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208 variant records found | [show instead phene records] |
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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 | Year Published | PubMed ID(s) | Acknowledgements |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| OMIA 002238-9913 | cattle | Shorthorn | Ichthyosis, ABCA12-related | ABCA12 | missense | yes | ARS‐UCD1.2 | 2 | g.103,016,791T>C | c.6776T>C | p.(Leu2259Pro) | NM_001191294.2:c.6776T>C; NP_001178223.2:p.(Leu2259Pro) | 2019 | 31568573 | |||
| OMIA 002238-9913 | cattle | Chianina | Ichthyosis, ABCA12-related | ABCA12 | missense | yes | UMD3.1 | 2 | g.103,543,077A>G | c.5,804A>G | p.H1,935R | 2008 | 18344998 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001271-9913 | cattle | Miniature Zebu | Bulldog calf | ACAN | insertion, small (<=20) | yes | UMD 3.1 | 21 | g.20850999insC | c.5686insC | p.Val1898fsTer9 | 2018 | 30305023 | ||||
| OMIA 001271-9913 | cattle | Dexter | Bulldog calf | ACAN | BD2 | regulatory | yes | UMD3.1 | 21 | g.20800319C>T | c.-198C>T | 2007 | 17952705 | Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001271-9913 | cattle | Dexter Scottish Highland | Bulldog calf | ACAN | BD1 | insertion, small (<=20) | yes | UMD3.1 | 21 | g.20844569_20844570insGGCA | c.2266_2267insGGCA | 2007 | 17952705 | Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000328-9913 | cattle | Belgian Blue | Ehlers-Danlos syndrome, type VII (Dermatosparaxis) | ADAMTS2 | indel, small (<=20) | yes | UMD3.1 | 7 | g.1957955_1957971delinsAGC | c.464_480delinsAGC | 1999 | 10417273 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||||
| OMIA 001562-9913 | cattle | Slovenian Cika | Pulmonary hypoplasia and anasarca syndrome | ADAMTS3 | missense | yes | ARS‐UCD1.2 | 6 | g.87,462,016G>A | c.1222C>T | p.(His408Tyr) | NM_001192797.1: c.1222C>T; NP_001179726.1: p.(His408Tyr) (Häfliger et al., 2020) | 2020 | 32069517 | |||
| OMIA 001511-9913 | cattle | Angus | Contractual arachnodactyly (Fawn calf syndrome) | ADAMTSL3 | deletion, gross (>20) | yes | 21 | "a large (~58 kilobase pair) deletion affecting the ADAMTSL3 gene" | 2014 | Reference not in PubMed; see OMIA 001511-9913 for reference details | |||||||
| OMIA 002135-9913 | cattle | Angus | Arthrogryposis multiplex congenita, AGRN-related | AGRN | deletion, gross (>20) | yes | A 23,363 bp deletion "encompasses the entirety of the ISG15 ubiquitin-like modifier (ISG15) gene . . . one or both of the 5' regulatory region of the hairy and enhancer split 4 (HES4) and of the agrin (AGRN) gene and of the first two exons of the AGRN gene" (Beever and Marron, 2011) | 2011 | Reference not in PubMed; see OMIA 002135-9913 for reference details | ||||||||
| OMIA 001009-9913 | cattle | Shorthorn | Tibial hemimelia | ALX4 | deletion, gross (>20) | yes | Deletion of 45,694 bp including exon 1 of ALX4 | 2012 | Reference not in PubMed; see OMIA 001009-9913 for reference details | ||||||||
| OMIA 001009-9913 | cattle | Galloway | Tibial hemimelia | ALX4 | duplication | yes | AC_000172; UMD3.1 | g.75154399_75154418dup | 2015 | 26076463 | |||||||
| OMIA 002083-9913 | cattle | Japanese Black | Abortion (embryonic lethality), ANXA10-related | ANXA10 | repeat variation | yes | "a "34-kb deleted-type" CNV "associated with embryonic mortality at 30-60 days after artificial insemination. The CNV harbors exon 2 to 6 of ANNEXIN A10 (ANXA10). . . . Western blot analysis showed that the CNV results in a null allele of ANXA10." | 2016 | 27881083 | ||||||||
