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96 variant records found

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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.

OMIA ID(s) Species Name Breed(s) Variant Phenotype Gene Allele Type of Variant Deleterious? Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
OMIA 001271-9796 horse Miniature Dwarfism, ACAN-related ACAN D4 deletion, small (<=20) yes Ecab 3.0 1 g.95257458_95257500del p.Phe2017-Asp2023del rs1095048839 2018 30058072
OMIA 001271-9796 horse Miniature Shetland Dwarfism, ACAN-related ACAN D3* missense yes Ecab 3.0 1 g.95282140C>G p.A505P This variant was named D3* by Eberth et al. (2018) rs1095048823 2017 27942904 Variant coordinates obtained from Eberth et al. (2018)
OMIA 001271-9796 horse Miniature Dwarfism, ACAN-related ACAN D2 missense yes Ecab 3.0 1 g.95284530C>T p.Val424Met 2018 30058072
OMIA 001271-9796 horse Miniature Dwarfism, ACAN-related ACAN D1 deletion, small (<=20) yes Ecab 3.0 1 g.95291270del p.Lys82fx rs1095048841 2018 30058072
OMIA 000991-9796 horse Warmblood Androgen insensitivity syndrome AR deletion, gross (>20) yes X c.1630_1654del "a 25-bp deletion of the DNA-binding domain [of the AR gene]" 2017 28192783 c. coordinates obtained from Villagomez et al. (2019)
OMIA 000991-9796 horse Quarter Horse Androgen insensitivity syndrome (AIS) AR regulatory yes X c.1A>G mutation in start codon 2012 22095250
OMIA 000991-9796 horse Thoroughbred Androgen insensitivity syndrome AR missense yes X c.2042G>C p.Trp681Ser 2016 27073903 p. coordinates obtained from Villagomez et al. (2019)
OMIA 000991-9796 horse Tennessee Walking Horse Androgen insensitivity syndrome (AIS) AR deletion, small (<=20) yes GenBank horse AR reference sequence (NC_009175.3, NM_001163891.1) X c.183delT p.Ser61fs Villagomez et al. (2020): NM_001163891.1:c.183delT; NP_001157363.1:p.(Ser61fs) 2020 31936796
OMIA 000991-9796 horse Thoroughbred Androgen insensitivity syndrome (AIS) AR missense yes GenBank horse AR reference sequence (NC_009175.3, NM_001163891.1) X c.2132C>T p.(Ala711Val) Villagomez et al. (2020): NM_001163891.1:c.2132C>T; NP_001157363.1:p.(Ala711Val) 2020 31936796
OMIA 000201-9796 horse Coat colour, recessive black ASIP a deletion, small (<=20) no g.2174_2184del11 c.191_201del 2001 11353392
OMIA 000487-9796 horse Belgian draft horse Friesian Hydrocephalus B3GALNT2 nonsense (stop-gain) yes EquCab3 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
OMIA 002068-9796 horse Friesian Dwarfism, Friesian B4GALT7 splicing yes EquCab3 14 g.3,772,591C>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.
OMIA 000698-9796 horse New Forest Pony Myotonia CLCN1 missense yes EquCab3.0 4 g.96,499,709A>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)
OMIA 000735-9796 horse Belgian Haflinger Percheron Ocular squamous cell carcinoma DDB2 missense yes EquCab3 12 g.11726667C>T c.1013C>T p.(T338M) The EquCab2 coordinates, obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool, are g.11608667, c.1013C>T and p.T338M rs1139682898 2017 28425625 The EquCab3 g. coordinates were provided by by Meredith O’Connell, working under the guidance of Professor Ernie Bailey, 5 March 2019
OMIA 000629-9796 horse American Paint Horse Miniature Horse Pinto Horse Quarter Horse Thoroughbred Megacolon EDNRB frame overo delins, small (<=20) yes EquCab2 17 c.353_354delinsAG p. I118K 1998 9530628 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124 200922: g. info removed to here (g.50624658) until can be standardised
OMIA 000420-9796 horse American Quarter Horse Glycogen storage disease IV GBE1 nonsense (stop-gain) yes c.102C>A p.Y34* 2004 15366377
