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54 variant records found

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

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 Inferred EVA rsID Year Published PubMed ID(s) Acknowledgements
OMIA 002178-9823 pig Large White Abortion, BBS9 and BMPER-related BBS9 deletion, gross (>20) 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
OMIA 002306-9823 pig German Landrace Infertility and increased litter size BMP15 nonsense (stop-gain) yes Sscrofa11.1 X g.44618787C>T p.(R212*) "NP_001005155.2:p.R212X" (Flossmann et al., 2021) 2021 33413103
OMIA 000576-9823 pig Yorkshire Knobbed acrosome defect BOLL deletion, gross (>20) yes Sscrofa11.1 15 g.101549770_101604750del 2020 32975846
OMIA 001752-9823 pig Resistance to PRRS virus CD163 deletion, gross (>20) no 5 Burkhard et al (2018): "the deletion of exon 7 of CD163 using CRISPR/Cas9 editing" 2018 29925651
OMIA 000636-9823 pig Membranoproliferative glomerulonephritis type II CFH missense yes Sscrofa11.1 10 g.2553907T>G c.3610T>G p.(I1166R) CFH is located on Chr10 in Sscrofa10.2, 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)
OMIA 001718-9823 pig Dwarfism, Schmid metaphyseal chondrodysplasia COL10A1 missense yes Sscrofa11.1 1 g.81767089C>T c.1768G>A p.(G590R) 2000 11130976 The genomic and CDS position was determined by Stephanie Shields and the effect was confirmed with Ensembl VEP (27/05/2020)
OMIA 000837-9823 pig Vitamin D-deficiency rickets, type I CYP27B1 deletion, gross (>20) yes 5 the first of two deletions (173 bp or 329 bp) in the gene for cytochromome P450C1 (otherwise known as CYP27B1) 2003 12915218
OMIA 000837-9823 pig Vitamin D-deficiency rickets, type I CYP27B1 deletion, gross (>20) yes 5 the second of two deletions (173 bp or 329 bp) in the gene for cytochromome P450C1 (otherwise known as CYP27B1) 2003 12915218
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 yes Sscrofa11.1 10 g. 46845535G>A 2015 26320255
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) yes Sscrofa11.1 10 g.46851262G>A p.(Trp267*) 2015 26320255
OMIA 001685-9823 pig Stress syndrome DMD missense 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
OMIA 002210-9823 pig Bama miniature Congenital hypothyroidosis DUOX2 missense 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) 2019 30651277
OMIA 000862-9823 pig Resistance to oedema disease (F18 receptor) FUT1 missense no Sscrofa11.1 6 g.54079560 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 2000 11132149
OMIA 001089-9823 pig Blood group system ABO GGTA1 O deletion, gross (>20) no 1 "the 0 allele has a large deletion between exon 7 of the A0 blood group gene and the neighbouring SURF6". 2011 21554350
OMIA 002268-9823 pig Danish Landrace Vitamin C deficiency GULO od deletion, gross (>20) 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
OMIA 001461-9823 pig Wild boar Gangliosidosis, GM2, type I HEXA missense yes Sscrofa11.1 7 g.60910365C>T c.1495C>T p.(R499C) cDNA positions based on NM_001123221.1 2021 34119419
OMIA 001952-9823 pig Microtia HOXA1 delins, small (<=20) 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)
OMIA 002283-9823 pig Swiss Large White Arthrogryposis multiplex congenita, KIF21A-related KIF21A insertion, gross (>20) yes Sscrofa11.1 5 g.70964237_70964238insAAGATAGAGGTTCTTTCCTCTAGACTTGAGGTTCTCCTGGTGTGACAGATGGTTCTTTCCTCT p.(V41_F42ins*) (NC_010447.5:g70964237_ g70964238insAAGATAGAGGTTCTTTCCTCTAGACTTGAGGTTCTCCTGGTGTGACAGATGGTTCTTTCCTCT; p.Val41_Phe42insTer) (Fang et al., 2020) 2020 32686171
OMIA 001216-9823 pig Coat colour, roan KIT splicing no 8 a U(26) repeat in intron 5 of the KIT gene, which is likely to mediate skipping of exon 5 of the gene in some tissues including skin 2011 21749430
OMIA 001743-9823 pig Coat colour, patch KIT duplication no 8 the patch allele comprises a 450kb duplication that includes KIT (roughly in the middle) 1998 9724328
OMIA 001745-9823 pig Bavarian Landschwein Essex Hampshire Wessex Saddleback White belt KIT complex rearrangement no 8 Hampshire pigs (belted phenotype) have "a 4.3-kb duplication (DUP2) located ~¼100 kb upstream of KIT and a 23-kb duplication (DUP3) ~100 kb downstream of KIT, which in turn contained a fourth ~4.3-kb duplication (DUP4) not present on wild-type chromosomes". Across four breeds, belted pigs always had DUP2 and DUP4, but some lacked DUP3. 2012 23151514