| OMIA 000001-9913 | cattle | Friesian Holstein | Abortion due to a nonsense mutation in APAF1 on haplotype HH1 | APAF1 | nonsense (stop-gain) | yes | UMD 3.1 | 5 | g.63150400C>T | c.1741C>T | p.Q581* | rs448942533 | 2016 | 27289157 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 001965-9913 | cattle | Holstein | Holstein cholesterol deficiency | APOB | insertion, gross (>20) | yes | "1.3kb insertion of a transposable LTR element (ERV2-1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing [p.Gly135ValfsX10)]" | 2016 | 26763170 | ||||||||
| OMIA 001334-9913 | cattle | Swedish Red | Sperm, short tail | ARMC3 | deletion, small (<=20) | yes | UMD3.1 | 13 | g.24301426delG | c.1442delG | p.A451fs26 | rs797454424 | 2016 | 26923438 | Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||
| OMIA 000201-9913 | cattle | Normande | Coat colour, agouti | ASIP | insertion, gross (>20) | no | "insertion of a full-length Bos taurus LINE element" | 2006 | 16827753 | ||||||||
| OMIA 000194-9913 | cattle | Holstein-Friesian | Citrullinaemia | ASS1 | nonsense (stop-gain) | yes | UMD 3.1 | 11 | g.100802781C>T | c.256C>T | p.R86* | 1989 | 2813370 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001450-9913 | cattle | Belgian Blue Red and White Dutch | Congenital muscular dystonia 1 | ATP2A1 | missense | yes | UMD3.1 | 25 | g.26191380C>T | c.1675C>T | p.R559C | 2008 | 18344998 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001464-9913 | cattle | Romagnola | Pseudomyotonia, congenital | ATP2A1 | missense | yes | UMD3.1 | 25 | g.26197204G>T | c.857G>T | p.G286V | 2012 | 23046865 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001464-9913 | cattle | Romagnola | Pseudomyotonia, congenital | ATP2A1 | missense | yes | UMD3.1 | 25 | g.26197429G>T | c.632G>T | p.G211V | 2012 | 23046865 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001464-9913 | cattle | Chianina | Pseudomyotonia, congenital | ATP2A1 | missense | yes | UMD3.1 | 25 | g.26198573G>A | c.491G > A | p.R164H | 2008 | 18786632 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000627-9913 | cattle | Polled Hereford | Maple syrup urine disease | BCKDHA | nonsense (stop-gain) | yes | UMD 3.1 | 18 | g.50828859C>T | c.154C>T | p.Q52* | rs479967962 | 1990 | 2303405 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 000627-9913 | cattle | Shorthorn | Maple syrup urine disease | BCKDHA | missense | yes | UMD3.1 | 18 | g.50837932C>T | c.1380C>T | p.P372L | 1999 | 10425233 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001079-9913 | cattle | Holstein | Yellow fat | BCO2 | nonsense (stop-gain) | yes | UMD3.1 | 15 | g.22877552 | c.306G>A | p.W102* | 2009 | 19398771 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 001991-9913 | cattle | Nordic Red | Stillbirth | BTBD9 | deletion, gross (>20) | yes | UMD3.1 | 23 | "∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8)" | 2016 | 27091210 | ||||||
| OMIA 002201-9913 | cattle | Normande | Abortion due to haplotype NH7 | CAD | missense | yes | 11 | g.72,399,397T>C | p.Tyr452Cys | 2019 | 31056337 | ||||||
| OMIA 002167-9913 | cattle | Nordic Red | Asthenospermia | CCDC189 | splicing | yes | UMD3.1 | 25 | 27138357C>T | Touru et al. (2019): "ARS-UCD1.2-assembly, the variant is located on Chr25:26880841C>T"; "a variant disrupting a canonical 5’ splice donor site (GCA_000003055.3:Chr25:g.27138357C>T) in CCDC189 (transcript - ID:ENSBTAT00000045037) encoding the coiled-coil domain containing protein 189." | 2019 | 30975085 | |||||
