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115 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 | domestic horse | Miniature Horse (Horse) | Dwarfism, ACAN-related | ACAN | D4 | deletion, gross (>20) | deletion (in-frame) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 1 | NC_009144.3:g.95257479_95257499del | XM_005602799.2:c.7633_7653del | XP_005602856.2:p.(F2545_C2551del) | Genomic positions were previosuly incorreclty listed in OMIA as g.95257458_95257500del (until 10/01/2022) and g.95257480_95257500del (until 13/06/2024). Coordinates presented in the table reflect the published rs1095048839. IT is thanking Rebecca Bellone for spotting an error in the genomic coordinates which are now corrected (26/11/2024). |
rs1095048839 | 2018 | 30058072 | |
| 1792 | OMIA:001271-9796 | domestic horse | Miniature Horse (Horse) | Dwarfism, ACAN-related | ACAN | D5 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 1 | NC_009144.3:g.95258999C>T | XM_005602799.2:c.7435G>A | XP_005602856.2:p.(A2479T) | 2023 | Reference not in PubMed; see OMIA 001271-9796 for reference details | |||
| 788 | OMIA:001271-9796 | domestic horse | Miniature Horse (Horse) Shetland Pony (Horse) | Dwarfism, ACAN-related | ACAN | D3* | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 1 | NC_009144.3:g.95282140C>G | XM_023650286.1:c.1513G>C | XP_023506054.1: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 | domestic horse | Miniature Horse (Horse) Quarter Horse (Horse) Warmblood (Horse) | Dwarfism, ACAN-related | ACAN | D2 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 1 | NC_009144.3:g.95284530C>T | XP_023506054.1:c.1270C>T | XP_023506054.1:p.(V424M) | rs3091781465 | 2018 | 30058072 | Breed information updated based on PMID: 38600096 | |
| 999 | OMIA:001271-9796 | domestic horse | Miniature Horse (Horse) Shetland Pony (Horse) | Dwarfism, ACAN-related | ACAN | D1 | deletion, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 1 | NC_009144.3:g.95291271del | XM_023650281.1:c.245del | XP_023506054.1: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 | Breed information updated based on PMID: 38600096 |
| 436 | OMIA:000991-9796 | domestic horse | Quarter Horse (Horse) | Androgen insensitivity syndrome (AIS) | AR | substitution | regulatory | Naturally occurring variant | Not currently 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 | domestic horse | Tennessee Walking Horse (Horse) | Androgen insensitivity syndrome (AIS) | AR | deletion, small (<=20) | frameshift | Naturally occurring variant | Not currently 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 | domestic horse | Warmblood (Horse) | Androgen insensitivity syndrome | AR | deletion, gross (>20) | frameshift | Naturally occurring variant | Not currently 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 | domestic horse | Thoroughbred (Horse) | Androgen insensitivity syndrome | AR | substitution | missense | Naturally occurring variant | Not currently 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 | domestic horse | Thoroughbred (Horse) | Androgen insensitivity syndrome (AIS) | AR | substitution | missense | Naturally occurring variant | Not currently 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 | domestic horse | American Trotter (Horse) Arab (Horse) Belgian Draft (Horse) Clydesdale (Horse) Freiberger (Horse) Icelandic Horse (Horse) Morgan (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Thoroughbred (Horse) Warmblood (Horse) Welsh Pony (Horse) | Coat colour, recessive black | ASIP | a | deletion, small (<=20) | Naturally occurring variant | Not currently 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. Breed information based on PMID: 38600096 | ||
| 348 | OMIA:000487-9796 | domestic horse | Belgian Draft (Horse) Friesian (Horse) Warmblood (Horse) | Hydrocephalus | B3GALNT2 | substitution | nonsense (stop-gain) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 1 | NC_009144.3:g.76887901C>T | XM_001491545.6:c.1423C>T | XP_001491595.2: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. Breed information updated based on PMID: 38600096 | |
| 421 | OMIA:002068-9796 | domestic horse | Friesian (Horse) | Dwarfism, Friesian | B4GALT7 | substitution | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 14 | NC_009157.3:g.3772591C>T | XM_023617086.1:c.50G>A | XP_023472854.1: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. | ||
| 161 | OMIA:000698-9796 | domestic horse | New Forest Pony (Horse) | Myotonia | CLCN1 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 4 | NC_009147.3:g.96518592A>C | XM_001915636.4:c.1775A>C | XP_001915671.3:p.(D592A) | c.1775A>C, Genbank acc. XM_001915636; p.D592A, Genbank acc. XP_001915671 (Wijnberg et al., 2014) | rs5334475185 | 2012 | 22197188 | (FN thanks Izabela De Assis Rocha, who provided genomic location in EquCab3.0 and the Genbank acc IDs, working under the supervision of Professor Ernie Bailey; 15 April 2020) Revised genomic location kindly provided by Cord Drögemüller; 21 May 2021 | |
| 167 | OMIA:000735-9796 | domestic horse | Belgian Draft (Horse) Connemara Pony (Horse) Haflinger (Horse) Noric (Horse) Rocky Mountain Horse (Horse) Warmblood (Horse) Welsh Pony (Horse) | Ocular squamous cell carcinoma | DDB2 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 12 | NC_009155.3:g.11726667C>T | XM_023654000.1:c.1013C>T | XP_023509768.1: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. Breed information updated based on PMID: 38600096; 40218305 | |