OMIA 001158-9796 horse American Paint Horse Appaloosa Draft Quarter Horse Warmblood Polysaccharide storage myopathy/Exertional rhabdomyolysis GYS1 missense yes EquCab2 10 g.18940324G>A c.926G>A p.R309H 2008 18358695 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 000081-9796 horse Arabian Atlanto occipital fusion HOXD3 deletion, gross (>20) yes "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
OMIA 001899-9796 horse Quarter Horse Warmblood Incontinentia pigmenti IKBKG nonsense (stop-gain) yes EquCab 2 X g.122833887C>T c.202C>T p.R68* 2013 24324710 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 001000-9796 horse Quarter Horse Thoroughbred Thrombasthenia ITGA2B missense yes c.122G>C p.(R41P) 2006 16407493 c. coordinates obtained from Leite et al. (2019)
OMIA 001000-9796 horse Peruvian Paso Quarter Horse Thrombasthenia ITGA2B deletion, small (<=20) yes EquCab3.0 11 g.19247983_19247992delCAGGTGAGGA 2007 17338169 g. coordinates obtained from Dahlgren et al. (2020)
OMIA 000209-9796 horse Thoroughbred Coat colour, dominant white KIT W27 missense unknown 3 c.1473T>G p.Cys491Trp 2018 29333746
OMIA 000209-9796 horse Thoroughbred Coat colour, dominant white KIT W26 deletion, small (<=20) unknown 3 c.2536delA p.Ser846Valfs*15 2018 29333746
OMIA 000209-9796 horse Icelandic Coat colour, dominant white KIT W8 splicing no Equ cab 2 3 200922: g. and c. infom moved here (g.77736688; c.2222-1) until can be standardised 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
OMIA 000209-9796 horse South German Draft Coat colour, dominant white KIT W11 splicing no Equ cab 2 3 g.77731743G>A 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
OMIA 000209-9796 horse Miniature Horse Quarter Horse Coat colour, dominant white KIT W13 splicing no Equ cab 2 3 g.77735380G>C 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
OMIA 000209-9796 horse Appaloosa Haflinger Lipizzan Noriker Quarter Horse Coat colour, dominant white KIT sabino 1 (SB1) splicing no Equ cab 2 3 g.77735520A>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
OMIA 000209-9796 horse Swiss Warmblood Coat colour, dominant white KIT W18 splicing no Equ cab 2 3 g.77745065G>A 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
OMIA 000209-9796 horse Thoroughbred Coat colour, dominant white KIT W7 splicing no Equ cab 2 3 g.77771305G>C 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
OMIA 000209-9796 horse German Riding Pony White spotting KIT W28 deletion, gross (>20) no EquCab 3 3 g.79579925_79581197del 2019 31463981
OMIA 000209-9796 horse Thoroughbred White spotting KIT W22 deletion, gross (>20) no EquCab2 3 g.77,740,239_77,742,136del1898 2017 28444912
OMIA 000209-9796 horse Oldenburg Coat colour, dominant white KIT W16 missense no EquCab2 3 g.77732055A>T 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
OMIA 000209-9796 horse Thoroughbred Coat colour, dominant white KIT W14 deletion, gross (>20) no EquCab2 3 g.77735465_77735518del 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
OMIA 000209-9796 horse Icelandic White spotting KIT W21 deletion, small (<=20) no EquCab2 3 g.77735488delG c.2369delC p.Ala790Glufs*20 2015 26059442 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
OMIA 000209-9796 horse Thoroughbred Coat colour, dominant white KIT W5 deletion, small (<=20) no EquCab2 3 g.77737214delG c.2193delG p.T732QfsX9 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
OMIA 000209-9796 horse Franches-Montagnes Coat colour, dominant white KIT W1 nonsense (stop-gain) no EquCab2 3 g.77737256C>G 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
OMIA 000209-9796 horse American Paint Horse Appaloosa German Riding Pony Gipsy Noriker Old-Tori Oldenberg Quarter Horse Thoroughbred Warmblood Welsh Pony Coat colour, dominant white KIT W20 missense unknown EquCab2 3 g.77739534G>A c.2045G>A p.R682H 2013 23659293 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
