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103 variant records found

[show instead phene records]

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

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

OMIA Variant ID OMIA Phene-Species ID(s) Species Name Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Deleterious? Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Inferred EVA rsID Year Published PubMed ID(s) Acknowledgements
1001 OMIA:001271-9796 horse Miniature Horse (Horse) Dwarfism, ACAN-related ACAN D4 deletion, small (<=20) Naturally occurring variant yes EquCab3.0 1 g.95257480_95257500del c.7633_7653del p.(F2545_D2551del) 220110: corrected genomic position from g.95257458_95257500del to 95257480_95257500 and updated cDNA and published protein coordinates (p.(F2017_D2023del)) based on the following transcripts: ENSECAT00000040213.1:c.7633_7653del ENSECAP00000032890.1:p.Phe2545_Cys2551del rs1095048839 2018 30058072
788 OMIA:001271-9796 horse Miniature Horse (Horse) Shetland Pony (Horse) Dwarfism, ACAN-related ACAN D3* missense Naturally occurring variant yes EquCab3.0 1 g.95282140C>G c.1513G>C p.(A505P) ENSECAT00000040213.1:c.1513G>C ENSECAP00000032890.1:p.Ala505Pro This variant was named D3* by Eberth et al. (2018) rs1095048823 rs1095048823 2017 27942904 Variant coordinates obtained from Eberth et al. (2018) and EVA_ID link
1000 OMIA:001271-9796 horse Miniature Horse (Horse) Dwarfism, ACAN-related ACAN D2 missense Naturally occurring variant yes EquCab3.0 1 g.95284530C>T p.(V424M) rs3091781465 2018 30058072
999 OMIA:001271-9796 horse Miniature Horse (Horse) Dwarfism, ACAN-related ACAN D1 deletion, small (<=20) Naturally occurring variant yes EquCab3.0 1 g.95291271del c.245del p.(K82Rfs*54) 220110: changed g.95291270del to g.95291271del based on HGVS 3'rule. ENSECAT00000040213.1:c.245del ENSECAP00000032890.1:p.Lys82ArgfsTer54 rs1095048841 rs1095048841 2018 30058072
436 OMIA:000991-9796 horse Quarter Horse (Horse) Androgen insensitivity syndrome (AIS) AR regulatory Naturally occurring variant yes EquCab3.0 X g.52728703A>G c.1A>G NM_001163891.1; NP_001157363.1; mutation in start codon 2012 22095250 The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022
1143 OMIA:000991-9796 horse Tennessee Walking Horse (Horse) Androgen insensitivity syndrome (AIS) AR deletion, small (<=20) Naturally occurring variant yes EquCab3.0 X g.52728885del c.183del p.(R63Gfs) NM_001163891.1; NP_001157363.1; published as c.183delT and p.(Ser61fs); c. and p. information in the table has been updated to HGVS nomenclature 2020 31936796 The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022
783 OMIA:000991-9796 horse Androgen insensitivity syndrome AR deletion, gross (>20) Naturally occurring variant yes EquCab3.0 X g.52808634_52808658del c.1630_1654del NM_001163891.1; NP_001157363.1; the deletion is predicted to create a frameshift: "resulting in altered amino acid composition from p.543Lys and a premature stop codon 44 amino acid residues downstream in exon 3" 2017 28192783
786 OMIA:000991-9796 horse Thoroughbred (Horse) Androgen insensitivity syndrome AR missense Naturally occurring variant yes EquCab3.0 X g.52872393G>C c.2042G>C p.(W681S) NM_001163891.1; NP_001157363.1 2016 27073903 The genomic position in EquCab3.0 was provided by Ceara Mulvey, working under the guidance of Professor Ernie Bailey in April 2022; p. coordinates obtained from Villagomez et al. (2019)
1144 OMIA:000991-9796 horse Thoroughbred (Horse) Androgen insensitivity syndrome (AIS) AR missense Naturally occurring variant yes EquCab3.0 X g.52878093C>T c.2132C>T p.(A711V) NM_001163891.1; NP_001157363.1 2020 31936796
509 OMIA:000201-9796 horse Coat colour, recessive black ASIP a deletion, small (<=20) Naturally occurring variant no 22 g.2174_2184del c.191_201del 2001 11353392
