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101 variant records found

[show instead phene records]

By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.

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 OMIA001271-9796 horse Miniature 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 OMIA001271-9796 horse Miniature Shetland 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 OMIA001271-9796 horse Miniature Dwarfism, ACAN-related ACAN D2 missense Naturally occurring variant yes EquCab3.0 1 g.95284530C>T p.(V424M) 2018 30058072
999 OMIA001271-9796 horse Miniature 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 OMIA000991-9796 horse Quarter 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 OMIA000991-9796 horse Tennessee Walking 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 OMIA000991-9796 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 OMIA000991-9796 horse Thoroughbred 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 OMIA000991-9796 horse Thoroughbred 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 OMIA000201-9796 horse Coat colour, recessive black ASIP a deletion, small (<=20) Naturally occurring variant no 22 g.2174_2184del c.191_201del 2001 11353392
348 OMIA000487-9796 horse Belgian draft horse Friesian horse Hydrocephalus B3GALNT2 nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 1 g.76887901C>T c.1423C>T p.(Q475*) Ducro et al./ (2015): "The nomenclature for the mutation is c.1423C>T [GenBank:XM_001491545] corresponding to p.Gln475* [GenBank:XP_001491595]". As at 25 April 2019, Ensembl's Variant Effect Predictor (VEP) gives the EquCab3 c. and p. coordinates as having not changed from the EquCab2 coordinates reported by Ducro et al. (2015). The Ensembl ref is ENSECAT00000049072 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 OMIA002068-9796 horse Friesian horse Dwarfism, Friesian B4GALT7 splicing Naturally occurring variant yes EquCab3.0 14 g.3772591C>T c.50G>A p.(R17K) 2016 27793082 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. FN thanks Elizabeth Huffman, who updated the g. coordinates to EquCab3, working under the supervision of Professor Ernie Bailey; 23 April 2020.
161 OMIA000698-9796 horse New Forest Pony Myotonia CLCN1 missense Naturally occurring variant yes EquCab3.0 4 g.96518592A>C c.1775A>C p.(D592A) c.1775A>C, Genbank acc. XM_001915636); p.D592A, Genbank acc. XP_001915671 (Wijnberg et al., 2014) 2012 22197188 (FN thanks Izabela De Assis Rocha, who provided genomic location in EquCab3.0 and the Genbank acc IDs, working under the supervision of Professor Ernie Bailey; 15 April 2020) Revised genomic location kindly provided by Cord Drögemüller; 21 May 2021
167 OMIA000735-9796 horse Belgian Connemara pony Haflinger Rocky Mountain 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 OMIA000629-9796 horse American Paint Horse Miniature Horse Quarter Horse Thoroughbred 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 OMIA000420-9796 horse American Paint Horse American Quarter 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 2004 15366377 The genomic position in EquCab3.0 was provided by Elizabeth Clark, working under the guidance of Professor Ernie Bailey in April 2022
163 OMIA001158-9796 horse American Paint Horse Appaloosa Quarter 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 OMIA000081-9796 horse Arabian 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 OMIA001899-9796 horse Quarter Horse Incontinentia pigmenti IKBKG nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 X g.126898409C>T c.202C>T p.(R68*) 2013 24324710 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
164 OMIA001000-9796 horse Quarter Horse Thoroughbred 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 OMIA001000-9796 horse Peruvian Paso Quarter 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 OMIA000209-9796 horse American Paint Horse Quarter 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 OMIA000209-9796 horse South German Draft Coat colour, dominant white KIT W11 splicing Naturally occurring variant no EquCab3.0 3 g.79540429C>T c.2684+1G>A 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
939 OMIA000209-9796 horse Thoroughbred 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 2018 29333746
873 OMIA000209-9796 horse Oldenburger Coat colour, dominant white KIT W16 missense Naturally occurring variant no EquCab3.0 3 g.79540741T>A c.2489A>T p.(K830I) 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
883 OMIA000209-9796 horse Miniature Horse Quarter Horse Shetland Pony Coat colour, dominant white KIT W13 splicing Naturally occurring variant no EquCab3.0 3 g.79544066C>G c.2472+5G>C 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
889 OMIA000209-9796 horse Thoroughbred Coat colour, dominant white KIT W14 deletion, gross (>20) Naturally occurring variant no EquCab3.0 3 g.79544151_79544204del c.2392_2445del p.(H798_N815del) 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
