Search Results

Advanced search

50 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
1379 OMIA:002238-9823 pig Bama Xiang Zhu, China (Pig) Ichthyosis ABCA12 splicing Chemical mutagenesis (ENU) unknown Sscrofa11.1 15 g.117250799T>C Intronic mutation IVS49-727 A>G results in splicing alteration resulting in a 132-nt insertion and a premature stop codon (Wang et al., 2019) 2019 30925591
1049 OMIA:002178-9823 pig Large White (Pig) Abortion, BBS9 and BMPER-related BBS9 deletion, gross (>20) Naturally occurring variant yes Sscrofa11.1 18 g.39817373_40029300del Derks et al. (2018): "a large deletion in complete LD with the SSC18 haplotype of approximately 212kb (position 39,817,373 to 40,029,300), spanning a part of the BBS9 gene ... [and reducing] expression of the downstream BMPER gene" 2018 30231021
1281 OMIA:002306-9823 pig German Landrace (Pig) Infertility and increased litter size BMP15 nonsense (stop-gain) Naturally occurring variant yes Sscrofa11.1 X g.44618787C>T p.(R212*) "NP_001005155.2:p.R212X" (Flossmann et al., 2021) 2021 33413103
1254 OMIA:000576-9823 pig Yorkshire (Pig) Knobbed acrosome defect BOLL deletion, gross (>20) Naturally occurring variant yes Sscrofa11.1 15 g.101549770_101604750del 2020 32975846
177 OMIA:000636-9823 pig Membranoproliferative glomerulonephritis type II CFH missense Naturally occurring variant yes Sscrofa11.1 10 c.3610T>G p.(I1166R) CFH is located on Chr10 in Sscrofa10.2 g.2553907T>G, but recorded as 'unplaced/NW_018085100.1' in Sscrofa11.1. 2002 12466119 The genomic location on Sscrofa11.1 was determined by Stephanie Shields (27/05/2020)
1365 OMIA:000698-9823 pig Myotonia CLCN1 deletion, gross (>20) Naturally occurring variant yes Sscrofa11.1 18 g.6912538_6916702del 2019 31666547
172 OMIA:001718-9823 pig Dwarfism, Schmid metaphyseal chondrodysplasia COL10A1 missense Naturally occurring variant yes Sscrofa11.1 1 g.81767089C>T c.1768G>A p.(G590R) rs5334475171 2000 11130976 The genomic and CDS position was determined by Stephanie Shields and the effect was confirmed with Ensembl VEP (27/05/2020)
656 OMIA:000837-9823 pig Vitamin D-deficiency rickets, type I CYP27B1 deletion, gross (>20) Naturally occurring variant yes 5 the first of two deletions (173 bp or 329 bp) in the gene for cytochromome P450C1 (otherwise known as CYP27B1) 2003 12915218
657 OMIA:000837-9823 pig Vitamin D-deficiency rickets, type I CYP27B1 deletion, gross (>20) Naturally occurring variant yes 5 the second of two deletions (173 bp or 329 bp) in the gene for cytochromome P450C1 (otherwise known as CYP27B1) 2003 12915218
784 OMIA:001986-9823 pig Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive, with sensitivity to ionizing radiation DCLRE1C splicing Naturally occurring variant yes Sscrofa11.1 10 g.46845535G>A rs5334475180 2015 26320255
785 OMIA:001986-9823 pig Severe combined immunodeficiency disease, autosomal, T cell-negative, B cell-negative, NK cell-positive, with sensitivity to ionizing radiation DCLRE1C nonsense (stop-gain) Naturally occurring variant yes Sscrofa11.1 10 g.46851262G>A p.(Trp267*) rs5334475181 2015 26320255
1395 OMIA:001081-9823 pig Duchenne muscular dystrophy DMD DMD^ex52del delins, gross (>20) Transgenesis via somatic cell nuclear transfer (SCNT) yes X gene targeting and somatic cell nuclear transfer was used to replace DMD exon 52 with a neomycin resistance cassette 2013 23784375
1457 OMIA:001888-9823 pig Becker muscular dystrophy DMD insertion, gross (>20) Naturally occurring variant yes Sscrofa11.1 X Aihara et al. (2022): "Analysis of dystrophin mRNA showed a 62 base pair insertion between exons 26 and 27. The insertion was derived from intron 26." 2022 35220848
179 OMIA:001685-9823 OMIA:001888-9823 pig Stress syndrome DMD missense Naturally occurring variant yes Sscrofa11.1 X g.28309227G>A c.5872C>T p.(R1958W) Ensembl VEP was used to identify cDNA position in transcript ENSSSCT00000089893.1, SIFT score 0.01 rs196952080 rs196952080 2012 22691118