OMIA 000209-9796 horse Japanese Draft Coat colour, dominant white KIT W17b missense no EquCab2 3 g.77739558T>C 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
OMIA 000209-9796 horse Japanese Draft Coat colour, dominant white KIT w17a missense no EquCab2 3 g.77739579A>T 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
OMIA 000209-9796 horse Thoroughbred Coat colour, dominant white KIT W2 missense no EquCab2 3 g.77740854G>A 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
OMIA 000209-9796 horse Camarillo White Horse Coat colour, dominant white KIT W4 missense no EquCab2 3 g.77741094C>T 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
OMIA 000209-9796 horse Holstein Coat colour, dominant white KIT W9 missense no EquCab2 3 g.77741111G>A 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
OMIA 000209-9796 horse Arabian Coat colour, dominant white KIT W15 missense no EquCab2 3 g.77741665T>C 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
OMIA 000209-9796 horse Arabian Coat colour, dominant white KIT W19 missense no EquCab2 3 g.77745090A>G 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
OMIA 000209-9796 horse Quarter Horse Coat colour, dominant white KIT W10 deletion, small (<=20) no EquCab2 3 g.77758240_77758243del c.1126_1129delGAAC p.E376FfsX3 2009 19456317 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
OMIA 000209-9796 horse Thoroughbred Coat colour, dominant white KIT W6 missense no EquCab2 3 g.77765059G>A 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
OMIA 000209-9796 horse Arabian White spotting KIT W23 splicing unknown EquCab2 3 g.77769789C>G c.756+1G>C ss2137493881 2017 28378922
OMIA 000209-9796 horse Arabian Coat colour, dominant white KIT W3 nonsense (stop-gain) no EquCab2 3 g.77769840A>T 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
OMIA 000209-9796 horse Thoroughbred Coat colour, dominant white KIT W12 deletion, small (<=20) unknown EquCab2 3 g.77771079_77771083delTCTGC c.559_563delTCTGC p.Ser187ArgfsX10 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
OMIA 000209-9796 horse Italian Trotter Coat colour, dominant white KIT W24 splicing no EquCab2.0 3 g.77736559C>T 2017 28856698
OMIA 000209-9796 horse Thoroughbred Coat colour, dominant white KIT W25 missense unknown EquCab2.0 3 g.77769878A>G c.668T>C p.Leu223Pro 2018 29333746
OMIA 000209-9796 horse Berber Extensive coat white patterning KIT W30 missense no EquCab3.0 g.79548244T>A c.2020T>A p.L674H g.79548244, c.2020T>A; p.L674H (Martin et al., 2020) 2020 33111383
OMIA 000245-9796 horse Bashkir Curly Horse Curly Curly coat KRT25 Crd missense no EquCab3.0 11 g.21962991G>A c.266G>A p.Arg89His rs1095048844 2018 29686323 29141579 Variant coordinates obtained from and/or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 001677-9796 horse American Saddlebred Epidermolysis bullosa, junctionalis, LAMA3-related LAMA3 deletion, gross (>20) yes "6589-bp deletion spanning exons 24-27 . . . in the LAMA3 gene in American Saddlebred foals" 2009 19016681
OMIA 001678-9796 horse Belgian Italian draft horse Trait Breton Trait Comtois Epidermolysis bullosa, junctionalis, LAMC2-related LAMC2 insertion, small (<=20) yes c.1368insC 2002 12230513
OMIA 001715-9796 horse Numerous breeds Gaitedness LOC100147177 nonsense (stop-gain) no 23 g.22999655C>A p.S301* 2012 22932389
OMIA 002021-9796 horse Quarter Horse Coat colour, brindle 1 MBTPS2 splicing no c.1437+4T>C 2016 27449517
OMIA 001199-9796 horse Coat colour, chesnut MC1R missense no EquCab2 3 g.36259552C>T c.248C>T p.S83F 1996 8995760 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 001199-9796 horse Coat colour, chesnut MC1R missense no EquCab2 3 g.36259554G>A c.250G>A p.D84N 2000 11086549 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 002197-9796 horse Shetland Pony Mushroom MFSD12 not known no 7 p.(Asp201fs) 2019 Reference not in PubMed; see OMIA 002197-9796 for reference details