| OMIA 001830-9913 | cattle | Holstein | Abortion due to haplotype HH7 | CENPU | deletion, small (<=20) | yes | UMD3.1 | 27 | g.14168130_14168133delTACT | Hozé et al. (2019): "Considering that CENPU is transcribed in the antisense orientation, this mutation is predicted to result in deletion of the nucleotides located at position +3 to + 6 bp after the splicing donor site of exon 11. Using cross-species nucleotide alignment, we observed that the nucleotide at position +3 is entirely conserved among vertebrates . . . , which suggests that it plays an important role in regulation of CENPU splicing. If modified after exon 11, the abnormal splicing of CENPU could cause mRNA decay or the production of a protein modified after residue 319 out of 409 AA. Based on these factors, we assumed that mutation g.14168130_14168133delTACT on chromosome 27 alters the splicing of CENPU and is embryonic lethal." | 2020 | 31733857 | |||||
| OMIA 001502-9913 | cattle | Montbeliarde | Caprine-like Generalized Hypoplasia Syndrome | CEP250 | nonsense (stop-gain) | yes | UMD3.1 | 13 | g.65369074C>T | c.493C>T | p.Q165* | 2015 | 25902731 | Coordinates obtained from and/or confirmed by EBI's VEP | |||
| OMIA 002125-9913 | cattle | Montbeliarde | Neurocristopathy | CHD7 | deletion, small (<=20) | yes | UMD3.1 | 14 | g.28085731_28085735del | p.K594AfsX29 | 2017 | 28904385 | |||||
| OMIA 002022-9913 | cattle | Red Danish | Arthrogryposis multiplex congenita, CHRNB1-related | CHRNB1 | deletion, small (<=20) | yes | c.55delG | p.Ala19Profs47* | 2016 | 27364156 | |||||||
| OMIA 000685-9913 | cattle | Brahman | Myasthenic syndrome, congenital, CHRNE-related | CHRNE | deletion, small (<=20) | yes | UMD3.1 | 19 | g.27119615 | c.448_467del | 2002 | 12481987 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||||
| OMIA 001887-9913 | cattle | Belgian Blue | Osteopetrosis with gingival hamartomas | CLCN7 | missense | yes | c2248T>C + c2250C>A | p. Y750Q | 2014 | 24159188 | |||||||
| OMIA 001135-9913 | cattle | Japanese Black | Renal dysplasia | CLDN16 | Type 1 | deletion, gross (>20) | yes | 37kb deletion of exons 1-4 | 2000 | 10810088 | |||||||
| OMIA 001135-9913 | cattle | Japanese Black | Renal dysplasia | CLDN16 | Type 2 | deletion, gross (>20) | yes | UMD3.1 | 1 | g.77528017_? | "a 56-kb deletion that eliminates exons 1-4 and 21-bp of exon 5" | 2002 | 12047224 | Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 001482-9913 | cattle | Devon | Neuronal ceroid lipofuscinosis, 5 | CLN5 | insertion, small (<=20) | yes | UMD3.1 | 12 | g.52461241insG | c.662insG | p.Arg221GlyfsX6 | 2006 | 16935476 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 002127-9913 | cattle | Red Angus | Osteogenesis imperfecta, type II, COL1A1-related | COL1A1 | missense | yes | ARS-UCD1.2 | 19 | g.36463798G>A | c.1063G>A | p.Gly355Ser | Petersen et al. (2019): "PolyPhen-2 predicted the mutation to be “probably damaging” with a score of 1.000 (sensitivity 0.00; specificity 1.00). Similarly, PROVEAN prediction classified the variant as “Deleterious” with a score of − 4.615, exceeding both the default (− 2.5) and stringent (− 4.1) thresholds for this classification." The genomic coordinate in the UMD3.1 assembly is g.37094333G>A (Petersen et al., 2019). The coding sequence coordinates are c.1063G>A (ENSBTAT00000017420.4) (Petersen, pers. comm.) | ss1342331437356 | 2019 | 30788588 | ||
| OMIA 002127-9913 | cattle | Fleckvieh | Osteogenesis imperfecta, type II, COL1A1-related | COL1A1 | indel, small (<=20) | yes | UMD3.1 | 19 | g.37101299_37101302delinsT | p.A1049_P1050DelInsS | 2017 | 28904385 | |||||