348 OMIA:000487-9796 horse Belgian Draft (Horse) Friesian (Horse) Hydrocephalus B3GALNT2 nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 1 g.76887901C>T c.1423C>T p.(Q475*) XM_001491545; XP_001491595; Ducro et al. (2015): "The nomenclature for the mutation is c.1423C>T [GenBank:XM_001491545] corresponding to p.Gln475* [GenBank:XP_001491595]". As at 25 April 2019, Ensembl's Variant Effect Predictor (VEP) gives the EquCab3 c. and p. coordinates as having not changed from the EquCab2 coordinates reported by Ducro et al. (2015). The Ensembl ref is ENSECAT00000049072 rs3429464524 rs3429464524 2015 26452345 c. and p. variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. EquCab3 g. coordinate provided by Meredith O’Connell, working under the supervision of Professor Ernie Bailey, 24 April 2019
421 OMIA:002068-9796 horse Friesian (Horse) Dwarfism, Friesian B4GALT7 splicing Naturally occurring variant yes EquCab3.0 14 g.3772591C>T c.50G>A p.(R17K) rs3447120064 2016 27793082 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. FN thanks Elizabeth Huffman, who updated the g. coordinates to EquCab3, working under the supervision of Professor Ernie Bailey; 23 April 2020.
161 OMIA:000698-9796 horse New Forest Pony (Horse) Myotonia CLCN1 missense Naturally occurring variant yes EquCab3.0 4 g.96518592A>C c.1775A>C p.(D592A) c.1775A>C, Genbank acc. XM_001915636); p.D592A, Genbank acc. XP_001915671 (Wijnberg et al., 2014) rs5334475185 2012 22197188 (FN thanks Izabela De Assis Rocha, who provided genomic location in EquCab3.0 and the Genbank acc IDs, working under the supervision of Professor Ernie Bailey; 15 April 2020) Revised genomic location kindly provided by Cord Drögemüller; 21 May 2021
167 OMIA:000735-9796 horse Belgian Draft (Horse) Connemara Pony (Horse) Haflinger (Horse) Rocky Mountain, United States of America (Bighorn sheep) Ocular squamous cell carcinoma DDB2 missense Naturally occurring variant yes EquCab3.0 12 g.11726667C>T c.1013C>T p.(T338M) The EquCab2 coordinates, obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool, are g.11608667, c.1013C>T and p.T338M rs1139682898 rs1139682898 2017 28425625 The EquCab3 g. coordinates were provided by by Meredith O’Connell, working under the guidance of Professor Ernie Bailey, 5 March 2019
160 OMIA:000629-9796 horse American Paint (Horse) Miniature Horse (Horse) Quarter Horse (Horse) Thoroughbred (Horse) Megacolon EDNRB frame overo delins, small (<=20) Naturally occurring variant yes EquCab3.0 17 g.50503041_50503042delinsCT c.353_354delinsAG p.(I118K) NM_001081837.2; NP_001075306.2 1998 9530628
322 OMIA:000420-9796 horse American Paint (Horse) Quarter Horse (Horse) Glycogen storage disease IV GBE1 nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 26 g.8667651C>A c.102C>A p.(Y34*) NM_001081940.2; NP_001075409.1 rs3437568674 rs3437568674 2004 15366377 The genomic position in EquCab3.0 was provided by Elizabeth Clark, working under the guidance of Professor Ernie Bailey in April 2022
1552 OMIA:002692-9796 horse American Saddle Horse (Horse) American Trotter (Horse) Miniature Horse (Horse) Missouri Fox Trotting Horse, United States of America (Horse) Morgan (Horse) Quarter Horse (Horse) Racking Horse (Horse) Rocky Mountain, United States of America (Horse) Spotted Saddle Horse (Horse) Tennessee Walking Horse (Horse) Night blindness, congenital stationary, GRM6-related GRM6 missense Naturally occurring variant yes EquCab3 14 g.2655618C>T c.533C>T p.(T178M) XM_001916934.4; XP_001916969.3; variant initially reported in Tennessee Walking horse and later reported in other breeds [PMID:37815029] rs1138010744 rs1138010744 2021 32654228
163 OMIA:001158-9796 horse American Paint (Horse) Appaloosa (Horse) Quarter Horse (Horse) Polysaccharide storage myopathy/Exertional rhabdomyolysis GYS1 missense Naturally occurring variant yes EquCab3.0 10 g.19203501C>T c.926G>A p.(R309H) ENSECAT00000023453.3:c.926G>A ENSECAP00000019426.2:p.Arg309His rs1150416011 rs1150416011 2008 18358695 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