OMIA 000214-9796 horse American Paint Horse White spotting, blue eyes and deafness MITF SW5 deletion, gross (>20) yes 16 g.21503211_21566617del 2019 30644113
OMIA 000214-9796 horse American Paint Horse Splashed white MITF SW6 deletion, gross (>20) no Ecab3.0 16 g.21551060_21559770del NC_009159.3:g.21551060-21559770del (Magdesian et al., 2020) 2020 32242630
OMIA 000214-9796 horse Quarter Horse Splashed white MITF SW3 deletion, small (<=20) no EquCab2 16 c.519_523delGTGTC p.C174Sfs*20 200922: g. info moved to here (g.20105348) until it can be standardised 2012 22511888 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
OMIA 000214-9796 horse American Standardbred White MITF MITF^244Glu missense no EquCab2 16 g.20094630C>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
OMIA 000214-9796 horse Franches-Montagnes Macchiato MITF macchiato missense no EquCab2 16 g.20103081A>G 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
OMIA 000214-9796 horse American Miniature Horse American Paint Horse Appaloosa Icelandic Morgan Old-Tori Quarter Horse Shetland Pony Trakehner Splashed white MITF SW1 delins, small (<=20) no EquCab2 16 g.20117302Tdelins11 2012 22511888 Variant coordinates gleaned from or confirmed by Table S1 of Durig et al. (2017) Anim Genet 48:123-124
OMIA 000214-9796 horse Menorca White splashing MITF regulatory no EquCab2 16 g.20147039C>T 2017 28084638
OMIA 001538-9796 horse Racing distance MSTN insertion, gross (>20) no 18 A "227 bp SINE insertion positioned upstream of exon 1" 2018 30379863
OMIA 000175-9796 horse Arabian Bashkir Curly Horse Trakehner Welsh Pony Cerebellar abiotrophy MUTYH not known yes EquCab 3.0 2 g.13122415G>A 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. 2011 21126570
OMIA 002141-9796 horse Quarter Horse Immune-mediated myositis MYH1 missense 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
OMIA 001501-9796 horse Arabian Lavender foal syndrome MYO5A deletion, small (<=20) yes g.138235715delC 2010 20419149
OMIA 001688-9796 horse Lipizzan Noriker Quarter Horse Splashed white PAX3 SW2 missense no EquCab2 6 g.11429753G>A 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
OMIA 001688-9796 horse Appaloosa Splashed white PAX3 SW4 missense no EquCab2.0 6 g.11429867G>C c.95C>G p.Pro32Arg 2013 23659293
OMIA 001982-9796 horse Warmblood Fragile Foal Syndrome PLOD1 missense yes EquCab3.0 2 g.39927817C>T c.2032G>A p.G678R rs1136065234 2015 25637337 rsID and Variant coordinates obtained from Zhang et al. (2020): "g.39927817C>T (rs1136065234; NC_009145.3, Equ-Cab3.0)" c. and p. coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 001438-9796 OMIA 000733-9796 horse American Miniature Horse Icelandic Rocky Mountain Coat colour, silver AND Multiple congenital ocular anomalies PMEL missense no g.73665304C>T p.R625C 2006 17029645
OMIA 000327-9796 horse American Quarter Horse Ehlers-Danlos syndrome PPIB missense yes EquCab2 1 g.128056148G>A c.115G>A p.G39R 2007 17498917 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 000220-9796 horse Arabian Severe combined immunodeficiency disease, autosomal PRKDC deletion, small (<=20) yes Ecab3.0 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
OMIA 000621-9796 horse American Quarter Horse Malignant hyperthermia RYR1 missense yes c.7360C>G p.R2454G 2004 15318347
OMIA 000785-9796 horse Quarter Horse HYPP SCN4A H missense yes Ecab3.0 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 1992 1338908
OMIA 001897-9796 horse Connemara pony Hoof wall separation syndrome SERPINB11 insertion, small (<=20) yes EquCab3.0 8 g.83,600,643_83,600,644insC c.504_505insC p.(Thr169Hisfs*3) 2015 25875171 FN thanks Daniel J. Schmidt, working under the supervision of Professor Ernie Bailey, for updating the coordinates to EquCab3.0.