891 OMIA000209-9796 horse Icelandic White spotting KIT W21 deletion, small (<=20) Naturally occurring variant no EquCab3.0 3 g.79544174del c.2369delC p.(A790Efs*20) 2015 26059442 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
885 OMIA000209-9796 horse Appaloosa Haflinger Lipizzan Noriker Quarter 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) 2005 16284805 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
893 OMIA000209-9796 horse Italian Trotter Coat colour, dominant white KIT W24 splicing Naturally occurring variant no EquCab3.0 3 g.79545245C>T 2017 28856698
1462 OMIA000209-9796 horse Standardbred 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 OMIA000209-9796 horse Icelandic Coat colour, dominant white KIT W8 splicing Naturally occurring variant no EquCab3.0 3 g.79545374C>T c.2222-1G>A NM_001163866.1; NP_001157338.1 2009 19456317
886 OMIA000209-9796 horse Thoroughbred Coat colour, dominant white KIT W5 deletion, small (<=20) Naturally occurring variant no EquCab3.0 3 g.79545900del c.2193delG p.(T732Qfs*9) 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
878 OMIA000209-9796 horse Franches-Montagnes Coat colour, dominant white KIT W1 nonsense (stop-gain) Naturally occurring variant no EquCab3.0 3 g.79545942G>C c.2151C>G p.(Y717*) 2007 17997609 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
877 OMIA000209-9796 horse American Paint Horse Appaloosa German Riding Pony Gipsy Noriker Old-Tori Oldenburger Quarter Horse Thoroughbred Welsh Pony 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 OMIA000209-9796 horse Japanese Draft Coat colour, dominant white KIT W17b missense Naturally occurring variant no EquCab3.0 3 g.79548244A>G c.2021T>C p.(L674P) 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
1261 OMIA000209-9796 horse Berber 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) 2020 33111383
874 OMIA000209-9796 horse Japanese Draft Coat colour, dominant white KIT w17a missense Naturally occurring variant no EquCab3.0 3 g.79548265T>A c.2001A>T p.(E667D) 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
890 OMIA000209-9796 horse Thoroughbred White spotting KIT W22 deletion, gross (>20) Naturally occurring variant no EquCab3.0 3 g.79548925_79550822del 1898bp deletion 2017 28444912
868 OMIA000209-9796 horse Thoroughbred Coat colour, dominant white KIT W2 missense Naturally occurring variant no EquCab3.0 3 g.79549540C>T c.1960G>A p.(G654R) 2007 17997609 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
869 OMIA000209-9796 horse Camarillo White Horse Coat colour, dominant white KIT W4 missense Naturally occurring variant no EquCab3.0 3 g.79549780G>A c.1805C>T p.(A602V) 2007 17997609 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
871 OMIA000209-9796 horse Holsteiner Coat colour, dominant white KIT W9 missense Naturally occurring variant no EquCab3.0 3 g.79549797C>T c.1789G>A p.(G597R) 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
872 OMIA000209-9796 horse Arabian Coat colour, dominant white KIT W15 missense Naturally occurring variant no EquCab3.0 3 g.79550351A>G c.1597T>C p.(C533R) 2011 21554354 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
940 OMIA000209-9796 horse Thoroughbred 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 2018 29333746
884 OMIA000209-9796 horse Swiss Warmblood Coat colour, dominant white KIT W18 splicing Naturally occurring variant no EquCab3.0 3 g.79553751C>T c.1346+1G>A 2013 23659293 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
876 OMIA000209-9796 horse Arabian Coat colour, dominant white KIT W19 missense Naturally occurring variant no EquCab3.0 3 g.79553776T>C c.1322A>G p.(Y441C) 2013 23659293 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
887 OMIA000209-9796 horse Quarter Horse Coat colour, dominant white KIT W10 deletion, small (<=20) Naturally occurring variant no EquCab3.0 3 g.79566926_79566929del c.1126_1129delGAAC p.(E376Ffs*3) 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
870 OMIA000209-9796 horse Thoroughbred Coat colour, dominant white KIT W6 missense Naturally occurring variant no EquCab3.0 3 g.79573754C>T c.856G>A p.(G286R) 2009 19456317 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
892 OMIA000209-9796 horse Arabian White spotting KIT W23 splicing Naturally occurring variant unknown EquCab3.0 3 g.79578484C>G c.756+1G>C rs1095048836 rs1095048836 2017 28378922
879 OMIA000209-9796 horse Arabian Coat colour, dominant white KIT W3 nonsense (stop-gain) Naturally occurring variant no EquCab3.0 3 g.79578535T>A c.706A>T p.(K236*) 2007 17997609 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
938 OMIA000209-9796 horse Thoroughbred 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 OMIA000209-9796 horse Thoroughbred Coat colour, dominant white KIT W12 deletion, small (<=20) Naturally occurring variant unknown EquCab3.0 3 g.79579774_79579778del c.559_563delTCTGC p.(S187Rfs*10) 2010 Reference not in PubMed; see OMIA 000209-9796 for reference details Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
1091 OMIA000209-9796 horse German Riding Pony White spotting KIT W28 deletion, gross (>20) Naturally occurring variant no EquCab3.0 3 g.79579925_79581197del 2019 31463981
