from Table S2 of Holl et al. (2019) | ||
| 1074 | OMIA:001344-9796 | horse | Standardbred x Tennessee Walking Horse cross (Horse) | Coat colour, sunshine | SLC45A2 | C^sun | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 21 | g.31705726G>A | c.568G>A | p.(G190R) | Holl et al. (2019): "The exon sequence containing this variant was deposited in Genbank under accession no. MF688761." | 2019 | 31006892 | |||
| 1069 | OMIA:001344-9796 | horse | American Paint (Horse) Lusitanian (Horse) Purebred Spanish (Horse) Quarter Horse (Horse) | Coat colour, pearl | SLC45A2 | C^prl | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 21 | g.31709690G>A | c.985G>A | p.(A329T) | 2019 | 30968968 | EquCab3 g. coordinate kindly provided by Natalia Sevane | |||
| 158 | OMIA:001578-9796 | horse | Dales (Horse) Fell Pony (Horse) | Foal immunodeficiency syndrome in the Fell and Dales Pony | SLC5A3 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 26 | g.31894278C>T | c.1352C>T | p.(P451L) | NM_001247992.1; NP_001234921.1; previously listed in OMIA as g.30660224G>T in EquCab2.0, c.1337G>T and published as p.(P446L); coordinates in the table have been updated to a recent reference genome and / or transcript | 2011 | 21750681 | Briana Moreno, working under the guidance of Professor Ernie Bailey, provided genomic coordinates in EquCab3.0 in April 2022 | |||
| 1040 | OMIA:002175-9796 | horse | Bashkir Curly (Horse) Missouri Fox Trotter, Germany (Horse) | Curly coat with/without hypotrichosis | SP6 | missense | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 11 | g.24096309C>T | c.1090G>A | p.(D364N) | Thomer et al. (2018): "SP6; NC_009154.2:g.24022045C>T, ss3021042887" with respect to EquCab2. Updated coordinates in this entry obtained from EVA rs1095048852; 14 Mar 2019 | rs1095048852 | 2018 | 29686323 | |||
| 659 | OMIA:001230-9796 | horse | American Trotter (Horse) | XY sex reversal | SRY | deletion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | Y | "at least the DNA-binding domain of the SRY gene was deleted from the Y chromosome of the XY mare" | 1995 | 7558880 | ||||||||
| 354 | OMIA:002096-9796 | horse | Akhal-Teke (Horse) | Naked foal syndrome | ST14 | nonsense (stop-gain) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 7 | NC_009150.3:g.39710628G>T | XM_005611718.2:c.388G>T | XP_005611775.1:p.(E130*) | 2017 | 28235824 | (FN thanks Emily Rogers for providing the genomic location (determined using BLAT with the XM_005611718.2 sequence against Equcab 3.0) and the sequence refs for the cDNA and protein variants, working under the supervision of Professor Ernie Bailey; 24 April 2020) | ||||
| 438 | OMIA:001356-9796 | horse | Coat colour, grey/gray | STX17 | duplication | Naturally occurring variant | Not currently ISAG evaluated | 25 | a 4.6kb intronic duplication in the gene for syntaxin-17 (STX17). This duplication appears to increase the expression of both syntaxin-17 and a neighbouring gene NR4A3, | 2008 | 18641652 | |||||||||
| 1028 | OMIA:001972-9796 | horse | Non-dun | TBX3 | nd1 | regulatory | Naturally occurring variant | Not currently ISAG evaluated | EquCab2.0 | 8 | Differs from the wild-type allele by a SNP downstream of the wild-type TBX3 sequence (located 1067bp downstream of the start of the larger nd2 deletion described in the nd2 entry), with allele nd1 = T compared with the wild-type D allele = G); an ancient variant | 2016 | 26691985 | |||||||
| 1029 | OMIA:001972-9796 | horse | Non-dun | TBX3 | nd2 | regulatory | Naturally occurring variant | Not currently ISAG evaluated | EquCab2.0 | 8 | A 1609bp deletion (18 227 267–18 227 279; EquCab2) downstream of the wild-type TBX3 sequence plus an 8bp deletion 11 bases upstream of the larger deletion; a recent variant | 2016 | 26691985 | |||||||
| 725 | OMIA:001341-9796 OMIA:002139-9796 | horse | American Miniature Horse (Horse) Appaloosa (Horse) British Spotted Pony, Spotted Pony, United Kingdom of Great Britain and Northern Ireland (Horse) English Spotted Pony, Australia (Horse) Knabstrupper (Horse) Noric (Horse) Pony Of the Americas, Germany (Horse) Thoroughbred (Horse) | Stationary congenital night blindness & Leopard Complex/Appaloosa spotting | TRPM1 | insertion, gross (>20) | Naturally occurring variant | Not currently ISAG evaluated | EquCab3.0 | 1 | NC_009144.3:g.109211964_109211965insN[1378] | "a 1378 bp retroviral LTR insertion in intron 1 of TRPM1", EquCab2.0: g.108297929_108297930insN[1378] | 2013 | 24167615 | Coordinates in EquCab3.0 kindly provided by Haley Rutstein, working under the guidance of Professor Ernie Bailey. |
* Variant pathogenicity for single gene diseases as evaluated by an expert panel of the International Society of Animal Genetics (ISAG) Animal Genetic Testing Standardization Standing Committee
| Overall Statistics | |
|---|---|
| Total number of variants | 107 |
| Variants with genomic location | 101 (94.4% ) |
| Variants in a variant database, i.e. with rs ID | 26 (24.3%) |
| Variant Type | Count | Percent |
|---|---|---|
| deletion, gross (>20) | 13 | 12.1% |
| deletion, small (<=20) | 14 | 13.1% |
| delins, small (<=20) | 2 | 1.9% |
| duplication | 2 | 1.9% |
| insertion, gross (>20) | 2 | 1.9% |
| insertion, small (<=20) | 3 | 2.8% |
| missense | 47 | 43.9% |
| nonsense (stop-gain) | 9 | 8.4% |
| not known | 1 | 0.9% |
| regulatory | 4 | 3.7% |
| splicing | 10 | 9.3% |
| Variant Effect | Count | Percent |
|---|---|---|
| unknown | 107 | 100.0% |
| Year First Reported | Count | Percent |
|---|---|---|
| 1992 | 1 | 0.9% |
| 1993 | 0 | 0.0% |
| 1994 | 0 | 0.0% |
| 1995 | 1 | 0.9% |
| 1996 | 1 | 0.9% |
| 1997 | 1 | 0.9% |
| 1998 | 1 | 0.9% |
| 1999 | 0 | 0.0% |
| 2000 | 1 | 0.9% |
| 2001 | 1 | 0.9% |
| 2002 | 1 | 0.9% |
| 2003 | 1 | 0.9% |
| 2004 | 2 | 1.9% |
| 2005 | 1 | 0.9% |
| 2006 | 2 | 1.9% |
| 2007 | 6 | 5.6% |
| 2008 | 3 | 2.8% |
| 2009 | 8 | 7.5% |
| 2010 | 2 | 1.9% |
| 2011 | 8 | 7.5% |
| 2012 | 7 | 6.5% |
| 2013 | 6 | 5.6% |
| 2014 | 0 | 0.0% |
| 2015 | 4 | 3.7% |
| 2016 | 7 | 6.5% |
| 2017 | 13 | 12.1% |
| 2018 | 9 | 8.4% |
| 2019 | 5 | 4.7% |
| 2020 | 6 | 5.6% |
| 2021 | 3 | 2.8% |
| 2022 | 3 | 2.8% |
| 2023 | 3 | 2.8% |