Search Results
Advanced search
96 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.
| 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 | EquCab3.0 | 1 | g.95257458_95257500del | p.(F2017_D2023del) | rs1095048839 | 2018 | 30058072 | |||
| OMIA 001271-9796 | horse | Miniature Shetland | Dwarfism, ACAN-related | ACAN | D3* | missense | yes | EquCab3.0 | 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 | EquCab3.0 | 1 | g.95284530C>T | p.(V424M) | 2018 | 30058072 | ||||
| OMIA 001271-9796 | horse | Miniature | Dwarfism, ACAN-related | ACAN | D1 | deletion, small (<=20) | yes | EquCab3.0 | 1 | g.95291270del | p.(K82fs) | 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.(W681S) | 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 | EquCab3.0 | X | c.183delT | p.(S61fs) | 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 | EquCab3.0 | X | c.2132C>T | p.(A711V) | 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 | 22 | g.2174_2184del | c.191_201del | 2001 | 11353392 | ||||||
| OMIA 000487-9796 | horse | Belgian draft horse Friesian | Hydrocephalus | B3GALNT2 | nonsense (stop-gain) | 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 | ||
| OMIA 002068-9796 | horse | Friesian | Dwarfism, Friesian | B4GALT7 | splicing | 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. | |||
| OMIA 000698-9796 | horse | New Forest Pony | Myotonia | CLCN1 | missense | 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 | ||
| OMIA 000735-9796 | horse | Belgian Haflinger Percheron | Ocular squamous cell carcinoma | DDB2 | missense | 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 | 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 | EquCab2.0 | 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 | 26 | 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 | EquCab2.0 | 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 | 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 | |||||||
| OMIA 001899-9796 | horse | Quarter Horse Warmblood | Incontinentia pigmenti | IKBKG | nonsense (stop-gain) | yes | EquCab2.0 | 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 | 11 | 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.(C491W) | 2018 | 29333746 | |||||
| OMIA 000209-9796 | horse | Thoroughbred | Coat colour, dominant white | KIT | W26 | deletion, small (<=20) | unknown | 3 | c.2536delA | p.(S846Vfs*15) | 2018 | 29333746 | |||||
| OMIA 000209-9796 | horse | Icelandic | Coat colour, dominant white | KIT | W8 | splicing | no | EquCab2.0 | 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 | EquCab2.0 | 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 | Oldenburg | Coat colour, dominant white | KIT | W16 | missense | no | EquCab2.0 | 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 | Miniature Horse Quarter Horse | Coat colour, dominant white | KIT | W13 | splicing | no | EquCab2.0 | 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 | Thoroughbred | Coat colour, dominant white | KIT | W14 | deletion, gross (>20) | no | EquCab2.0 | 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 | EquCab2.0 | 3 | g.77735488delG | 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 | ||
| OMIA 000209-9796 | horse | Appaloosa Haflinger Lipizzan Noriker Quarter Horse | Coat colour, dominant white | KIT | sabino 1 (SB1) | splicing | no | EquCab2.0 | 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 | 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 | W5 | deletion, small (<=20) | no | EquCab2.0 | 3 | g.77737214delG | 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 | ||
| OMIA 000209-9796 | horse | Franches-Montagnes | Coat colour, dominant white | KIT | W1 | nonsense (stop-gain) | no | EquCab2.0 | 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 | EquCab2.0 | 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 | EquCab2.0 | 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 | EquCab2.0 | 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 | White spotting | KIT | W22 | deletion, gross (>20) | no | EquCab2.0 | 3 | g.77740239_77742136del1898 | 2017 | 28444912 | |||||
| OMIA 000209-9796 | horse | Thoroughbred | Coat colour, dominant white | KIT | W2 | missense | no | EquCab2.0 | 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 | EquCab2.0 | 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 | EquCab2.0 | 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 | EquCab2.0 | 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 | Swiss Warmblood | Coat colour, dominant white | KIT | W18 | splicing | no | EquCab2.0 | 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 | Arabian | Coat colour, dominant white | KIT | W19 | missense | no | EquCab2.0 | 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 | EquCab2.0 | 3 | g.77758240_77758243del | 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 | ||
| OMIA 000209-9796 | horse | Thoroughbred | Coat colour, dominant white | KIT | W6 | missense | no | EquCab2.0 | 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 | EquCab2.0 | 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 | EquCab2.0 | 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 | W25 | missense | unknown | EquCab2.0 | 3 | g.77769878A>G | c.668T>C | p.(L223P) | 2018 | 29333746 | |||
| OMIA 000209-9796 | horse | Thoroughbred | Coat colour, dominant white | KIT | W12 | deletion, small (<=20) | unknown | EquCab2.0 | 3 | g.77771079_77771083delTCTGC | 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 | ||