| 321 | OMIA:001715-9796 | domestic horse | American Trotter (Horse) Bhotia Pony, India (Horse) Chakouyi, China (Horse) French Trotter (Horse) Icelandic Horse (Horse) Kentucky Mountain Saddle, United States of America (Horse) Missouri Fox Trotting Horse (Horse) Morgan (Horse) Paso Fino (Horse) Peruvian Paso (Horse) Quarter Horse (Horse) Rocky Mountain Horse (Horse) Scandinavian Coldblood Trotter (Horse) Spiti Pony, India (Horse) Tennessee Walking Horse (Horse) Thoroughbred (Horse) Zaniskari Pony (Horse) | Gaitedness | DMRT3 | substitution | nonsense (stop-gain) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 23 | NC_009166.3:g.22391254C>A | NM_001317265.1:c.902C>A | NP_001304194.1:p.(S301*) | rs1150690013 | 2012 | 22932389 | Breed information updated based PMID:39571791 on PMID:38600096 and PMID:37149793 | ||
| 160 | OMIA:000629-9796 | domestic horse | American Paint (Horse) Miniature Horse (Horse) Quarter Horse (Horse) Thoroughbred (Horse) | Megacolon | EDNRB | frame overo | delins, small (<=20) | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 17 | NC_009160.3:g.50503041_50503042delinsCT | NM_001081837.2:c.353_354delinsAG | NP_001075306.2:p.(I118K) | NM_001081837.2; NP_001075306.2 | 1998 | 9530628 | ||
| 322 | OMIA:000420-9796 | domestic horse | American Paint (Horse) Quarter Horse (Horse) | Glycogen storage disease IV | GBE1 | substitution | nonsense (stop-gain) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 26 | NC_009169.3:g.8667651C>A | NM_001081940.2:c.102C>A | NP_001075409.1: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 | domestic 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 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 14 | NC_009157.3:g.2655618C>T | XM_001916934.4:c.533C>T | XP_001916969.3: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 | domestic horse | American Paint (Horse) Appaloosa (Horse) Belgian Draft (Horse) Quarter Horse (Horse) | Polysaccharide storage myopathy/Exertional rhabdomyolysis | GYS1 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 10 | NC_009153.3:g.19203501C>T | NM_001126125.2:c.926G>A | NP_001119597.2: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. Breed information updated based on PMID: 38600096 | |
| 1824 | OMIA:001968-9796 | domestic horse | German Riding Pony (Horse) New Forest Pony (Horse) Shetland Pony (Horse) Welsh Pony (Horse) | small size | HMGA2 | missense | missense | Naturally occurring variant | Not currently evaluated | TB-T2T | 6 | NC_091689.1:g.94527217G>A | NM_001433493.1:c.83G>A | NP_001420422.1:pG28E | 2015 | 26474182 | ||||
| 691 | OMIA:000081-9796 | domestic horse | Arab (Horse) | Atlanto occipital fusion | HOXD3 | deletion, gross (>20) | Naturally occurring variant | Not currently 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 | domestic horse | Quarter Horse (Horse) Warmblood (Horse) | Incontinentia pigmenti | IKBKG | substitution | nonsense (stop-gain) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | X | NC_009175.3:g.126898409C>T | NM_001284533.1:c.184C>T | NP_001271462.1:p.(R62*) | Previously listed as as c.202C>T and p.(R68*), updated in this table to reflect NM_001284533.1 transcript | rs3433281055 | 2013 | 24324710 | Breed information updated based on PMID: 38600096 | |
| 164 | OMIA:001000-9796 | domestic horse | Quarter Horse (Horse) Thoroughbred (Horse) | Thrombasthenia | ITGA2B | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 11 | NC_009154.3:g.19245752G>C | NM_001081793.1:c.215G>C | NP_001075262.1: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 | domestic horse | Peruvian Paso (Horse) Quarter Horse (Horse) | Thrombasthenia | ITGA2B | deletion, small (<=20) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 11 | NC_009154.3:g.19247983_19247992del | g.19247983_19247992delCAGGTGAGGA | 2007 | 17338169 | g. coordinates obtained from Dahlgren et al. (2020) | |||||
| 1331 | OMIA:000209-9796 | domestic horse | American Paint (Horse) American Trotter (Horse) Belgian Draft (Horse) Icelandic Horse (Horse) Quarter Horse (Horse) Thoroughbred (Horse) Welsh Pony (Horse) | White spotting | KIT | W32 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79538738C>T | NM_001163866.1:c.2878G>A | NP_001157338.1:p.(A960T) | cDNA position previously listed as c.3214G>A; p.(A1072T) based on transcript ENSECAT00000014037.3 [16/04/2024] | rs1141982296 | 2021 | 34223905 | Breed information updated based on PMID: 38600096 |
| 882 | OMIA:000209-9796 | domestic horse | Süddeutsches Kaltblut, Germany (Horse) | Coat colour, dominant white | KIT | W11 | substitution | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79540429C>T | NM_001163866.1:c.2684+1G>A | rs5334475183 | 2009 | 19456317 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||
| 939 | OMIA:000209-9796 | domestic horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W26 | deletion, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79540694del | NM_001163866.1:c.2536del | NP_001157338.1:p.(S846Vfs*15) | NM_001163866.1; NP_001157338.1; published as c.2536delA | rs3101685403 | 2018 | 29333746 | |
| 873 | OMIA:000209-9796 | domestic horse | Oldenburg (Horse) | Coat colour, dominant white | KIT | W16 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79540741T>A | NM_001163866.1:c.2489A>T | NP_001157338.1:p.(K830I) | rs5334475213 | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