691 OMIA:000081-9796 horse Arab (Horse) Atlanto occipital fusion HOXD3 deletion, gross (>20) Naturally occurring variant yes 18 "a 2.7-kb deletion located 4.4 kb downstream of the end of HOXD4 and 8.2 kb upstream of the start of HOXD3." 2017 28111759
337 OMIA:001899-9796 horse Quarter Horse (Horse) Incontinentia pigmenti IKBKG nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 X g.126898409C>T c.202C>T p.(R68*) rs3433281055 2013 24324710 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
164 OMIA:001000-9796 horse Quarter Horse (Horse) Thoroughbred (Horse) Thrombasthenia ITGA2B missense Naturally occurring variant yes EquCab3.0 11 g.19245752G>C c.215G>C p.(R72P) NM_001081793.1; NP_001075262.1; originally published as p.(R41P) and listed by Leite et al. (2019) as c.122G>C; coordinates in this table have been updated to a recent reference genome and / or transcript 2006 16407493
512 OMIA:001000-9796 horse Peruvian Paso (Horse) Quarter Horse (Horse) Thrombasthenia ITGA2B deletion, small (<=20) Naturally occurring variant yes EquCab3.0 11 g.19247983_19247992del g.19247983_19247992delCAGGTGAGGA 2007 17338169 g. coordinates obtained from Dahlgren et al. (2020)
1331 OMIA:000209-9796 horse American Paint (Horse) Quarter Horse (Horse) White spotting KIT W32 missense Naturally occurring variant unknown EquCab3.0 3 g.79538738C>T c.3214G>A p.(A1072T) cDNA position based on transcript ENSECAT00000014037.3 rs1141982296 rs1141982296 2021 34223905
882 OMIA:000209-9796 horse Süddeutsches Kaltblut, Germany (Horse) Coat colour, dominant white KIT W11 splicing Naturally occurring variant no EquCab3.0 3 g.79540429C>T c.2684+1G>A rs5334475183 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
939 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W26 deletion, small (<=20) Naturally occurring variant unknown EquCab3.0 3 g.79540694del c.2536del p.(S846Vfs*15) NM_001163866.1; NP_001157338.1; published as c.2536delA rs3101685403 2018 29333746
873 OMIA:000209-9796 horse Oldenburg (Horse) Coat colour, dominant white KIT W16 missense Naturally occurring variant no EquCab3.0 3 g.79540741T>A c.2489A>T p.(K830I) rs5334475213 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
883 OMIA:000209-9796 horse Miniature Horse (Horse) Quarter Horse (Horse) Shetland Pony (Horse) Coat colour, dominant white KIT W13 splicing Naturally occurring variant no EquCab3.0 3 g.79544066C>G c.2472+5G>C NM_001163866.1 rs3102773259 rs3102773259 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
889 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W14 deletion, gross (>20) Naturally occurring variant no EquCab3.0 3 g.79544098_79544151del c.2392_2445del p.(H798_N815del) NM_001163866.1; NP_001157338.1 2011 21554354 genomic coordinates updated from g.79544151_79544204del to g.79544098_79544151del in EquCab3.0 [17/09/2023]
891 OMIA:000209-9796 horse Iceland Pony (Horse) White spotting KIT W21 deletion, small (<=20) Naturally occurring variant no EquCab3.0 3 g.79544174del c.2369delC p.(A790Efs*20) rs5334475210 2015 26059442 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
885 OMIA:000209-9796 horse Appaloosa (Horse) Haflinger (Horse) Lipizzan horse (Horse) Noric (Horse) Quarter Horse (Horse) Coat colour, dominant white KIT sabino 1 (SB1) splicing Naturally occurring variant no EquCab3.0 3 g.79544206A>T "SNP AX-103727726 (ECA3:77735520; SB1, SNP KI16+1037A)" (Druml et al., 2018) rs5334475211 2005 16284805 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
893 OMIA:000209-9796 horse Trottatore Italiano, Italy (Horse) Coat colour, dominant white KIT W24 splicing Naturally occurring variant no EquCab3.0 3 g.79545245C>T rs3443588955 2017 28856698