1352 OMIA:002442-9823 pig Large White (Pig) Sperm flagella defect DNAH17 deletion, small (<=20) Naturally occurring variant yes Sscrofa11.1 12 g.3556402_3556414del Nosková et al. (2021): "intronic 13-bp deletion ... causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17" rs5334475172 2021 33724408
1115 OMIA:002210-9823 pig Bama Xiang Zhu, China (Pig) Congenital hypothyroidosis DUOX2 missense Naturally occurring variant yes Sscrofa11.1 1 g.126625620A>G c.1226A>G p.(D409G) ENU mutagenesis was used to create these pigs, the mutation is located within an exonic splicing enhancer motif and causes aberrant splicing of DUOX2 transcripts (Cao et al., 2019) rs5334475175 2019 30651277
1402 OMIA:000628-9823 pig Marfan syndrome FBN1 deletion, small (<=20) Genome-editing (ZFN) yes Sscrofa11.1 1 g.123246159del p.(E433Nfs98*) 2016 27074716
178 OMIA:000862-9823 pig Resistance to oedema disease (F18 receptor) FUT1 missense Naturally occurring variant no Sscrofa11.1 6 g.54079560T>C c.304A>G p.(T103A) The variant was initially described as c.307G>A and p.A103T by Vögeli et al. 1997. VEP analysis identified the variant as c.304A>G p.T102A in transcript ENSSSCT00000051297.2 rs335979375 rs335979375 2000 11132149
1195 OMIA:002268-9823 pig Danish Landrace (Pig) Vitamin C deficiency GULO od deletion, gross (>20) Naturally occurring variant yes 14 "This deletion includes 77 bp of exon VIII, 398 bp of intron 7 and 3.7 kbp of intron 8, which leads to a frame shift. The mutant protein is truncated to 356 amino acids, but only the first 236 amino acids are identical to the wild-type GULO protein." (Hasan et al., 2004) 2004 15112110
1318 OMIA:001461-9823 pig Wild boar Gangliosidosis, GM2, type I HEXA missense Naturally occurring variant yes Sscrofa11.1 7 g.60910365C>T c.1495C>T p.(R499C) cDNA positions based on NM_001123221.1 rs5334475169 2021 34119419
624 OMIA:001952-9823 pig Microtia HOXA1 delins, small (<=20) Naturally occurring variant yes Sscrofa11.1 18 g.45478109delinsTC c.451delinsTC p.(L151fs) 2015 26035869 The genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcript: XM_003134844.5 by Stephanie Shields (27/05/2020)
1231 OMIA:002283-9823 pig Large White (Pig) Arthrogryposis multiplex congenita, KIF21A-related KIF21A insertion, gross (>20) Naturally occurring variant yes Sscrofa11.1 5 g.70964237_70964238insAAGATAGAGGTTCTTTCCTCTAGACTTGAGGTTCTCCTGGTGTGACAGATGGTTCTTTCCTCT p.(V41_F42ins*) (NC_010447.5:g70964237_ g70964238insAAGATAGAGGTTCTTTCCTCTAGACTTGAGGTTCTCCTGGTGTGACAGATGGTTCTTTCCTCT; p.Val41_Phe42insTer) (Fang et al., 2020) rs5334475173 2020 32686171
1248 OMIA:002287-9823 pig Bama Xiang Zhu, China (Pig) Hypopigmentation (piebald) and deafness KIT missense Naturally occurring variant yes Sscrofa11.1 8 g.41485957T>A c.2418T>A p.(D806E) ENU mutagenesis was used to create these pigs, NM_001044525.1; c.2418T>A; NP_001037990.1; p.(D806E) (Xu et al., 2020) 2020 33042408
987 OMIA:000499-9823 pig Hypercholesterolaemia LDLR missense Naturally occurring variant yes Sscrofa11.1 2 g.69841413C>T c.250C>T p.(R84C) rs701604154 rs701604154 1998 9556295 The genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcripts: XM_021080444.1, XM_021080449.1, XM_021080452.1, XM_021080457.1 by Stephanie Shields (27/05/2020)
1401 OMIA:001213-9823 pig Yucatan Miniature, United States of America (Pig) Hutchinson-Gilford progeria syndrome LMNA splicing Genome-editing (CRISPR-Cas9) yes Sscrofa11.1 4 g.93900345G>A c.1824C>T 2019 30911407
1378 OMIA:001401-9823 pig Bama Xiang Zhu, China (Pig) Waardenburg syndrome, type 2A MITF missense Chemical mutagenesis (ENU) yes 13 c.740T>C p.(L247S) 2017 29094203