| 883 | OMIA:000209-9796 | domestic horse | Miniature Horse (Horse) Quarter Horse (Horse) Shetland Pony (Horse) | Coat colour, dominant white | KIT | W13 | substitution | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79544066C>G | NM_001163866.1: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 | domestic horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W14 | deletion, gross (>20) | deletion (in-frame) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79544098_79544151del | NM_001163866.1:c.2392_2445del | NP_001157338.1: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 | domestic horse | Icelandic Horse (Horse) | White spotting | KIT | W21 | deletion, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79544174del | NM_001163866.1:c.2369delC | NP_001157338.1:p.(A790Efs*20) | rs5334475210 | 2015 | 26059442 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
| 885 | OMIA:000209-9796 | domestic horse | Appaloosa (Horse) Haflinger (Horse) Lipizzan horse (Horse) Noric (Horse) Quarter Horse (Horse) | Coat colour, dominant white | KIT | sabino 1 (SB1) | substitution | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79544206A>T | "SNP AX-103727726 (ECA3:77735520; SB1, SNP KI16+1037A)" (Druml et al., 2018) | rs5334475211 | 2005 | 16284805 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||
| 893 | OMIA:000209-9796 | domestic horse | Trottatore Italiano, Italy (Horse) | Coat colour, dominant white | KIT | W24 | substitution | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79545245C>T | NM_001163866.1:c.2349+1G>A | rs3443588955 | 2017 | 28856698 | |||
| 1462 | OMIA:000209-9796 | domestic horse | American Trotter (Horse) | Dominant white spotting | KIT | W33 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79545248T>A | NM_001163866.1:c.2347A>T | NP_001157338.1:p.(N783Y) | NC_009146.3; previously listed as ENSECAT00000014037.3: c.2783A>T / p.(N895Y) [16/04/2024] | 2022 | 35641888 | ||
| 881 | OMIA:000209-9796 | domestic horse | Icelandic Horse (Horse) | Coat colour, dominant white | KIT | W8 | substitution | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79545374C>T | NM_001163866.1:c.2222-1G>A | NM_001163866.1 | rs3434854925 | 2009 | 19456317 | ||
| 1778 | OMIA:000209-9796 | domestic horse | Warmblood (Horse) | White spotting | KIT | W38 | substitution | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79545867C>A | NM_001163866.2:c.2221+5G>T | 2025 | 40218308 | ||||
| 886 | OMIA:000209-9796 | domestic horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W5 | deletion, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79545900del | NM_001163866.1:c.2193delG | NP_001157338.1:p.(T732Qfs*9) | rs5334475194 | 2009 | 19456317 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
| 878 | OMIA:000209-9796 | domestic horse | Freiberger (Horse) | Coat colour, dominant white | KIT | W1 | substitution | nonsense (stop-gain) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79545942G>C | NM_001163866.1:c.2151C>G | NP_001157338.1:p.(Y717*) | rs5334475201 | 2007 | 17997609 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
| 877 | OMIA:000209-9796 | domestic horse | American Paint (Horse) American Trotter (Horse) Appaloosa (Horse) Arab (Horse) Belgian Draft (Horse) Clydesdale (Horse) Freiberger (Horse) German Riding Pony (Horse) Morgan (Horse) Noric (Horse) Oldenburg (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Thoroughbred (Horse) Tori hobune, Estonia (Horse) Traditional Gypsy Cob, United Kingdom of Great Britain and Northern Ireland (Horse) Warmblood (Horse) Welsh Pony (Horse) | Coat colour, dominant white | KIT | W20 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79548220T>C | NM_001163866.1:c.2045G>A | NP_001157338.1:p.(R682H) | ENSECAT00000014037.3:c.2381A>G ENSECAP00000011188.2:p.His794Arg; reference genome corresponds to g.79548220T and the transcript NM_001163866.1 represents g.79548220C | rs1143160924 | 2013 | 23659293 | Variant coordinates initially gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124. Breed information updated based on PMID: 38600096 |
| 1261 | OMIA:000209-9796 | domestic horse | Berber, Germany (Horse) | Extensive coat white patterning | KIT | W30 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79548244A>T | NM_001163866.1:c.2021T>A | NP_001157338.1:p.(L674H) | published as g.79548244, c.2020T>A; p.L674H (Martin et al., 2020) - changed to NM_001163866.1:c.2021T>A [16/042024] | rs5334475224 | 2020 | 33111383 | |
| 890 | OMIA:000209-9796 | domestic horse | Thoroughbred (Horse) | White spotting | KIT | W22 | deletion, gross (>20) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79548925_79550822del | 1898bp deletion | 2017 | 28444912 | |||||
| 868 | OMIA:000209-9796 | domestic horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W2 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79549540C>T | NM_001163866.1:c.1960G>A | NP_001157338.1:p.(G654R) | rs5334475198 | 2007 | 17997609 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
| 869 | OMIA:000209-9796 | domestic horse | Camarillo White Horse, United States of America (Horse) | Coat colour, dominant white | KIT | W4 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79549781G>A | NM_001163866.1:c.1805C>T | NP_001157338.1:p.(A602V) | Previously incorrectly listed as g.79549780G>A [16/04/2024] | 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 | domestic horse | Holsteiner (Horse) | Coat colour, dominant white | KIT | W9 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79549797C>T | NM_001163866.1:c.1789G>A | NP_001157338.1:p.(G597R) | rs5334475209 | 2009 | 19456317 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