OMIA 000209-9823 pig Dominant white KIT I complex rearrangement no 8 This dominant white allele carries at least three causal polymorphisms, namely a 450 kb duplication (originally reported by Johansson Moller (1996); also present in Patch - see OMIA 001743-9825), the splice mutation reported by Marklund et al. (1998) (unique to Dominant white) and smaller duplication(s) (that occur within the 450kb duplication) causing Belt (see OMIA 001745-9825).(with thanks to Leif Andersson). To emphasise the original discovery of the duplication, the ref cited here is Johansson Moller (1996) 1996 8875890
OMIA 002287-9823 pig Bama miniature Hypopigmentation (piebald) and deafness KIT missense 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
OMIA 001745-9823 pig Cinta Senese White belt KIT not known no Sscrofa11.1 8 g.41488472C>T Sscrofa10.2 g.43,597,545C>T; Ensembl VEP analysis suggests that this can be a synonymous or 3_prime_UTR_variant depending on the transcript analysed rs328592739 rs328592739 2016 Reference not in PubMed; see OMIA 001745-9823 for reference details Ogorevc et al. (2017) reported the EVA ID of this variant as rs328592739
OMIA 000499-9823 pig FH-r strain Hypercholesterolaemia LDLR missense 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)
OMIA 001199-9823 pig Duroc Red MC1R e missense no Sscrofa11.1 6 g.181461C>T c.727G>A p.(A243T) Variant is called p.(A240T) in original paper (Kijas et al., 1998). Two substitutions were found in recessive red (e/e) animals p.(A161V) and p.(A240T) - the p.(A240T) was considered as causative (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2 rs321432333 1998 9799269
OMIA 001199-9823 pig Duroc Red MC1R e missense no Sscrofa11.1 6 g.181697G>A c.491C>T p.(A164V) Variant is called p.(A161V) in original paper (Kijas et al., 1998). Two substitutions were found in recessive red (e/e) animals p.(A161V) and p.(A240T) - the p.(A240T) was considered as causative (Kijas et al., 1998). cDNA and protein location based in this table are based on transcript ENSSSCT00000022534.2 rs45435032 1998 9799269
OMIA 001199-9823 pig Hampshire Dominant black MC1R E^D2 missense no Sscrofa11.1 6 g.181818C>T c.370G>A p.(D124N) Variant is called p.(D121N) in original paper (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. rs326921593 rs326921593 2016 27703696 9799269
OMIA 001199-9823 pig Large Black Meishan Dominant black MC1R E^D1 missense no Sscrofa11.1 6 g.181883A>G c.305T>C p.(L102P) Variant is called p.(L99P) in original paper (Kijas et al., 1998). Two silent (p.(A240A), p.(N118N)) and two missense substitutions p.(V92M) and p.(L99P) were found in dominant black Asian pigs (E^D1/E^D1) (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. rs45434630 rs45434630 1998 9799269
OMIA 001199-9823 pig Large Black Meishan Dominant black MC1R E^D1 missense no Sscrofa11.1 6 g.181905C>T c.283G>A p.(V95M) Variant is called p.(V92M) in original paper (Kijas et al., 1998). Two silent (p.(A240A), p.(N118N)) and two missense substitutions p.(V92M) and p.(L99P) were found in dominant black Asian pigs (E^D1/E^D1) (Kijas et al., 1998). cDNA and protein location in this table are based on transcript ENSSSCT00000022534.2. rs45434629 rs45434629 1998 9799269
OMIA 001199-9823 pig Bama miniature Pietrain Coat colour, black spotting on red or white background MC1R E^P, E^qy insertion, small (<=20) no Sscrofa11.1 6 g.182126_182127insGG c.67_68insCC p.(R23Pfs*33) Variant was published as nt67insCC (Kijas et al., 2001), g.462-463CC (Wu et al., 2017), c.67_68insCC (Jia et al. 2017) rs1113295336 2017 28002929 28411032 11404341
OMIA 002217-9823 pig fatness, growth, feed intake MC4R missense unknown Sscrofa11.1 1 g.160773437G>A p.(D298N) rs81219178 rs81219178 2000 10656927 Variant coordinates updated based on Johnsson and Jungnickel (2021)
OMIA 001401-9823 pig Rongchang Waardenburg syndrome, type 2A MITF insertion, small (<=20) 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" 2016 27349893
OMIA 000319-9823 pig Ear size MSRB3 repeat variation no Sscrofa11.1 5 "the 38.7-kb CNV . . . starts at 349,577 bp and ends at 388,246 bp of the corrected contig (MK028166) . . . , covering the last two exons 6 and 7 of the MSRB3 gene" (Chen et al., 2018) 2018 30587124