849 OMIA:001401-9823 pig Rongchang, China (Pig) Waardenburg syndrome, type 2A MITF insertion, small (<=20) Naturally occurring variant yes Sscrofa11.1 13 g.51377987_51377988insTTTAGTTTAAAAAA a 14 bp insertion "in the non-regulatory region of the melanocyte-specific promoter of microphthalmia-associated transcription factor (MITF) gene generated a novel silencer" rs5334475179 2016 27349893
1019 OMIA:002161-9823 pig Large White (Pig) Leg weakness, MSTN-related MSTN nonsense (stop-gain) Naturally occurring variant yes Sscrofa11.1 15 g.94623834C>A c.820G>T p.(E274*) rs3473215843 2019 30699111
598 OMIA:001200-9823 pig Tremor, high-frequency (Campus syndrome) MYH7 insertion, small (<=20) Naturally occurring variant yes Sscrofa11.1 7 g.75668349_75668350insGGCGGG c.4320_4321insCCCGCC p.(A1440_A1441insPA) rs5334475166 2012 23153285 The genomic location on Sscrofa10.2 was determined by Stephanie Shields (27/05/2020) and updated to the genomic Sscrofa11.1 location by Imke Tammen
1316 OMIA:002148-9823 pig Duroc (Pig) Vestibular dysfunction MYO7A nonsense (stop-gain) Naturally occurring variant yes Sscrofa11.1 9 g.11280403C>T c.541C>T p.(Q181*) cDNA position is based on transcript NM_001099928.1 rs5334475170 2021 33955556
1370 OMIA:002464-9823 pig Large White (Pig) Cryopyrin-associated periodic syndrome NLRP3 missense Genome editing (CRISPR/Cpf1) yes 2 p.(R259W) 2020 32958688
1288 OMIA:001128-9823 pig Duroc (Pig) Pale soft exudative meat PHKG1 splicing Naturally occurring variant yes Sscrofa11.1 3 g.16830320C>A c.919-5C>A ENSSSCT00000008491.4:c.919-5C>A Ma et al. 2014: "a point mutation (C>A) in a splice acceptor site of intron 9, resulting in a 32-bp deletion in the open reading frame and generating a premature stop codon" rs330928088 rs330928088 2014 25340394
1404 OMIA:000807-9823 pig Polycystic kidney disease PKD1 PKD1^insG/+ insertion, small (<=20) Genome-editing (CRISPR-Cas9) yes 3 c.152_153insG 2022 34980882
1406 OMIA:000807-9823 pig Polycystic kidney disease PKD1 PKD1^Tins/+ insertion, small (<=20) Genome-editing (ZFN) yes 3 c.642_643insT 2015 25798056
1405 OMIA:000807-9823 pig Polycystic kidney disease PKD1 PKD1^TGCTins/+ insertion, small (<=20) Genome-editing (ZFN) yes 3 c.642_643insTGCT 2015 25798056
1523 OMIA:002525-9823 pig PKD2 overexpression PKD2 insertion, gross (>20) Genome-editing (CRISPR-Cas9) yes insertion of transgene vector pCAG-muhPKD2 (c.1532A > T/p.511D > V)-3 × FLAG-floxP-neo-pH11 into the pH11 safe harbor site 2022 36452154
1054 OMIA:002183-9823 pig Landrace (Pig) Embryonic lethality PNKP missense Naturally occurring variant yes Sscrofa11.1 6 g.54880241T>C p.(Q96R) Derks et al. (2019): "deleterious missense mutation in the PNKP gene (6:g.54880241G>T), predicted to be strongly deleterious by SIFT (0.02) and PROVEAN (-2.9). The missense mutation causes a glutamine to arginine amino acid substitution (ENSSSCP00000003467:p.Gln96Arg)" rs5334475176 2019 30875370
1052 OMIA:002181-9823 pig Landrace (Pig) Embryonic lethality POLR1B splicing Naturally occurring variant yes Sscrofa11.1 3 g.43952776T>G Derks et al. (2019): "Skipping of exon 14 introduces a glutamic acid and a premature stop codon in the second codon of the terminal exon, lacking the final 370 amino acids located in the conserved subunit 2, hybrid-binding domain (binding to the DNA strand)" rs5334475168 2019 30875370
175 OMIA:001085-9823 pig Meat quality (Rendement Napole) PRKAG3 RN- missense Naturally occurring variant yes Sscrofa11.1 15 g.120863533C>T c.749G>A p.(R250Q) The paper by Milan et al. (2000) reported this variant as c.599G>A and p.R200Q rs1109104772 rs1109104772 2000 10818001 The genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcript: ENSSSCT00000017641.4 by Stephanie Shields (27/05/2020)
176 OMIA:001085-9823 pig Meat quality (Rendement Napole) PRKAG3 RN- missense Naturally occurring variant yes Sscrofa11.1 15 g.120863537C>T c.745G>A p.(I249V) rs1108399077 rs1108399077 2001 11729159 he genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcript: ENSSSCT00000017641.4 by Stephanie Shields (27/05/2020)