880 OMIA000209-9796 horse Thoroughbred Coat colour, dominant white KIT W7 splicing Naturally occurring variant no EquCab3.0 3 g.79580000C>G c.338-1G>C 2009 19456317 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
1330 OMIA000209-9796 horse Quarter 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 OMIA000245-9796 horse Bashkir Curly Horse Curly 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 OMIA001677-9796 horse American Saddlebred 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 OMIA001678-9796 horse Belgian Italian draft horse Trait Breton Trait Comtois 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]
321 OMIA001715-9796 horse Gaitedness LOC100147177 nonsense (stop-gain) Naturally occurring variant no EquCab3.0 23 g.22391254C>A c.902C>A p.(S301*) Transcript: XM_014735431.1 2012 22932389
413 OMIA002021-9796 horse Quarter Horse Coat colour, brindle 1 MBTPS2 splicing Naturally occurring variant no EquCab3.0 X g.17286855T>C c.1437+4T>C 2016 27449517
154 OMIA001199-9796 horse Coat colour, chesnut MC1R e missense Naturally occurring variant no EquCab3.0 3 g.36979560C>T c.248C>T p.(S83F) rs68458866 rs68458866 1996 8995760 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
155 OMIA001199-9796 horse Coat colour, chesnut MC1R e^a missense Naturally occurring variant no EquCab3.0 3 g.36979562G>A c.250G>A p.(D84N) 2000 11086549 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1426 OMIA002197-9796 horse Shetland Pony 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 OMIA000214-9796 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 OMIA000214-9796 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
166 OMIA000214-9796 horse American Standardbred White MITF MITF^244Glu missense Naturally occurring variant no EquCab3.0 16 g.21556522C>T c.731G>A p.(G244E) 2017 27592871 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; breed and allele information obtained from Table S1 of Durig et al. (2017) Anim Genet 48:123-124
156 OMIA000214-9796 horse Franches-Montagnes Macchiato MITF macchiato missense Naturally occurring variant no EquCab3.0 16 g.21564980T>C c.629A>G p.(N210S) 2012 22511888 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
793 OMIA000214-9796 horse Quarter 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 OMIA000214-9796 horse American Miniature Horse American Paint Horse Appaloosa Icelandic Morgan Old-Tori Quarter Horse Shetland Pony Trakehner Splashed white MITF SW1 delins, small (<=20) Naturally occurring variant no EquCab3.0 16 g.21579201delinsATAATAACCTA g.20117302Tdelins11 2012 22511888 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
806 OMIA000214-9796 horse Menorca White splashing MITF regulatory Naturally occurring variant no EquCab3.0 16 g.21608936C>T Published as g.20147039C>T (EquCab2.0) 2017 28084638
443 OMIA001538-9796 horse Racing distance MSTN insertion, gross (>20) Naturally occurring variant no 18 A "227 bp SINE insertion positioned upstream of exon 1" 2018 30379863
437 OMIA000175-9796 horse Arabian Bashkir Curly Horse Trakehner Welsh Pony 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 OMIA002141-9796 horse Quarter 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 2018 29510741
510 OMIA001501-9796 horse Arabian 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
791 OMIA001688-9796 horse Lipizzan Noriker Quarter Horse Splashed white PAX3 SW2 missense Naturally occurring variant no EquCab3.0 6 g.11199026C>T c.209G>A p.(C70Y) 2012 22511888 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
978 OMIA001688-9796 horse Appaloosa Splashed white PAX3 SW4 missense Naturally occurring variant no EquCab3.0 6 g.11199140G>C c.95C>G p.(P32R) 2013 23659293
165 OMIA001982-9796 horse Thoroughbred 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 OMIA001438-9796 OMIA000733-9796 horse American Miniature Horse Ardennes Icelandic Missouri Foxtrotter Morgan Rocky Mountain Trait Comtois 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 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 OMIA000327-9796 horse American Quarter 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 OMIA000220-9796 horse Arabian 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 1997 9103416
1369 OMIA002458-9796 horse Thoroughbred Hypoparathyroidism RAPGEF5 nonsense (stop-gain) Naturally occurring variant yes EquCab3.0 4 g.54108297G>T c.2624C>A p.(S875*) 2020 32986719
159 OMIA000621-9796 horse American Quarter 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 OMIA000785-9796 horse Quarter Horse HYPP SCN4A H missense Naturally occurring variant yes EquCab3.0 11 g.15474228C>G c.4248C>G p.(F1416L) 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 OMIA001897-9796 horse Connemara pony Hoof wall separation syndrome SERPINB11 insertion, small (<=20) Naturally occurring variant yes EquCab3.0 8 g.83600643_83600644insC c.504_505insC p.(T169Hfs*3) 2015 25875171 FN thanks Daniel J. Schmidt, working under the supervision of Professor Ernie Bailey, for updating the coordinates to EquCab3.0.