| OMIA 000209-9796 | horse | Thoroughbred | Coat colour, dominant white | KIT | W7 | splicing | no | EquCab2.0 | 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 | Berber | Extensive coat white patterning | KIT | W30 | missense | no | EquCab3.0 | 3 | g.79548244T>A | c.2020T>A | p.(L674H) | g.79548244, c.2020T>A; p.L674H (Martin et al., 2020) | 2020 | 33111383 | ||
| OMIA 000209-9796 | horse | German Riding Pony | White spotting | KIT | W28 | deletion, gross (>20) | no | EquCab3.0 | 3 | g.79579925_79581197del | 2019 | 31463981 | |||||
| OMIA 000245-9796 | horse | Bashkir Curly Horse Curly | Curly coat | KRT25 | Crd | missense | no | EquCab3.0 | 11 | g.21962991G>A | c.266G>A | p.(R89H) | 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 | 8 | "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 | 5 | 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 | X | c.1437+4T>C | 2016 | 27449517 | |||||||
| OMIA 001199-9796 | horse | Coat colour, chesnut | MC1R | missense | no | EquCab2.0 | 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 | EquCab2.0 | 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.(D201fs) | 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 | Quarter Horse | Splashed white | MITF | SW3 | deletion, small (<=20) | no | EquCab2.0 | 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 | EquCab2.0 | 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 | EquCab2.0 | 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 | EquCab2.0 | 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 | EquCab2.0 | 16 | g.20147039C>T | 2017 | 28084638 | ||||||
| OMIA 000214-9796 | horse | American Paint Horse | Splashed white | MITF | SW6 | deletion, gross (>20) | no | EquCab3.0 | 16 | g.21551060_21559770del | NC_009159.3:g.21551060-21559770del (Magdesian et al., 2020) | 2020 | 32242630 | ||||
| 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 | EquCab3.0 | 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 | 1 | g.138235715delC | 2010 | 20419149 | |||||||
| OMIA 001688-9796 | horse | Lipizzan Noriker Quarter Horse | Splashed white | PAX3 | SW2 | missense | no | EquCab2.0 | 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.(P32R) | 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 | 6 | g.73665304C>T | p.(R625C) | 2006 | 17029645 | ||||||
| OMIA 000327-9796 | horse | American Quarter Horse | Ehlers-Danlos syndrome | PPIB | missense | yes | EquCab2.0 | 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 | 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 | |||
| OMIA 000621-9796 | horse | American Quarter Horse | Malignant hyperthermia | RYR1 | missense | yes | 10 | c.7360C>G | p.(R2454G) | 2004 | 15318347 | ||||||
| OMIA 000785-9796 | horse | Quarter Horse | HYPP | SCN4A | H | missense | 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 | 1992 | 1338908 | |
| OMIA 001897-9796 | horse | Connemara pony | Hoof wall separation syndrome | SERPINB11 | insertion, small (<=20) | 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. | |||
| OMIA 002013-9796 | horse | Shetland Pony | Skeletal atavism | SHOX | deletion, gross (>20) | yes | PAR | "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 | EquCab2.0 | 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 | EquCab2.0 | 1 | g.141677402A>T | c.272A>T | p.(F91Y) | 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 | EquCab2.0 | 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.30664622G>A | c.305G>A | p.(R102Q) | 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 | EquCab3.0 | 21 | g.31690653G>A | c.457G>A | p.(D153N) | 2003 | 12605854 | EquCab3 coordinates obtained from Table S2 of Holl et al. (2019) | |||
| OMIA 001344-9796 | horse | Standardbred x Tennessee Walking Horse cross | Coat colour, sunshine | SLC45A2 | C^sun | missense | no | EquCab3.0 | 21 | g.31705368G>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 | ||
| OMIA 001344-9796 | horse | American Paint Horse Lusitano Purebred Spanish horse Quarter Horse | Coat colour, pearl | SLC45A2 | C^prl | missense | no | EquCab3.0 | 21 | g.31709690G>A | c.985G>A | p.(A329T) | 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 | EquCab2.0 | 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.(D364N) | Thomer et al. (2018): "SP6; NC_009154.2:g.24022045C>T, ss3021042887" with respect to EquCab2. Updated coordinates in this entry obtained from EVA rs1095048852; 14 Mar 2019 | rs1095048852 | 2018 | 29686323 | ||
| OMIA 001230-9796 | horse | Standardbred | Ovotesticular DSD (Disorder of Sexual Development) | SRY | deletion, gross (>20) | yes | Y | "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.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) | ||
| OMIA 001356-9796 | horse | Coat colour, grey/gray | STX17 | duplication | 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 | ||||||||
| OMIA 001972-9796 | horse | Non-dun | TBX3 | nd1 | regulatory | 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 | ||||||
| OMIA 001972-9796 | horse | Non-dun | TBX3 | nd2 | regulatory | 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 | ||||||
| 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 | EquCab2.0 | 1 | g.108297929_108297930ins1378 | "a 1378 bp retroviral LTR insertion in intron 1 of TRPM1" | 2013 | 24167615 |
| 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% |