| OMIA 001926-9913 | cattle | Charolais Salers | Bulldog calf | COL2A1 | missense | yes | UMD3.1 | 5 | g.32469820G>A | c.1791G>A | p.G600D | 2017 | 28904385 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001926-9913 | cattle | Holstein | Bulldog calf | COL2A1 | missense | yes | UMD3.1 | 5 | g.32471813G>A | c.2158G>A | p.G720S | 2017 | 28904385 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001926-9913 | cattle | Danish Holstein | bulldog calf | COL2A1 | splicing | yes | UMD3.1 | 5 | g.32473300G>A | c.2463 + 1G>A | 2016 | 27296271 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||||
| OMIA 001926-9913 | cattle | Holstein | Bulldog calf | COL2A1 | missense | yes | UMD3.1 | g.32475732G>A | p.G960R | 2014 | 25017103 | ||||||
| OMIA 001926-9913 | cattle | Holstein | Bulldog calf | COL2A1 | missense | yes | UMD3.1 | 5 | g.32476082G>A | c.2986G>A | p.G996S | rs876243579 | 2017 | 28904385 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 001926-9913 | cattle | Holstein | Bulldog calf | COL2A1 | missense | yes | UMD3.1 | g.32476808G>A | c.3166G>A | p.Gly1056Ser | 2019 | 30378686 | |||||
| OMIA 000341-9913 | cattle | Rotes Höhenvieh Vorderwald | Epidermolysis bullosa, dystrophic | COL7A1 | nonsense (stop-gain) | yes | UMD 3.1 | 22 | g. 51873390C>T | c.4762C>T | p.R1588* | rs876174537 | 2012 | 22715415 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed and some variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 001529-9913 | cattle | Holstein | Dominant red | COPA | DR^DR | missense | no | UMD3.1 | 3 | g.9479761C>T | c.478C>T | p.R160C | 2017 | 28904385 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 002111-9913 | cattle | Red Holstein Friesian | Cataract, recessive, CPAMD8-related | CPAMD8 | nonsense (stop-gain) | yes | UMD 3.1, AC_000164.1 | 7 | g.5995966C>T | c.220C>T | p.Gln74* | 2017 | 28683140 | ||||
| OMIA 002033-9913 | cattle | Numerous breeds | A2 milk | CSN2 | A2 | missense | no | UMD3.1 | 6 | g.87181619A>C | c.245A>C | p.H82P | Note that cattle cannot be genotyped for the A2 allele solely on the basis of the c.245A>C variant because this variant is common to 4 other alleles; see Table 2 of Caroli et al. (2009) J. Dairy Sci. 92, 5335-5352 (Matt McClure, pers. comm.) | rs43703011 | 2013 | 23102962 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool |
| OMIA 001697-9913 | cattle | Jersey | Abortion due to haplotype JH1 | CWC15 | nonsense (stop-gain) | yes | UMD 3.1 | 15 | g.15707169C>T | c.163C>T | p.R55* | 2013 | 23349982 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 002109-9913 | cattle | Brown Swiss | Tricho-dento-osseous-like syndrome | DLX3 | insertion, small (<=20) | yes | NM_001081622 | 19 | g.37298375_37298376insGGAGCACA | c.584_585insGGAGCACAGG | p.Ser198ArgfsTer99 | 2017 | 28670783 | ||||
| OMIA 000543-9913 | cattle | Holstein | Anhidrotic ectodermal dysplasia | EDA | deletion, small (<=20) | yes | "a 19 bp deletion in exon 1" | 2011 | 21410470 | ||||||||
| OMIA 000543-9913 | cattle | Japanese Black | Anhidrotic ectodermal dysplasia | EDA | insertion, small (<=20) | yes | c.280_281insAGGG | 2012 | 22497423 | ||||||||
| OMIA 000543-9913 | cattle | Danish Holstein | Anhidrotic ectodermal dysplasia | EDA | insertion, gross (>20) | yes | UMD3.1 | 13 | g.64234645_64255988del6576ins8 | c.1-21344del6576ins8402 | "a LINE1-derived pseudoexon between EDA exons 1 and 2. The 161-bp-long pseudoexon introduces a shift in reading frame and a premature stop codon early in EDA exon 2" | 2011 | 22034998 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 000543-9913 | cattle | German Holstein | Anhidrotic ectodermal dysplasia | EDA | splicing | yes | UMD3.1 | X | g.85710147G>T | c.924+2G>T | IVS8 +2T>G | 2002 | 12021844 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 000543-9913 | cattle | German Holstein | Anhidrotic ectodermal dysplasia | EDA | deletion, gross (>20) | yes | UMD3.1 | X | g.85821470 | c.397_502de | a large deletion including exon 3 in the gene for ectodysplasin (ED1; now called EDA) | 2001 | 11591646 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 000543-9913 | cattle | French Holstein | Generalized hypohidrotic ectodermal dysplasia | EDA | inversion | yes | UMD_3.1/bosTau6 | X | g.82,271,053_86,034,441inv | Escouflaire et al. (2019): The "first breakpoint . . . [is] between positions 82,271,052 and 82,271,053 bp on chromosome X . . . The second breakpoint is situated at position 86,034,441 bp within the EDA intron 1" | 2019 | 31533624 | |||||
| OMIA 002128-9913 | cattle | Charolais | Anhidrotic ectodermal dysplasia, EDAR-related | EDAR | insertion, small (<=20) | yes | UMD3.1 | 11 | g.44462236_44462237insC | p.P161RfsX97 | 2017 | 28904385 | |||||
| OMIA 001716-9913 | cattle | Holstein | Ehlers-Danlos syndrome, Holstein variant | EPYC | missense | yes | UMD3.1 | 5 | g.20922527 | c.258G>T | p.S87N | 1999 | 10357109 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 000187-9913 | cattle | Japanese Brown | Chondrodysplasia | EVC2 | splicing | yes | c.1356C>T | 2002 | 12136126 | ||||||||
| OMIA 000187-9913 | cattle | Japanese Brown | Chondrodysplasia | EVC2 | indel, small (<=20) | yes | c.2054_2055delCAinsG | 2002 | 12136126 | ||||||||
| OMIA 000187-9913 | cattle | Tyrolean Grey | Chondrodysplasia | EVC2 | deletion, small (<=20) | yes | c.2993delAC | p.Asp998GlufsTer13 | 2014 | 24733244 | |||||||
| OMIA 002042-9913 | cattle | Belgian Blue | Abortion (embryonic lethality), EXOSC4 | EXOSC4 | nonsense (stop-gain) | yes | UMD3.1 | 14 | g.1947890G>A | c.190G>A | p.R64* | 2016 | 27646536 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000363-9913 | cattle | Japanese Black | Factor XI deficiency | F11 | insertion, small (<=20) | yes | UMD3.1 | 27 | g.15362363C>ATATGTGCAGAATATA | c.870insC>ATATGTGCAGAATATA | p.Phe290LeuTyrValGlnAsnIle | "an insertion of 15 nucleotides in exon 9" | 2005 | 16104386 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 000363-9913 | cattle | Holstein Sahiwal | Factor XI deficiency | F11 | insertion, gross (>20) | yes | UMD3.1 | 27 | g.15367048 | c.1406ins76 | a 76-bp insertion in exon 12 of the Factor XI gene | 2004 | 15566468 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 000437-9913 | cattle | German Fleckvieh | Haemophilia A | F8 | missense | yes | UMD3.1 | X | g.38842314A>T | p.His45Leu | ss213751737 | 2018 | 29774585 | ||||
| OMIA 000437-9913 | cattle | Japanese Brown | Haemophilia A | F8 | missense | yes | UMD3.1 | X | g.38971744T>A | c.6458T>A | p.L2153H | 2009 | 19456318 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000151-9913 | cattle | Holstein | Brachyspina | FANCI | deletion, gross (>20) | yes | UMD3.1 | 21 | g.21184870_21188198del | c.526-64495_526-67824del | p.V877Lfs27X | 2012 | 22952632 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000628-9913 | cattle | Limousin | Marfan syndrome | FBN1 | missense | yes | UMD3.1 | 10 | g.62054844G>A | c.3598G>A | p.E1200K | 2005 | 15776436 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000628-9913 | cattle | Japanese Black | Marfan syndrome | FBN1 | splicing | yes | UMD3.1 | 10 | g.62141462 | c.8227-1G>A | 2012 | 22221020 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||||