686 OMIA002013-9796 horse Shetland Pony 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 OMIA002013-9796 horse Shetland Pony 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 OMIA002124-9796 horse Paso Fino 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 OMIA002124-9796 horse Paso Fino Tiger eye SLC24A5 Tiger-eye 1 missense Naturally occurring variant yes EquCab3.0 1 g.143145865A>T c.272A>T p.(F91Y) 2017 28655738 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
152 OMIA001263-9796 horse Coat colour, champagne SLC36A1 missense Naturally occurring variant no EquCab3.0 14 g.26012449G>C c.188C>G p.(T63R) 2008 18802473 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1140 OMIA001344-9796 horse Gypsy 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 2020 31961951
153 OMIA001344-9796 horse Coat colour, cream dilution SLC45A2 C^Cr missense Naturally occurring variant no EquCab3.0 21 g.31690653G>A c.457G>A p.(D153N) 2003 12605854 EquCab3 coordinates obtained from Table S2 of Holl et al. (2019)
1074 OMIA001344-9796 horse Standardbred x Tennessee Walking Horse cross 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." 2019 31006892
1069 OMIA001344-9796 horse American Paint Horse Lusitano Purebred Spanish horse Quarter Horse Coat colour, pearl SLC45A2 C^prl missense Naturally occurring variant no EquCab3.0 21 g.31709690G>A c.985G>A p.(A329T) 2019 30968968 EquCab3 g. coordinate kindly provided by Natalia Sevane
158 OMIA001578-9796 horse Dales Pony Fell Pony 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
1040 OMIA002175-9796 horse American Bashkir Curly horse Missouri Foxtrotter Curly coat with/without hypotrichosis SP6 missense Naturally occurring variant yes EquCab3.0 11 g.24096309C>T c.1090G>A p.(D364N) Thomer et al. (2018): "SP6; NC_009154.2:g.24022045C>T, ss3021042887" with respect to EquCab2. Updated coordinates in this entry obtained from EVA rs1095048852; 14 Mar 2019 rs1095048852 rs1095048852 2018 29686323
659 OMIA001230-9796 horse Standardbred Ovotesticular DSD (Disorder of Sexual Development) 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 OMIA002096-9796 horse Akhal-Teke 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*)) 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 OMIA001356-9796 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 OMIA001972-9796 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 OMIA001972-9796 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 OMIA001341-9796 OMIA002139-9796 horse American Miniature Horse Appaloosa Australian Spotted Pony British Spotted Pony Knabstrupper Noriker Pony of the Americas Thoroughbred Stationary congenital night blindness & Leopard Complex/Appaloosa spotting TRPM1 insertion, gross (>20) Naturally occurring variant no EquCab2.0 1 g.108297929_108297930ins1378 "a 1378 bp retroviral LTR insertion in intron 1 of TRPM1" 2013 24167615
Overall Statistics
Total number of variants 101
Variants with genomic location 93 (92.1% )
Variants in a variant database, i.e. with rs ID 15 (14.9%)
Variant Type Count Percent
deletion, gross (>20) 12 11.9%
deletion, small (<=20) 13 12.9%
delins, small (<=20) 2 2.0%
duplication 2 2.0%
insertion, gross (>20) 2 2.0%
insertion, small (<=20) 3 3.0%
missense 44 43.6%
nonsense (stop-gain) 8 7.9%
not known 1 1.0%
regulatory 4 4.0%
splicing 10 9.9%
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 2.0%
2005 1 1.0%
2006 2 2.0%
2007 6 5.9%
2008 3 3.0%
2009 8 7.9%
2010 2 2.0%
2011 8 7.9%
2012 7 6.9%
2013 6 5.9%
2014 0 0.0%
2015 4 4.0%
2016 7 6.9%
2017 13 12.9%
2018 9 8.9%
2019 5 5.0%
2020 6 5.9%
2021 2 2.0%
2022 1 1.0%