| 872 | OMIA:000209-9796 | domestic horse | Arab (Horse) | Coat colour, dominant white | KIT | W15 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79550351A>G | NM_001163866.1:c.1597T>C | NP_001157338.1:p.(C533R) | rs5334475202 | 2011 | 21554354 | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
| 1777 | OMIA:000209-9796 | domestic horse | Anglo-Arab (Horse) Zangersheide, Belgium (Horse) | White spotting | KIT | W37 | insertion, small (<=20) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79551903_79551904insA | NM_001163866.2:c.1512_1513insT | NP_001157338.2:p.(N505*) | published as g.79551897_79551898insA - coordinates in this table consider the 3'rule of the HGVS recommendations | 2025 | 40218308 | |||
| 940 | OMIA:000209-9796 | domestic horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W27 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79551937A>C | NM_001163866.1:c.1473T>G | NP_001157338.1:p.(C491W) | NM_001163866.1; NP_001157338.1 | rs3110307743 | 2018 | 29333746 | |
| 884 | OMIA:000209-9796 | domestic horse | CH-Warmblut, Switzerland (Horse) | Coat colour, dominant white | KIT | W18 | substitution | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79553751C>T | NM_001163866.1:c.1346+1G>A | rs5334475221 | 2013 | 23659293 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||
| 876 | OMIA:000209-9796 | domestic horse | Arab (Horse) | Coat colour, dominant white | KIT | W19 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79553776T>C | NM_001163866.1:c.1322A>G | NP_001157338.1:p.(Y441C) | rs5334475217 | 2013 | 23659293 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
| 1476 | OMIA:000209-9796 | domestic horse | American Paint (Horse) American Trotter (Horse) Appaloosa (Horse) Arab (Horse) Mangalarga (Horse) Morgan (Horse) Mustang (Horse) Quarter Horse (Horse) Rocky Mountain, United States of America (Bighorn sheep) Warmblood (Horse) | Increased white spotting | KIT | W34 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79566881T>C | NM_001163866.1:c.1171A>G | NP_001157338.1:p.(T391A) | Previously listed as ENSECAT00000014037.3:c.1495A>G; ENSECAP00000011188.2:p.(T499A) [16/04/2024] | rs1140732842 | 2022 | 35953947 | Breed information updated based on PMID: 38600096 |
| 887 | OMIA:000209-9796 | domestic horse | Quarter Horse (Horse) | Coat colour, dominant white | KIT | W10 | deletion, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79566923_79566926del | NM_001163866.1:c.1126_1129del | NP_001157338.1: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 | domestic horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W6 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79573754C>T | NM_001163866.1:c.856G>A | NP_001157338.1:p.(G286R) | rs5334475167 | 2009 | 19456317 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
| 892 | OMIA:000209-9796 | domestic horse | Arab (Horse) | White spotting | KIT | W23 | substitution | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79578484C>G | NM_001163866.1:c.756+1G>C | rs1095048836 | 2017 | 28378922 | |||
| 879 | OMIA:000209-9796 | domestic horse | Arab (Horse) | Coat colour, dominant white | KIT | W3 | substitution | nonsense (stop-gain) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79578535T>A | NM_001163866.1:c.706A>T | NP_001157338.1:p.(K236*) | rs5334475200 | 2007 | 17997609 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | |
| 938 | OMIA:000209-9796 | domestic horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W25 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79578573A>G | NM_001163866.1:c.668T>C | NP_001157338.1:p.(L223P) | NM_001163866.1; NP_001157338.1 | rs3103992630 | 2018 | 29333746 | |
| 888 | OMIA:000209-9796 | domestic horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W12 | deletion, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79579774_79579778del | NM_001163866.1:c.559_563del | NP_001157338.1:p.(S187Rfs*10) | NM_001163866.1; NP_001157338.1; published as c.559_563delTCTGC | rs5334475188 | 2010 | Reference not in PubMed; see OMIA 000209-9796 for reference details | Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 |
| 1779 | OMIA:000209-9796 | domestic horse | White spotting | KIT | W39 | substitution | nonsense (stop-gain) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79579796G>A | NM_001163866.2:c.541C>T | NP_001157338.2:p.(R181*) | 2025 | 40218308 | ||||
| 1091 | OMIA:000209-9796 | domestic horse | German Riding Pony (Horse) | White spotting | KIT | W28 | deletion, gross (>20) | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79579925_79581197del | 1273bp deletion affecting partial intron 2 and exon 3, may impact splicing | 2019 | 31463981 | ||||
| 880 | OMIA:000209-9796 | domestic horse | Thoroughbred (Horse) | Coat colour, dominant white | KIT | W7 | substitution | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79580000C>G | NM_001163866.1:c.338-1G>C | rs5334475216 | 2009 | 19456317 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124 | ||
| 1330 | OMIA:000209-9796 | domestic horse | Quarter Horse (Horse) | White spotting | KIT | W31 | insertion, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.79618532_79618533insA | NM_001163866.1:c.30_31insT | NP_001157338.1:p.(L11Sfs*115) | 2021 | 34223905 | |||
| 1854 | OMIA:000209-9796 | domestic horse | Japanese Draft, Japan (Horse) | Coat colour, dominant white | KIT | W17 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.[79548244A>G;79548265T>A] | NM_001163866.1:c.[2000A>T;2021T>C] | NP_001157338.1:p.[(E667D);(L674P)] | The two variants forming this haplotype were previously listed in OMIA as two variants (W17a; omia.variant:874; rs5334475222 and W17b; omia.variant:875; rs5334475224). Changed to this haplotype based on Tozaki et al. (2020, PMID:33376443) [28/11/2025]. | 2011 | 33376443 21554354 | Thanks to Tosso Leeb for bringing the information reported by Tozaki et al. (2020) to our attention. | |