OMIA 002013-9796 horse Shetland Pony Skeletal atavism SHOX deletion, gross (>20) yes "two partially overlapping large deletions [are] in the pseudoautosomal region (PAR) of chromosome X/Y"; "One of the identified deletions removes the entire coding region of the short stature homeobox (SHOX) gene and both deletions remove parts of the cytokine receptor-like factor 2 (CRLF2) gene located downstream of SHOX." 2016 27207956
OMIA 002124-9796 horse Paso Fino Tiger eye SLC24A5 Tiger-eye 2 deletion, gross (>20) yes EquCab2 1 g.141660611_141661239del c.875-340_1081+82del 2017 28655738
OMIA 002124-9796 horse Paso Fino Tiger eye SLC24A5 Tiger-eye 1 missense yes EquCab2 1 g.141677402A>T c.272A>T p.Phe91Tyr 2017 28655738 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 001263-9796 horse Coat colour, champagne SLC36A1 missense no EquCab2 14 g.26701092C>G c.188C>G p.T63R 2008 18802473 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 001344-9796 horse Gypsy Coat colour, snowdrop SLC45A2 C^sno missense no EquCab2.0 21 g.30,664,622G>A c.305G>A p.(Arg102Gln) Bisbee et al. (2020): transcript ENSECAT00000026240.1 in the Ensembl EquCab2.0 assembly 2020 31961951
OMIA 001344-9796 horse Coat colour, cream dilution SLC45A2 C^Cr missense no EquCab3 21 g.31,690,653G>A c.457G>A p.(Asp153Asn) 2003 12605854 EquCab3 coordinates obtained from Table S2 of Holl et al. (2019)
OMIA 001344-9796 horse Standardbred × Tennessee Walking Horse cross Coat colour, sunshine SLC45A2 C^sun missense no EquCab3 21 g.31,705,368G>A c.568G>A p.(Gly190Arg) Holl et al. (2019): "The exon sequence containing this variant was deposited in Genbank under accession no. MF688761." 2019 31006892
OMIA 001344-9796 horse American Paint Horse Lusitano Purebred Spanish horse Quarter Horse Coat colour, pearl SLC45A2 C^prl missense no EquCab3 21 g.31,709,690G>A c.985G>A p.(Ala329Thr) 2019 30968968 EquCab3 g. coordinate kindly provided by Natalia Sevane
OMIA 001578-9796 horse Dales Pony Fell Pony Foal immunodeficiency syndrome in the Fell and Dales Pony SLC5A3 missense yes EquCab2 26 g.30660224G>T c.1337G>T p.P446L 2011 21750681 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 002175-9796 horse American Bashkir Curly horse Missouri Foxtrotter Curly coat with/without hypotrichosis SP6 missense yes EquCab3.0 11 g.24096309C>T c.1090G>A p.Asp364Asn Thomer et al. (2018): "SP6; NC_009154.2:g.24022045C>T, ss3021042887" with respect to EquCab2. Updated coordinates in this entry obtained from EVA rs1095048852; 14 Mar 2019 rs1095048852 2018 29686323
OMIA 001230-9796 horse Standardbred Ovotesticular DSD (Disorder of Sexual Development) SRY deletion, gross (>20) yes "at least the DNA-binding domain of the SRY gene was deleted from the Y chromosome of the XY mare" 1995 7558880
OMIA 002096-9796 horse Akhal-Teke Naked foal syndrome ST14 nonsense (stop-gain) yes EquCab3.0 7 g.39,710,628G>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)
OMIA 001356-9796 horse Coat colour, grey/gray STX17 duplication no 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
OMIA 001972-9796 horse Non-dun TBX3 nd1 regulatory no EquCab2 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
OMIA 001972-9796 horse Non-dun TBX3 nd2 regulatory unknown EquCab2 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
OMIA 001341-9796 OMIA 002139-9796 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) no EquCab2 1 g.108297929_108297930ins1378 "a 1378 bp retroviral LTR insertion in intron 1 of TRPM1" 2013 24167615
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Overall Statistics
Total number of variants 96
Variants with genomic location 74 (77.1% )
Variants in a variant database, i.e. with rs ID 9 (9.4%)
Variant Type Count Percent
deletion, gross (>20) 11 11.5%
deletion, small (<=20) 13 13.5%
delins, small (<=20) 2 2.1%
duplication 1 1.0%
insertion, gross (>20) 2 2.1%
insertion, small (<=20) 2 2.1%
missense 42 43.8%
nonsense (stop-gain) 7 7.3%
not known 2 2.1%
regulatory 4 4.2%
splicing 10 10.4%
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 2.1%
2005 1 1.0%
2006 2 2.1%
2007 6 6.2%
2008 3 3.1%
2009 8 8.3%
2010 2 2.1%
2011 8 8.3%
2012 7 7.3%
2013 6 6.2%
2014 0 0.0%
2015 4 4.2%
2016 6 6.2%
2017 13 13.5%
2018 9 9.4%
2019 5 5.2%
2020 5 5.2%