174 OMIA:000621-9823 pig Malignant hyperthermia RYR1 missense Naturally occurring variant yes Sscrofa11.1 6 g.47357966T>C c.1843C>T p.(R615C) NM_001001534.1: c.1843C>T; p.(R615C) Interestingly, the reference allele in the Sscrofa11.1 assembly is T rather than C, meaning that the Duroc animal that is the basis of this reference genome assembly has the causal variant for malignant hyperthermia! rs344435545 rs344435545 1991 1862346 Effect was confirmed with Ensembl VEP in the following transcript: NM_001001534.1 by Stephanie Shields (27/05/2020)
1367 OMIA:002453-9823 pig Waardenburg syndrome SOX10 duplication Genome-editing (CRISPR-Cas9) yes 5 c.321dupC p.(K108Qfs*45) 2016 26442986
1366 OMIA:002453-9823 pig Bama Xiang Zhu, China (Pig) Waardenburg syndrome SOX10 missense Chemical mutagenesis (ENU) yes 5 c.325A>T p.(R109W) 2017 28639938
392 OMIA:002435-9823 pig Sperm, short tail SPEF2 splicing Naturally occurring variant yes 16 an inserted retrotransposon within an intron 2006 16549801
1149 OMIA:002232-9823 pig Large White (Pig) Myopathy, congenital, SPTBN4-related SPTBN4 deletion, small (<=20) Naturally occurring variant yes Sscrofa11.1 6 g.48801281_48801296del p.(R1902fs) Derks et al. (2019): ENSSSCP00000031537:p.Arg1902fs 2019 31850074
1051 OMIA:002180-9823 pig Duroc (Pig) Embryonic lethality TADA2A splicing Naturally occurring variant yes Sscrofa11.1 12 g.38922102G>A splice-donor mutation causing retention of intron 13 or exon skipping of exon 13 (Derks et al., 2019) rs5334475174 2019 30875370
912 OMIA:001673-9823 pig Large White, Finland (Pig) Spermatogenic arrest TEX14 splicing Naturally occurring variant yes 12 "a 51 bp insertion within exon 27, which caused differential splicing of the exon and created a premature translation stop codon" 2011 22136159
1519 OMIA:001472-9823 pig Yucatan Miniature, United States of America (Pig) Neuronal ceroid lipfuscinosis, 2 (CLN2) TPP1 nonsense (stop-gain) Transgenesis via viral vectors yes p.(R208X) 2022 36100791
1053 OMIA:002182-9823 pig Landrace (Pig) Embryonic lethality URB1 deletion, small (<=20) Naturally occurring variant yes Sscrofa11.1 13 g.195977038del p.(V1961fs) Derks et al. (2019): "[a] frameshift mutation in exon 38 of the URB1 gene (13:g.195977038delC) caused by a 1-bp deletion . . . The frameshift (ENSSSCP00000036505:p.Val1961fs) introduces 26 novel amino acids and a premature stop codon, producing a truncated protein of 1,986 amino acids, lacking the final 261 amino acids compared to the wild-type protein (2,247 AA)." rs5334475182 2019 30875370
969 OMIA:001058-9823 pig Mixed Breed (Dog) Von Willebrand disease III VWF duplication Naturally occurring variant yes 5 p.(V814Lfs*3) "a tandem duplication of exons 17 and 18, causing a frameshift and a premature termination codon (p.Val814LeufsTer3) . . . This duplication putatively originates from porcine SINE elements located within VWF introns 16 and 18 with high identity. 2018 29208651
Overall Statistics
Total number of variants 50
Variants with genomic location 34 (68.0% )
Variants in a variant database, i.e. with rs ID 7 (14.0%)
Variant Type Count Percent
deletion, gross (>20) 6 12.0%
deletion, small (<=20) 4 8.0%
delins, gross (>20) 1 2.0%
delins, small (<=20) 1 2.0%
duplication 2 4.0%
insertion, gross (>20) 3 6.0%
insertion, small (<=20) 5 10.0%
missense 15 30.0%
nonsense (stop-gain) 5 10.0%
splicing 8 16.0%
Year First Reported Count Percent
1991 1 2.0%
1992 0 0.0%
1993 0 0.0%
1994 0 0.0%
1995 0 0.0%
1996 0 0.0%
1997 0 0.0%
1998 1 2.0%
1999 0 0.0%
2000 3 6.0%
2001 1 2.0%
2002 1 2.0%
2003 2 4.0%
2004 1 2.0%
2005 0 0.0%
2006 1 2.0%
2007 0 0.0%
2008 0 0.0%
2009 0 0.0%
2010 0 0.0%
2011 1 2.0%
2012 2 4.0%
2013 1 2.0%
2014 1 2.0%
2015 5 10.0%
2016 3 6.0%
2017 2 4.0%
2018 2 4.0%
2019 10 20.0%
2020 4 8.0%
2021 4 8.0%
2022 4 8.0%