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70 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.
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 | 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 | |||||
| 1504 | OMIA:002594-9823 | pig | N-acetyl-galactosamine intestinal concentration | ABO | deletion, gross (>20) | Naturally occurring variant | unknown | 1 | 2.3kb deletion encompassing exon 8 | 2022 | 35477154 | ||||||||
| 1049 | OMIA:002178-9823 | pig | Landrace (Pig) Large White (Pig) Yorkshire (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". Initially reported in Large White and later reported in other breeds (PMID:39327728). | 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 | ||||||
| 1737 | OMIA:002886-9823 | pig | Large White (Pig) | Timothy syndrome 1 | CACNA1C | missense | Genome-editing (CRISPR-Cas9) | unknown | Sscrofa11.1 | 5 | NC_010447.5:g.69316114G>A | XM_021092981.1:c.1216G>A | XP_020948640.1:p.(G406R) | 2023 | 38665938 | ||||
| 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 | NC_010460.4: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 | 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 | 2000 | 11132149 | |||
| 655 | OMIA:001089-9823 | pig | Blood group system ABO | GGTA1 | O | deletion, gross (>20) | Naturally occurring variant | no | 1 | "the 0 allele has a large deletion between exon 7 of the A0 blood group gene and the neighbouring SURF6". | 2011 | 21554350 | |||||||
| 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 | ||
| 1728 | OMIA:002878-9823 | pig | Diabetes mellitus, HNF1A-related | HNF1A | insertion, gross (>20) | Transgenesis via somatic cell nuclear transfer (SCNT) | yes | integration of human HNF1⍺ gene with a P291fsinC mutation | 2009 | 19357985 | |||||||||
| 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 | |||
| 715 | OMIA:001743-9823 | pig | Coat colour, patch | KIT | duplication | Naturally occurring variant | no | 8 | the patch allele comprises a 450kb duplication that includes KIT (roughly in the middle) | 1998 | 9724328 | ||||||||
| 743 | OMIA:001745-9823 | pig | Essex, United Kingdom of Great Britain and Northern Ireland (Pig) Hampshire Down (Sheep) Schwäbisch Hällisches Schwein, Germany (Pig) Wessex Saddleback (Pig) | White belt | KIT | complex rearrangement | Naturally occurring variant | 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 | |||||||
| 391 | OMIA:001216-9823 | pig | Coat colour, roan | KIT | splicing | Naturally occurring variant | 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 | ||||||||
| 979 | OMIA:000209-9823 | pig | Dominant white | KIT | I | complex rearrangement | Naturally occurring variant | 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 | |||||||
| 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 | |||
| 1135 | OMIA:001745-9823 | pig | Cinta Senese, Italy (Pig) | White belt | KIT | not known | Naturally occurring variant | no | Sscrofa11.1 | 8 | g.41488472C>T | c.2499C>T | p.(P833P) | ENSSSCT00000009679.4:c.2499C>T ENSSSCP00000009430.3:p.Pro833= ENSSSCT00000062378.2:c.*1559C>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 | 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 | |
| 987 | OMIA:000499-9823 | pig | Hypercholesterolaemia | LDLR | missense | Naturally occurring variant | yes | Sscrofa11.1 | 2 | g.69841413C>T | c.250C>T | p.(R84C) | 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 | |||||
| 170 | OMIA:001199-9823 | pig | Duroc (Pig) | Red | MC1R | e | missense | Naturally occurring variant | 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 | |
| 171 | OMIA:001199-9823 | pig | Duroc (Pig) | Red | MC1R | e | missense | Naturally occurring variant | 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 | |
| 169 | OMIA:001199-9823 | pig | Hampshire Down (Sheep) | Dominant black | MC1R | E^D2 | missense | Naturally occurring variant | 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 | 2016 | 27703696 9799269 | |