1462 OMIA:000209-9796 horse American Trotter (Horse) Dominant white spotting KIT W33 missense Naturally occurring variant no EquCab3.0 3 g.79545248T>A c.2783A>T p.(N895Y) NC_009146.3; ENSECAT00000014037.3 2022 35641888
881 OMIA:000209-9796 horse Iceland Pony (Horse) Coat colour, dominant white KIT W8 splicing Naturally occurring variant no EquCab3.0 3 g.79545374C>T c.2222-1G>A NM_001163866.1 rs3434854925 rs3434854925 2009 19456317
886 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W5 deletion, small (<=20) Naturally occurring variant no EquCab3.0 3 g.79545900del c.2193delG p.(T732Qfs*9) rs5334475194 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
878 OMIA:000209-9796 horse Freiberger (Horse) Coat colour, dominant white KIT W1 nonsense (stop-gain) Naturally occurring variant no EquCab3.0 3 g.79545942G>C c.2151C>G p.(Y717*) rs5334475201 2007 17997609 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
877 OMIA:000209-9796 horse American Paint (Horse) Appaloosa (Horse) German Riding Pony (Horse) Noric (Horse) Oldenburg (Horse) Quarter Horse (Horse) Thoroughbred (Horse) Tori hobune, Estonia (Horse) Traditional Gypsy Cob, United Kingdom of Great Britain and Northern Ireland (Horse) Welsh Pony (Horse) Coat colour, dominant white KIT W20 missense Naturally occurring variant unknown EquCab3.0 3 g.79548220C>T c.2045G>A p.(R682H) ENSECAT00000014037.3:c.2381A>G ENSECAP00000011188.2:p.His794Arg rs1143160924 rs1143160924 2013 23659293 Variant coordinates initially gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
875 OMIA:000209-9796 horse Japanese Draft, Japan (Horse) Coat colour, dominant white KIT W17b missense Naturally occurring variant no EquCab3.0 3 g.79548244A>G c.2021T>C p.(L674P) rs5334475224 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
1261 OMIA:000209-9796 horse Berber, Germany (Horse) Extensive coat white patterning KIT W30 missense Naturally occurring variant no EquCab3.0 3 g.79548244A>T c.2020T>A p.(L674H) g.79548244, c.2020T>A; p.L674H (Martin et al., 2020) rs5334475224 2020 33111383
874 OMIA:000209-9796 horse Japanese Draft, Japan (Horse) Coat colour, dominant white KIT w17a missense Naturally occurring variant no EquCab3.0 3 g.79548265T>A c.2001A>T p.(E667D) rs5334475222 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
890 OMIA:000209-9796 horse Thoroughbred (Horse) White spotting KIT W22 deletion, gross (>20) Naturally occurring variant no EquCab3.0 3 g.79548925_79550822del 1898bp deletion 2017 28444912
868 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W2 missense Naturally occurring variant no EquCab3.0 3 g.79549540C>T c.1960G>A p.(G654R) rs5334475198 2007 17997609 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
869 OMIA:000209-9796 horse Camarillo White Horse, United States of America (Horse) Coat colour, dominant white KIT W4 missense Naturally occurring variant no EquCab3.0 3 g.79549780G>A c.1805C>T p.(A602V) rs5334475223 2007 17997609 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
871 OMIA:000209-9796 horse Holsteiner (Horse) Coat colour, dominant white KIT W9 missense Naturally occurring variant no EquCab3.0 3 g.79549797C>T c.1789G>A p.(G597R) rs5334475209 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
872 OMIA:000209-9796 horse Arab (Horse) Coat colour, dominant white KIT W15 missense Naturally occurring variant no EquCab3.0 3 g.79550351A>G c.1597T>C p.(C533R) rs5334475202 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
940 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W27 missense Naturally occurring variant unknown EquCab3.0 3 g.79551937A>C c.1473T>G p.(C491W) NM_001163866.1; NP_001157338.1 rs3110307743 2018 29333746
884 OMIA:000209-9796 horse CH-Warmblut, Switzerland (Horse) Coat colour, dominant white KIT W18 splicing Naturally occurring variant no EquCab3.0 3 g.79553751C>T c.1346+1G>A rs5334475221 2013 23659293 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