| 856 | OMIA:000245-9796 | domestic horse | Bashkir Curly (Horse) Curly Horse (Horse) | Curly coat | KRT25 | Crd | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 11 | NC_009154.3:g.21962991G>A | NM_001346190.1:c.266G>A | NP_001333119.1: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 | domestic horse | American Saddle Horse (Horse) | Epidermolysis bullosa, junctionalis, LAMA3-related | LAMA3 | deletion, gross (>20) | Naturally occurring variant | Not currently 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 | domestic 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) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 5 | NC_009148.3:g.17498175dup | NM_001081768.1:c.1372dup | NP_001075237.1: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] | ||
| 1823 | OMIA:002977-9796 | domestic horse | Freiberger (Horse) | Hypertriglyceridemia-induced pancreatitis | LMF1 | HIP | delins, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | NC_009156.3:g.42,935,259_42,935,263delinsTCT | XM_023616679.1:c.369_373delinsTCT | XP_023472447.1:p.(L125Rfs*193 | 2025 | 40764662 | ||||
| 413 | OMIA:002021-9796 | domestic horse | Quarter Horse (Horse) Warmblood (Horse) | Coat colour, brindle 1 | MBTPS2 | substitution | splicing | Naturally occurring variant | Not currently evaluated | EquCab3.0 | X | NC_009175.3:g.17286855T>C | XM_023634090.1:c.1340+4T>C | Published as c.1437+4T>C - updated in this table to reflect XM_023634090.1 transcript coordinates | rs3434246715 | 2016 | 27449517 | Breed information updated based on PMID: 38600096 | ||
| 154 | OMIA:001199-9796 | domestic horse | American Trotter (Horse) Arab (Horse) Belgian Draft (Horse) Clydesdale (Horse) Freiberger (Horse) Icelandic Horse (Horse) Morgan (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Thoroughbred (Horse) Warmblood (Horse) Welsh Pony (Horse) | Coat colour, chesnut | MC1R | e | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.36979560C>T | NM_001114534.1:c.248C>T | NP_001108006.1:p.(S83F) | rs68458866 | 1996 | 8995760 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. Breed information updated based on PMID: 38600096 | |
| 155 | OMIA:001199-9796 | domestic horse | Belgian Draft (Horse) | Coat colour, chesnut | MC1R | e^a | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 3 | NC_009146.3:g.36979562G>A | NM_001114534.1:c.250G>A | NP_001108006.1:p.(D84N) | rs3443929753 | 2000 | 11086549 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. Breed information updated based on PMID: 38600096 | |
| 1426 | OMIA:002197-9796 | domestic horse | Shetland Pony (Horse) | Coat colour, dilution (mushroom) | MFSD12 | Mu | duplication | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 7 | NC_009150.3:g.2544518dup | XM_023646425.1:c.600dup | XP_023502193.1: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 | domestic horse | American Paint (Horse) | White spotting, blue eyes and deafness | MITF | SW5 | deletion, gross (>20) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 16 | NC_009159.3:g.21503211_21566617del | "~63-kb deletion spanning exons 6-9 of the MITF gene" | 2019 | 30644113 | |||||
| 1180 | OMIA:000214-9796 | domestic horse | American Paint (Horse) | Splashed white | MITF | SW6 | deletion, gross (>20) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 16 | NC_009159.3:g.21551060_21559770del | NC_009159.3:g.21551060-21559770del (Magdesian et al., 2020) | 2020 | 32242630 | |||||
| 1626 | OMIA:000214-9796 | domestic horse | Thoroughbred (Horse) | Splashed white | MITF | SW8 | deletion, gross (>20) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 16 | NC_009159.3:g.21555811_21558139delinsAAAT | 2023 | 37697831 | ||||||
| 166 | OMIA:000214-9796 | domestic horse | American Trotter (Horse) | White | MITF | MITF^244Glu | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 16 | NC_009159.3:g.21556522C>T | NM_001163874.1:c.1031G>A | NP_001157346.1:p.(G344E) | Published as XM_005600318.1:c.731G>A; XP_005600375.1:p.Gly244Glu) - updated in this table to reflect recent transcript ID | rs3435075789 | 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 | domestic horse | Purebred Spanish (Horse) | Splashed white | MITF | SW9 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 16 | NC_009159.3:g.21559940T>A | NM_001163874.1:c.961A>T | NP_001157346.1:p.(N321Y) | NM_001163874.1; NP_001157346.1; published as c.993A>T, variant associated with increased depigmentation | 2023 | 37406837 | ||
| 1488 | OMIA:000214-9796 | domestic horse | American Paint (Horse) Quarter Horse (Horse) | Splashed white | MITF | SW7 | deletion, small (<=20) | deletion (in-frame) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 16 | NC_009159.3:g.21559953_21559955del | NM_001163874.1:c.949_951del | NP_001157346.1:p.R317del | NM_001163874.1; NP_001157346.1; published as c.949_951delTCT | 2022 | 35672910 | ||
| 156 | OMIA:000214-9796 | domestic horse | Freiberger (Horse) | Macchiato | MITF | macchiato | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 16 | NC_009159.3:g.21564980T>C | NM_001163874.1:c.629A>G | NP_001157346.1:p.(N310S) | rs5334475186 | 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 | domestic horse | Quarter Horse (Horse) | Splashed white | MITF | SW3 | deletion, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 16 | NC_009159.3:g.21567245_21567249del | NM_001163874.1:c.837_841del | NP_001157346.1:p.(C280Sfs*20) | NM_001163874.1; NP_001157346.1; published as c.837_841delGTGTC | 2012 | 22511888 | ||