| 168 | OMIA:001199-9823 | pig | Large Black (Pig) Meishan (Pig) | Dominant black | MC1R | E^D1 | missense | Naturally occurring variant | 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 | 1998 | 9799269 | |
| 1290 | OMIA:001199-9823 | pig | Large Black (Pig) Meishan (Pig) | Dominant black | MC1R | E^D1 | missense | Naturally occurring variant | 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 | 1998 | 9799269 | |
| 597 | OMIA:001199-9823 | pig | Bama Xiang Zhu, China (Pig) Pietrain (Pig) | Coat colour, black spotting on red or white background | MC1R | E^P, E^qy | insertion, small (<=20) | Naturally occurring variant | 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 | |
| 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 | ||||
| 1189 | OMIA:000319-9823 | pig | Ear size | MSRB3 | repeat variation | Naturally occurring variant | 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 | |||||||
| 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 | |||
| 441 | OMIA:000683-9823 | pig | Pietrain (Pig) | Muscular hypertrophy (double muscling) | MSTN | regulatory | Naturally occurring variant | 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 | 2008 | 18822098 | ||||
| 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 | |||||||
| 1749 | OMIA:002130-9823 | pig | Bama Xiang Zhu, China (Pig) | Albinism, oculocutaneous, type II | OCA2 | missense | Chemical mutagenesis (ENU) | unknown | Sscrofa11.1 | 15 | NC_010457.5:g.56825733C>T | NM_214094.2:c.2228 C>T | NP_999259.2:p.(S743L) | 2019 | 31636960 | ||||
| 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 | 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 | 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 | 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 | 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 | ||||||||
| 508 | OMIA:001249-9823 | pig | Dahe, China (Pig) Tibetan, China (Pig) Wujin - Kele, China (Pig) Wujin - Liangshan, China (Pig) | Brown | TYRP1 | deletion, small (<=20) | Naturally occurring variant | no | Sscrofa11.1 | 1 | g.209726927_209726932del | c.1484_1489del | p.(M495_G496del) | 2011 | 20978532 | ||||
| 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 | ||||||
| 1376 | OMIA:002468-9823 | pig | Bama Xiang Zhu, China (Pig) | ZBED6 knock-out | ZBED6 | deletion, small (<=20) | Genome-editing (CRISPR-Cas9) | no | c.1320del | c.1320del causes a frameshift after codon 134 and a premature stop occurs at codon 224 (Wang et al., 2021) | 2021 | 34710100 |
| Overall Statistics | |
|---|---|
| Total number of variants | 70 |
| Variants with genomic location | 46 (65.7% ) |
| Variants in a variant database, i.e. with rs ID | 30 (42.9%) |
| Variant Type | Count | Percent |
|---|---|---|
| complex rearrangement | 2 | 2.9% |
| deletion, gross (>20) | 8 | 11.4% |
| deletion, small (<=20) | 6 | 8.6% |
| delins, gross (>20) | 1 | 1.4% |
| delins, small (<=20) | 1 | 1.4% |
| duplication | 3 | 4.3% |
| insertion, gross (>20) | 4 | 5.7% |
| insertion, small (<=20) | 6 | 8.6% |
| missense | 22 | 31.4% |
| nonsense (stop-gain) | 5 | 7.1% |
| not known | 1 | 1.4% |
| regulatory | 1 | 1.4% |
| repeat variation | 1 | 1.4% |
| splicing | 9 | 12.9% |
| Year First Reported | Count | Percent |
|---|---|---|
| 1991 | 1 | 1.4% |
| 1992 | 0 | 0.0% |
| 1993 | 0 | 0.0% |
| 1994 | 0 | 0.0% |
| 1995 | 0 | 0.0% |
| 1996 | 1 | 1.4% |
| 1997 | 0 | 0.0% |
| 1998 | 7 | 10.0% |
| 1999 | 0 | 0.0% |
| 2000 | 3 | 4.3% |
| 2001 | 2 | 2.9% |
| 2002 | 1 | 1.4% |
| 2003 | 2 | 2.9% |
| 2004 | 1 | 1.4% |
| 2005 | 0 | 0.0% |
| 2006 | 1 | 1.4% |
| 2007 | 0 | 0.0% |
| 2008 | 1 | 1.4% |
| 2009 | 1 | 1.4% |
| 2010 | 0 | 0.0% |
| 2011 | 4 | 5.7% |
| 2012 | 3 | 4.3% |
| 2013 | 1 | 1.4% |
| 2014 | 1 | 1.4% |
| 2015 | 5 | 7.1% |
| 2016 | 4 | 5.7% |
| 2017 | 2 | 2.9% |
| 2018 | 3 | 4.3% |
| 2019 | 11 | 15.7% |
| 2020 | 4 | 5.7% |
| 2021 | 5 | 7.1% |
| 2022 | 5 | 7.1% |
| 2023 | 1 | 1.4% |