876 OMIA:000209-9796 horse Arab (Horse) Coat colour, dominant white KIT W19 missense Naturally occurring variant no EquCab3.0 3 g.79553776T>C c.1322A>G p.(Y441C) rs5334475217 2013 23659293 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
1476 OMIA:000209-9796 horse American Paint (Horse) Appaloosa (Horse) Arab (Horse) Mangalarga (Horse) Morgan (Horse) Mustang (Horse) Quarter Horse (Horse) Rocky Mountain, United States of America (Bighorn sheep) Warmblood breeds Increased white spotting KIT W34 missense Naturally occurring variant no EquCab3.0 3 g.79566881T>C c.1495A>G p.(T499A) ENSECAT00000014037.3; ENSECAP00000011188.2 rs1140732842 rs1140732842 2022 35953947
887 OMIA:000209-9796 horse Quarter Horse (Horse) Coat colour, dominant white KIT W10 deletion, small (<=20) Naturally occurring variant no EquCab3.0 3 g.79566923_79566926del c.1126_1129del p.(E376Ffs*3) NM_001163866.1; NP_001157338.1; published as c.1126_1129delGAAC 2009 19456317 Genomic coordinates updated in this table from g.79566926_79566929del in EquCab3.0 after feedback from Micaela Vierra identified that these coordinates were incorrect [27/09/2023].
870 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W6 missense Naturally occurring variant no EquCab3.0 3 g.79573754C>T c.856G>A p.(G286R) rs5334475167 2009 19456317 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
892 OMIA:000209-9796 horse Arab (Horse) White spotting KIT W23 splicing Naturally occurring variant unknown EquCab3.0 3 g.79578484C>G c.756+1G>C rs1095048836 rs1095048836 2017 28378922
879 OMIA:000209-9796 horse Arab (Horse) Coat colour, dominant white KIT W3 nonsense (stop-gain) Naturally occurring variant no EquCab3.0 3 g.79578535T>A c.706A>T p.(K236*) rs5334475200 2007 17997609 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
938 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W25 missense Naturally occurring variant unknown EquCab3.0 3 g.79578573A>G c.668T>C p.(L223P) NM_001163866.1; NP_001157338.1 rs3103992630 2018 29333746
888 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W12 deletion, small (<=20) Naturally occurring variant unknown EquCab3.0 3 g.79579774_79579778del c.559_563del p.(S187Rfs*10) NM_001163866.1; NP_001157338.1; published as c.559_563delTCTGC rs5334475188 2010 Reference not in PubMed; see OMIA 000209-9796 for reference details Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
880 OMIA:000209-9796 horse Thoroughbred (Horse) Coat colour, dominant white KIT W7 splicing Naturally occurring variant no EquCab3.0 3 g.79580000C>G c.338-1G>C rs5334475216 2009 19456317 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
1330 OMIA:000209-9796 horse Quarter Horse (Horse) White spotting KIT W31 insertion, small (<=20) Naturally occurring variant unknown EquCab3.0 3 g.79618532_79618533insA c.30_31insT p.(L11Sfs*115) 2021 34223905
856 OMIA:000245-9796 horse Bashkir Curly (Horse) Curly Horse (Horse) Curly coat KRT25 Crd missense Naturally occurring variant no EquCab3.0 11 g.21962991G>A c.266G>A p.(R89H) rs1095048844 rs1095048844 2018 29686323 29141579 Variant coordinates obtained from and/or confirmed by EBI's Some Effect Predictor (VEP) tool
658 OMIA:001677-9796 horse American Saddle Horse (Horse) Epidermolysis bullosa, junctionalis, LAMA3-related LAMA3 deletion, gross (>20) Naturally occurring variant yes 8 "6589-bp deletion spanning exons 24-27 . . . in the LAMA3 gene in American Saddlebred foals" 2009 19016681
599 OMIA:001678-9796 horse Belgian Draft (Horse) Breton, France (Horse) Cavallo Agricolo Italiano da Tiro Pesante Rapido, Italy (Horse) Comtois (Horse) Epidermolysis bullosa, junctionalis, LAMC2-related LAMC2 insertion, small (<=20) Naturally occurring variant yes EquCab3.0 5 g.17498175dup c.1372dup p.(R458Pfs) NM_001081768.1; NP_001075237.1; published as c.1368insC; coordinates in the table have been updated to HGVS nomenclature (3'-rule) and recent reference genome and / or transcript inforamtion 1,372 Protein position: 458 2002 12230513 The genomic position in EquCab3.0 was provided by Margaret Higgins, working under the guidance of Professor Ernie Bailey [April 2022]