OMIA 002161-9823 pig Large White Leg weakness, MSTN-related MSTN nonsense (stop-gain) yes Sscrofa11.1 15 g.94623834C>A c.820G>T p.(E274*) 2019 30699111
OMIA 000683-9823 pig Pietrain Muscular hypertrophy (double muscling) MSTN regulatory yes Sscrofa11.1 15 g.94629236T>C Stinckens et al. (2008) describe polymorphism located at position 447 of the porcine MSTN promoter, EF490986 EF490990 g.447A>G rs332188828 rs332188828 2008 18822098
OMIA 001200-9823 pig Tremor, high-frequency (Campus syndrome) MYH7 insertion, small (<=20) yes Sscrofa11.1 7 g.75668349_75668350insGGCGGG c.4320_4321insCCCGCC p.(A1440_A1441insPA) 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
OMIA 002148-9823 pig Duroc vestibular dysfunction MYO7A nonsense (stop-gain) yes Sscrofa11.1 9 g.11280403C>T c.541C>T p.(Q181*) cDNA position is based on transcript NM_001099928.1 2021 33955556
OMIA 001128-9823 pig Duroc Pale soft exudative meat PHKG1 splicing yes Sscrofa11.1 3 g.16830320C>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
OMIA 002183-9823 pig Landrace Embryonic lethality PNKP missense yes Sscrofa11.1 6 g.54880241G>T 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)" 2019 30875370
OMIA 002181-9823 pig Landrace Embryonic lethality POLR1B splicing 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)" 2019 30875370
OMIA 001579-9823 pig Chinese Erhualian Large floppy ears PPARD missense no Sscrofa11.1 7 g.31281804G>A c.95G>A p.(G32E) rs80909573 2011 21573137 The genomic location on Sscrofa11.1 was determined and the effect was confirmed with Ensembl VEP in the following transcripts: XM_005665910.3, XM_013977808.2 by Stephanie Shields (27/05/2020)
OMIA 001085-9823 pig Meat quality (Rendement Napole) PRKAG3 RN- missense 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)
OMIA 001085-9823 pig Meat quality (Rendement Napole) PRKAG3 RN- missense 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)
OMIA 000621-9823 pig Malignant hyperthermia RYR1 missense 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)
OMIA 001334-9823 pig Sperm, short tail SPEF2 splicing yes 16 an inserted retrotransposon within an intron 2006 16549801
OMIA 002232-9823 pig Synthetic Myopathy, congenital, SPTBN4-related SPTBN4 deletion, small (<=20) yes Sscrofa11.1 6 g.48801281_48801296del p.(R1902fs) Derks et al. (2019): ENSSSCP00000031537:p.Arg1902fs 2019 31850074
OMIA 002180-9823 pig Duroc Embryonic lethality TADA2A splicing 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) 2019 30875370
OMIA 001673-9823 pig Finnish Yorkshire Spermatogenic arrest TEX14 splicing 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
OMIA 001249-9823 pig Chinese-Tibetan Dahe Kele Liangshan Brown TYRP1 deletion, small (<=20) no Sscrofa11.1 1 g.209726927_209726932del c.1484_1489del p.(M495_G496del) 2011 20978532
OMIA 001436-9823 pig Non-shivering thermiogenesis, absence of UCP1 deletion, gross (>20) yes 8 "exons 3 to 5 were eliminated by a deletion in the pig sequence" 2006 16933999
OMIA 002182-9823 pig Landrace Embryonic lethality URB1 deletion, small (<=20) 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)." 2019 30875370
OMIA 001058-9823 pig Mixed breed Von Willebrand disease III VWF duplication 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. 2017 29208651
OMIA 001579-9823 pig Large White Minzhu Ear size WIF1 missense no Sscrofa11.1 5 g.29463165C>G c.1167C>G p.(F236L) rs338733115 2019 30815903
Overall Statistics
Total number of variants 54
Variants with genomic location 41 (75.9% )
Variants in a variant database, i.e. with rs ID 17 (31.5%)
Variant Type Count Percent
complex rearrangement 2 3.7%
deletion, gross (>20) 8 14.8%
deletion, small (<=20) 3 5.6%
delins, small (<=20) 1 1.9%
duplication 2 3.7%
insertion, gross (>20) 1 1.9%
insertion, small (<=20) 3 5.6%
missense 20 37.0%
nonsense (stop-gain) 4 7.4%
not known 1 1.9%
regulatory 1 1.9%
repeat variation 1 1.9%
splicing 7 13.0%
Year First Reported Count Percent
1991 1 1.9%
1992 0 0.0%
1993 0 0.0%
1994 0 0.0%
1995 0 0.0%
1996 1 1.9%
1997 0 0.0%
1998 7 13.0%
1999 0 0.0%
2000 4 7.4%
2001 2 3.7%
2002 1 1.9%
2003 2 3.7%
2004 1 1.9%
2005 0 0.0%
2006 2 3.7%
2007 0 0.0%
2008 1 1.9%
2009 0 0.0%
2010 0 0.0%
2011 5 9.3%
2012 3 5.6%
2013 0 0.0%
2014 1 1.9%
2015 3 5.6%
2016 2 3.7%
2017 1 1.9%
2018 3 5.6%
2019 8 14.8%
2020 3 5.6%
2021 3 5.6%