| 792 | OMIA:000214-9796 | domestic horse | American Miniature Horse (Horse) American Paint (Horse) Appaloosa (Horse) Icelandic Horse (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 evaluated | EquCab3.0 | 16 | NC_009159.3:g.21579201delinsATAATAACCTA | g.20117302Tdelins11 | rs5334475212 | 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 | domestic horse | American Trotter (Horse) Arab (Horse) Belgian Draft (Horse) Cavall Menorquí, Spain (Horse) Clydesdale (Horse) Freiberger (Horse) Icelandic Horse (Horse) Morgan (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Thoroughbred (Horse) Warmblood (Horse) Welsh Pony (Horse) | White splashing | MITF | substitution | regulatory | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 16 | NC_009159.3:g.21608936C>T | Published as g.20147039C>T (EquCab2.0); may not be causal as the variant was identified to be a common variant across multiple breeds in a later study: PMID: 38600096 | 2017 | 28084638 | Breed information updated based on PMID: 38600096 | ||||
| 443 | OMIA:001538-9796 | domestic horse | Racing distance, association with | MSTN | insertion, gross (>20) | Naturally occurring variant | Not currently evaluated | 18 | A "227 bp SINE insertion positioned upstream of exon 1" | 2015 | 26503543 | |||||||||
| 437 | OMIA:000175-9796 | domestic horse | Arab (Horse) Bashkir Curly (Horse) Quarter Horse (Horse) Trakehner (Horse) Welsh Pony (Horse) | Cerebellar abiotrophy | MUTYH | substitution | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 2 | NC_009145.3:g.13122415C>T | ENSECAT00000009202.3: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. Additional breeds added based on supplementary table 6 of Durward-Akhurst et al. (2024, PMID: 38600096). | rs397160943 | 2011 | 21126570 | ||||
| 973 | OMIA:002141-9796 | domestic horse | Belgian Draft (Horse) Quarter Horse (Horse) Welsh Pony (Horse) | Immune-mediated myositis | MYH1 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 11 | NC_009154.3:g.53345548T>C | NM_001081759.1:c.959A>G | NM_001081759.1:p.(E320G) | 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 and p.(E320G) | rs3435577028 | 2018 | 29510741 | Breed information updated based on PMID: 38600096 | |
| 510 | OMIA:001501-9796 | domestic horse | Arab (Horse) | Lavender foal syndrome | MYO5A | deletion, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 1 | NC_009144.3:g.139290592del | XM_023617258.1:c.4249del | XP_023473026.1: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 | domestic horse | Purebred Spanish (Horse) | Splashed white | PAX3 | SW10 | substitution | nonsense (stop-gain) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 6 | NC_009149.3:g.11196181G>A | XM_005610643.3:c.583C>T | XP_005610700.1:p.(R195*) | XM_005610643.3; XP_005610700.1; association with increased depigmentation, published as c.927C>T | 2023 | 37406837 | ||
| 791 | OMIA:001688-9796 | domestic horse | Lipizzan horse (Horse) Noric (Horse) Quarter Horse (Horse) | Splashed white | PAX3 | SW2 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 6 | NC_009149.3:g.11199026C>T | XM_001495160.4:c.209G>A | XP_001495210.1:p.(C70Y) | rs5334475189 | 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 | domestic horse | Appaloosa (Horse) | Splashed white | PAX3 | SW4 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 6 | NC_009149.3:g.11199140G>C | XM_001495160.4:c.95C>G | XP_001495210.1:p.(P32R) | rs5334475206 | 2013 | 23659293 | ||
| 165 | OMIA:001982-9796 | domestic horse | Thoroughbred (Horse) Warmblood (Horse) | Fragile Foal Syndrome | PLOD1 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 2 | NC_009145.3:g.39927817C>T | XM_001491331.6:c.2032G>A | XP_001491381.1: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 | domestic horse | American Miniature Horse (Horse) Ardennes (Horse) Comtois (Horse) Icelandic Horse (Horse) Missouri Fox Trotter, Germany (Horse) Morgan (Horse) Rocky Mountain, United States of America (Bighorn sheep) Shetland Pony (Horse) | Coat colour, silver AND Multiple congenital ocular anomalies | PMEL | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 6 | NC_009149.3:g.74569773G>A | NM_001163889.1:c.1849C>T | NP_001157361.1: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. Breed information updated based on PMID: 38600096 | |
| 157 | OMIA:000327-9796 | domestic horse | Quarter Horse (Horse) | Ehlers-Danlos syndrome | PPIB | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 1 | NC_009144.3:g.129307092G>A | NM_001099761.1:c.115G>A | NP_001093231.1:p.(G39R) | rs396329681 | 2007 | 17498917 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| 511 | OMIA:000220-9796 | domestic horse | Arab (Horse) | Severe combined immunodeficiency disease, autosomal | PRKDC | deletion, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 9 | NC_009152.3:g.36395752_36395756del | NM_001163858.1:c.9478_9482del | NP_001157330.1: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. The g. coordinates were previously listed incorrectly in this table as g.36395752_36395759del [03/06/2024] |
1997 | 9103416 | |||
| 1369 | OMIA:002458-9796 | domestic horse | Thoroughbred (Horse) | Hypoparathyroidism | RAPGEF5 | substitution | nonsense (stop-gain) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 4 | NC_009147.3:g.54108297G>T | XM_023639352.1:c.2624C>A | XP_023495120.1:p.(S875*) | 2020 | 32986719 | ||||