413 OMIA:002021-9796 horse Quarter Horse (Horse) Coat colour, brindle 1 MBTPS2 splicing Naturally occurring variant no EquCab3.0 X g.17286855T>C c.1437+4T>C rs3434246715 2016 27449517
154 OMIA:001199-9796 horse Coat colour, chesnut MC1R e missense Naturally occurring variant no EquCab3.0 3 g.36979560C>T c.248C>T p.(S83F) ENSECAT00000129995.1; ENSECAP00000088247.1 rs68458866 rs68458866 1996 8995760 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
155 OMIA:001199-9796 horse Coat colour, chesnut MC1R e^a missense Naturally occurring variant no EquCab3.0 3 g.36979562G>A c.250G>A p.(D84N) ENSECAT00000129995.1; ENSECAP00000088247.1 rs3443929753 rs3443929753 2000 11086549 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1426 OMIA:002197-9796 horse Shetland Pony (Horse) Coat colour, dilution (mushroom) MFSD12 Mu duplication Naturally occurring variant no EquCab3.0 7 g.2544518dup c.600dup p.(D201fs) XM_023646425.1; XP_023502193.1; published as NC_009150.3: g.2544512dup (XM_023646425.1:c.600dupC, p.Asp201fs); coordinates in the table have been updated to reflect HGVS nomenclature 2019 31635058
1023 OMIA:000214-9796 horse American Paint (Horse) White spotting, blue eyes and deafness MITF SW5 deletion, gross (>20) Naturally occurring variant yes EquCab3.0 16 g.21503211_21566617del "~63-kb deletion spanning exons 6-9 of the MITF gene" 2019 30644113
1180 OMIA:000214-9796 horse American Paint (Horse) Splashed white MITF SW6 deletion, gross (>20) Naturally occurring variant no EquCab3.0 16 g.21551060_21559770del NC_009159.3:g.21551060-21559770del (Magdesian et al., 2020) 2020 32242630
1626 OMIA:000214-9796 horse Thoroughbred (Horse) Splashed white MITF SW8 deletion, gross (>20) Naturally occurring variant yes EquCab3.0 16 g.21555811_21558139delinsAAAT 2023 37697831
166 OMIA:000214-9796 horse American Trotter (Horse) White MITF MITF^244Glu missense Naturally occurring variant no EquCab3.0 16 g.21556522C>T c.731G>A p.(G244E) 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 horse Purebred Spanish (Horse) Splashed white MITF SW9 missense Naturally occurring variant yes 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 yes 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 no EquCab3.0 16 g.21564980T>C c.629A>G p.(N210S) 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 horse Quarter Horse (Horse) Splashed white MITF SW3 deletion, small (<=20) Naturally occurring variant no 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 no EquCab3.0 16 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 horse Cavall Menorquí, Spain (Horse) White splashing MITF regulatory Naturally occurring variant no EquCab3.0 16 g.21608936C>T Published as g.20147039C>T (EquCab2.0) 2017 28084638
437 OMIA:000175-9796 horse Arab (Horse) Bashkir Curly (Horse) Trakehner (Horse) Welsh Pony (Horse) Cerebellar abiotrophy MUTYH not known Naturally occurring variant yes 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 rs397160943 2011 21126570
973 OMIA:002141-9796 horse Quarter Horse (Horse) Immune-mediated myositis MYH1 missense Naturally occurring variant yes 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 rs3435577028 2018 29510741
510 OMIA:001501-9796 horse Arab (Horse) Lavender foal syndrome MYO5A deletion, small (<=20) Naturally occurring variant yes 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 unknown 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 no EquCab3.0 6 g.11199026C>T c.209G>A 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 horse Appaloosa (Horse) Splashed white PAX3 SW4 missense Naturally occurring variant no EquCab3.0 6 g.11199140G>C c.95C>G p.(P32R) rs5334475206 2013 23659293
165 OMIA:001982-9796 horse Thoroughbred (Horse) Warmblood breeds Fragile Foal Syndrome PLOD1 missense Naturally occurring variant yes EquCab3.0 2 g.39927817C>T c.2032G>A p.(G678R) rs1136065234 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 no 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 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 yes EquCab3.0 1 g.129307092G>A c.115G>A p.(G39R) rs396329681 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 yes 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 rs5334475184 1997 9103416
1369 OMIA:002458-9796 horse Thoroughbred (Horse) Hypoparathyroidism RAPGEF5 nonsense (stop-gain) Naturally occurring variant yes 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 yes 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 yes 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 rs1148998534 1992 1338908
965 OMIA:001897-9796 horse Connemara Pony (Horse) Hoof wall separation syndrome SERPINB11 insertion, small (<=20) Naturally occurring variant yes EquCab3.0 8 g.83600643_83600644insC c.504_505insC 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 horse Shetland Pony (Horse) Skeletal atavism SHOX Del-1 deletion, gross (>20) Naturally occurring variant yes 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 yes 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 yes 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 yes EquCab3.0 1 g.143145865A>T c.272A>T p.(F91Y) rs5334475205 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 no EquCab3.0 14 g.26012449G>C c.188C>G p.(T63R) rs5334475190 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 no EquCab3.0 21 g.31688649G>A c.305G>A p.(R102Q) Bisbee et al. (2020): transcript ENSECAT00000026240.1 in the Ensembl EquCab2.0 assembly rs5334475197 2020 31961951
153 OMIA:001344-9796 horse Coat colour, cream dilution SLC45A2 C^Cr missense Naturally occurring variant no EquCab3.0 21 g.31690653G>A c.457G>A p.(D153N) ENSECAT00000066600.2; ENSECAP00000054416.1 rs1140980396 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 no 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." rs394940514 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 no EquCab3.0 21 g.31709690G>A c.985G>A p.(A329T) rs3101690631 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 yes 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
659 OMIA:001230-9796 horse American Trotter (Horse) XY sex reversal SRY deletion, gross (>20) Naturally occurring variant yes 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 yes EquCab3.0 7 g.39710628G>T c.388G>T p.(E130*) 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 horse Coat colour, grey/gray STX17 duplication Naturally occurring variant no 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 no 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 unknown 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 no EquCab2.0 1 g.108297929_108297930insN[1378] "a 1378 bp retroviral LTR insertion in intron 1 of TRPM1" 2013 24167615
Overall Statistics
Total number of variants 103
Variants with genomic location 96 (93.2% )
Variants in a variant database, i.e. with rs ID 23 (22.3%)
Variant Type Count Percent
deletion, gross (>20) 12 11.7%
deletion, small (<=20) 14 13.6%
delins, small (<=20) 2 1.9%
duplication 2 1.9%
insertion, gross (>20) 1 1.0%
insertion, small (<=20) 3 2.9%
missense 46 44.7%
nonsense (stop-gain) 8 7.8%
not known 1 1.0%
regulatory 4 3.9%
splicing 10 9.7%
Year First Reported Count Percent
1992 1 1.0%
1993 0 0.0%
1994 0 0.0%
1995 1 1.0%
1996 1 1.0%
1997 1 1.0%
1998 1 1.0%
1999 0 0.0%
2000 1 1.0%
2001 1 1.0%
2002 1 1.0%
2003 1 1.0%
2004 2 1.9%
2005 1 1.0%
2006 2 1.9%
2007 6 5.8%
2008 3 2.9%
2009 8 7.8%
2010 2 1.9%
2011 8 7.8%
2012 6 5.8%
2013 6 5.8%
2014 0 0.0%
2015 4 3.9%
2016 7 6.8%
2017 13 12.6%
2018 7 6.8%
2019 4 3.9%
2020 6 5.8%
2021 3 2.9%
2022 3 2.9%
2023 3 2.9%