| 159 | OMIA:000621-9796 | domestic horse | American Paint (Horse) Appaloosa (Horse) Quarter Horse (Horse) | Malignant hyperthermia | RYR1 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 10 | NC_009153.3:g.9678680C>G | XM_023649662.1:c.7363C>G | XP_023505430.1: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. Additional breed inforamtion based on PMID:40298507 | ||
| 162 | OMIA:000785-9796 | domestic horse | Quarter Horse (Horse) | HYPP | SCN4A | H | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 11 | NC_009154.3:g.15474228C>G | NM_001081761.1:c.4248C>G | NP_001075230.1: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 | |
| 1819 | OMIA:002272-9796 | domestic horse | Thoroughbred (Horse) | Thrombasthenia, atypical | SEL1L | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 24 | NC_009167.3:g.26081856T>C | NM_001317264.1:c.1810A>G | NP_001304193.1:p.Ile604Val | 2025 | 40654876 | ||||
| 965 | OMIA:001897-9796 | domestic horse | Connemara Pony (Horse) | Hoof wall separation syndrome | SERPINB11 | insertion, small (<=20) | frameshift | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 8 | NC_009151.3:g.83600643_83600644insC | XM_001491598.3:c.504_505insC | XP_001491648.1:p.(T169Hfs*3) | rs3447216148 | 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 | domestic horse | Shetland Pony (Horse) | Skeletal atavism | SHOX | Del-1 | deletion, gross (>20) | Naturally occurring variant | Not currently 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 | domestic horse | Shetland Pony (Horse) | Skeletal atavism | SHOX | Del-2 | deletion, gross (>20) | Naturally occurring variant | Not currently 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 | domestic horse | Paso Fino (Horse) | Tiger eye | SLC24A5 | Tiger-eye 2 | deletion, gross (>20) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 1 | NC_009144.3:g.143129074_143129702del | published as a 628bp deletion: chr1:141660611–141661239; ENSECAT00000019866.1:c.875-340_1081 + 82del | 2017 | 28655738 | |||||
| 810 | OMIA:002124-9796 | domestic horse | Paso Fino (Horse) | Tiger eye | SLC24A5 | Tiger-eye 1 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 1 | NC_009144.3:g.143145865A>T | XM_023618043.1:c.272A>T | XP_023473811.1:p.(F91Y) | rs5334475205 | 2017 | 28655738 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |
| 152 | OMIA:001263-9796 | domestic horse | American Cream Draft (Horse) American Miniature Horse (Horse) American Paint (Horse) American Saddle Horse (Horse) Appaloosa (Horse) Kentucky Mountain Saddle, United States of America (Horse) Missouri Fox Trotting Horse (Horse) Quarter Horse (Horse) Tennessee Walking Horse (Horse) | Coat colour, champagne | SLC36A1 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 14 | NC_009157.3:g.26012449G>C | XM_023617382.1:c.188C>G | XP_023473150.1:p.(T63R) | rs5334475190 | 2008 | 18802473 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| 1140 | OMIA:001344-9796 | domestic horse | Traditional Gypsy Cob, United Kingdom of Great Britain and Northern Ireland (Horse) | Coat colour, snowdrop | SLC45A2 | C^sno | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 21 | NC_009164.3:g.31688649G>A | XM_001498110.4:c.449G>A | XP_001498160.2:p.(R150Q) | Bisbee et al. (2020): transcript ENSECAT00000026240.1 in the Ensembl EquCab2.0 assembly, previously listed as c.305G>A and p.(R102Q). Coordinates in this table are based on a recent reference genome and in accordance with HGVS recommendations. | rs5334475197 | 2020 | 31961951 | EquCab3.0 c. and p. coordinates kindly provided by Robin Everts. |
| 153 | OMIA:001344-9796 | domestic horse | Morgan (Horse) Quarter Horse (Horse) Welsh Pony (Horse) | Coat colour, cream dilution | SLC45A2 | C^Cr | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 21 | NC_009164.3:g.31690653G>A | XM_001498110.4:c.601G>A | XP_001498160.2:p.(D201N) | Variant published as equCab3 chr21:g. 31,690,653G>A exon 2 c.457G>A p.Asp153Asn; coordinates in this table are based on a recent reference genome and in accordance with HGVS recommendations. | rs1140980396 | 2003 | 12605854 | EquCab3.0 g. coordinates obtained from Table S2 of Holl et al. (2019); c. and p. coordinates kindly provided by Robin Everts. Breed information updated based on PMID: 38600096 |
| 1074 | OMIA:001344-9796 | domestic horse | Standardbred x Tennessee Walking Horse cross (Horse) | Coat colour, sunshine | SLC45A2 | C^sun | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 21 | NC_009164.3:g.31705404G>A | XM_001498110.4:c.712G>A | XP_001498160.2:p.(G238R) | Variant published as equCab3 chr21:g. 31,705,368G>A exon 3 c.568G>A p.Gly190Arg; genomic coordinates in OMIA were previously incorrectly listed as EquCab3.0 chr21 g.31705726G>A and corrected based on feedback from Robin Everts [12/04/2024]. Coordinates in this table are based on a recent reference genome and in accordance with HGVS recommendations. | rs394940514 | 2019 | 31006892 | EquCab3.0 g., c. and p. kindly provided by Robin Everts. |
| 1069 | OMIA:001344-9796 | domestic horse | American Paint (Horse) Lusitanian (Horse) Purebred Spanish (Horse) Quarter Horse (Horse) | Coat colour, pearl | SLC45A2 | C^prl | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 21 | NC_009164.3:g.31709690G>A | XM_001498110.4:c.1129G>A | XP_001498160.2:p.(A377T) | Variant published as equCab3 chr21:g. 31,709,654G>A exon 4 c.985G>A p.Ala329Thr; coordinates in this table are based on a recent reference genome and in accordance with HGVS recommendations. | rs3101690631 | 2019 | 30968968 | EquCab3 g. coordinate kindly provided by Natalia Sevane; c. and p. coordinates kindly provided by Robin Everts. |
| 158 | OMIA:001578-9796 | domestic horse | Dales (Horse) Fell Pony (Horse) | Foal immunodeficiency syndrome in the Fell and Dales Pony | SLC5A3 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 26 | NC_009169.3:g.31894278C>T | NM_001247992.1:c.1352C>T | NP_001234921.1: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 | domestic horse | Bashkir Curly (Horse) Missouri Fox Trotter, Germany (Horse) | Curly coat with/without hypotrichosis | SP6 | substitution | missense | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 11 | NC_009154.3:g.24096309C>T | XM_023652659.1:c.1090G>A | XP_023508427.1:p.(G364S) | 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. Protein coordinates in this table previously inocrrectly shown as p.(D346N); corrected 13/06/2024. | rs1095048852 | 2018 | 29686323 | ||
| 659 | OMIA:001230-9796 | domestic horse | American Trotter (Horse) | XY sex reversal | SRY | deletion, gross (>20) | Naturally occurring variant | Not currently 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 | domestic horse | Akhal-Teke (Horse) | Naked foal syndrome | ST14 | substitution | nonsense (stop-gain) | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 7 | NC_009150.3:g.39710628G>T | XM_005611718.2:c.388G>T | XP_005611775.1:p.(E130*) | rs5334475187 | 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 | domestic horse | Coat colour, grey/gray (slow greying) | STX17 | G2 | repeat variation | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 25 | NC_009168.3:g.6625295_6629872dup | two tandom copies of a 4.6kb intronic region in STX17, which increase the expression of both STX17 and a neighbouring gene NR4A3 | 2008 | 18641652 | ||||||
| 1732 | OMIA:001356-9796 | domestic horse | Coat colour, grey/gray (fast greying) | STX17 | G3 | repeat variation | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 25 | NC_009168.3:g.6625295_6629872[3] | three tandom copies of a 4.6kb intronic region in STX17 which increase the expression of both syntaxin-17 and a neighbouring gene NR4A3 | 2024 | 39209879 | ||||||
| 1029 | OMIA:001972-9796 | domestic horse | Non-dun without primitive markings | TBX3 | nd2 | reference sequence allele | regulatory | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 8 | allele is represented by the reference genome EquCab3.0 | 2016 | 26691985 | [IT thanks Haley Rutstein, working under the guidance of Professor Ernie Bailey, for contributions to this entry in April 2024] | |||||
| 1701 | OMIA:001972-9796 | domestic horse | Curly Horse (Horse) Fjord (Horse) Icelandic Horse (Horse) Polish Konik (Horse) Quarter Horse (Horse) Vyatka (Horse) | Dun | TBX3 | D | haplotype | regulatory | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 8 | NC_009151.3:g.[20665796_20665797insCCTTCTGGC;20665807_20665808ins[1609]] | 2016 | 26691985 | [IT thanks Haley Rutstein, working under the guidance of Professor Ernie Bailey, for contributions to this entry in April 2024]. Additional breed information based on Stefaniuk-Szmukier et al. (2017) and Belousova et al. (2023). | ||||
| 1028 | OMIA:001972-9796 | domestic horse | American Trotter (Horse) Arab (Horse) Curly Horse (Horse) Faeroes Pony (Horse) Gotland Pony (Horse) Mongolian (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Swedish Warmblood (Horse) Vyatka (Horse) | Non-dun with primitive markings | TBX3 | nd1 | haplotype | regulatory | Naturally occurring variant | Not currently evaluated | EquCab3.0 | 8 | NC_009151.3:g.[20665796_20665797insCCTTCTGGC;20665807_20665808ins[1610]] | 2016 | 26691985 | [IT thanks Haley Rutstein, working under the guidance of Professor Ernie Bailey, for contributions to this entry in April 2024]. Additional breed information based on Belousova et al. (2023). | ||||
| 725 | OMIA:001341-9796 OMIA:002139-9796 | domestic 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) Malopolski (Horse) Noric (Horse) Pony Of the Americas, Germany (Horse) Shetland Pony (Horse) Thoroughbred (Horse) | Stationary congenital night blindness & Leopard Complex/Appaloosa spotting | TRPM1 | insertion, gross (>20) | Naturally occurring variant | Not currently 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 | 115 |
| Variants with genomic location | 110 (95.7% ) |
| Variants in a variant database, i.e. with rs ID | 64 (55.7%) |
| Variant Type | Count | Percent |
|---|---|---|
| deletion, gross (>20) | 14 | 12.2% |
| deletion, small (<=20) | 13 | 11.3% |
| delins, small (<=20) | 3 | 2.6% |
| duplication | 1 | 0.9% |
| haplotype | 2 | 1.7% |
| insertion, gross (>20) | 2 | 1.7% |
| insertion, small (<=20) | 4 | 3.5% |
| missense | 1 | 0.9% |
| reference sequence allele | 1 | 0.9% |
| repeat variation | 2 | 1.7% |
| substitution | 72 | 62.6% |
| Variant Effect | Count | Percent |
|---|---|---|
| deletion (in-frame) | 3 | 2.6% |
| frameshift | 16 | 13.9% |
| missense | 50 | 43.5% |
| nonsense (stop-gain) | 10 | 8.7% |
| regulatory | 5 | 4.3% |
| splicing | 12 | 10.4% |
| unknown | 19 | 16.5% |
| 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 | 1.7% |
| 2005 | 1 | 0.9% |
| 2006 | 2 | 1.7% |
| 2007 | 6 | 5.2% |
| 2008 | 3 | 2.6% |
| 2009 | 8 | 7.0% |
| 2010 | 2 | 1.7% |
| 2011 | 7 | 6.1% |
| 2012 | 7 | 6.1% |
| 2013 | 6 | 5.2% |
| 2014 | 0 | 0.0% |
| 2015 | 6 | 5.2% |
| 2016 | 8 | 7.0% |
| 2017 | 13 | 11.3% |
| 2018 | 8 | 7.0% |
| 2019 | 5 | 4.3% |
| 2020 | 6 | 5.2% |
| 2021 | 3 | 2.6% |
| 2022 | 3 | 2.6% |
| 2023 | 4 | 3.5% |
| 2024 | 1 | 0.9% |
| 2025 | 5 | 4.3% |