| OMIA 000836-9913 | cattle | Blonde d'Aquitaine Limousin | Protoporphyria | FECH | extension (stop-lost) | yes | UMD3.1 | 24 | g.57298883G>T | c.1250G>T | p.*417Lext*27 | 1998 | 9784594 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 002090-9913 | cattle | Holstein | Facial dysplasia syndrome | FGFR2 | missense | yes | UMD3.1 | 26 | g.41861956G>T | c.927G>T | p.Trp309Cys | 2017 | 28768473 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001703-9913 | cattle | Holstein | Chondrodysplasia, disproportionate | FGFR3 | extension (stop-lost) | yes | ARS‐UCD1.2 | 6 | g.116,767,863C>A | c.2408G>T | p.(Ter803Leuext*93) | NM_174318.3: c.2408G>T; [XM_024992994.1: p.(Ter803Leuext*93) | 2020 | 32239744 | |||
| OMIA 001360-9913 | cattle | Swedish Red and White | Trimethylaminuria (fishy taint) | FMO3 | nonsense (stop-gain) | yes | UMD 3.1 | 16 | g.39523051C>T | c.712C>T | p.R238* | rs797790546 | 2002 | 12466292 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; rsID gleaned from or confirmed by Table 1 of  Sharma et al. (2017) Animal Genetics 48(3):369-370 | ||
| OMIA 000419-9913 | cattle | Brahman | Glycogen storage disease II | GAA | E13 | nonsense (stop-gain) | yes | UMD 3.1 | 19 | g.53105979C>T | c1783C>T | p.R595* | 2000 | 10723725 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 000419-9913 | cattle | Shorthorn | Glycogen storage disease II | GAA | E18 | deletion, small (<=20) | yes | UMD3.1 | 19 | g.53102004 | c.2454_2455delCA | p.T819R | 2000 | 10723725 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||
| OMIA 000419-9913 | cattle | Brahman Droughtmaster | Glycogen storage disease II | GAA | E7 | deletion, small (<=20) | yes | UMD3.1 | 19 | g.53109436_53109437delAT | c.1057_1058delAT | p.Y353L | 2000 | 10723725 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||
| OMIA 001826-9913 | cattle | Holstein | Abortion due to haplotype HH4 | GART | missense | yes | UMD3.1 | 1 | g.1277227A>C | c.869A>C | p.N290T | rs465495560 | 2013 | 23762392 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 001442-9913 | cattle | Japanese Black | Forelimb-girdle muscular anomaly | GFRA1 | nonsense (stop-gain) | yes | UMD 3.1 | 26 | g.36951312C>T | c.430C>T | p.Q144* | 2013 | Reference not in PubMed; see OMIA 001442-9913 for reference details | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001473-9913 | cattle | Brahman | Dwarfism, growth-hormone deficiency | GH1 | missense | yes | UMD3.1 | 19 | g.48768780C>T | c.593C>T | p.T198M | 2009 | 19524387 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000689-9913 | cattle | Polled Hereford | Myoclonus | GLRA1 | nonsense (stop-gain) | yes | UMD 3.1 | 7 | g.65080197C>A | c.156C>A | p.Y52* | 2001 | 11178872 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001985-9913 | cattle | Fleckvieh | Dwarfism, Fleckvieh | GON4L | deletion, small (<=20) | yes | UMD3.1 | 3 | g.15079217delC | c.4285_4287delCCCinsCC | p.Glu1430LysfsX66 | rs723240647 | 2016 | 27036302 | Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||
| OMIA 002230-9913 | cattle | Belted Galloway | Hypotrichosis | HEPHL1 | nonsense (stop-gain) | yes | UMD 3.1 | 29 | g.695072A>T | c.1684A>T | p.K562* | 2012 | Reference not in PubMed; see OMIA 002230-9913 for reference details | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000317-9913 | cattle | Highland | Ears, crop | HMX1 | insertion, gross (>20) | no | 76bp duplication of 106,720058 to 106,720,133 on BTA6; UMD3 reference assembly | 2013 | 24194898 | ||||||||
| OMIA 001319-9913 | cattle | Holstein-Friesian | Myopathy of the diaphragmatic muscles | HSPA1A | deletion, gross (>20) | yes | 23 | Deletion of one of two HSP70 (heat-shock protein) genes in the bovine major histocompatibility complex | 2003 | 12755819 | |||||||
| OMIA 001817-9913 | cattle | Japanese Black | Perinatal weak calf syndrome | IARS | missense | yes | UMD3.1 | 8 | g.85341291G>C | c.235G>C | p.V79L | 2013 | 23700453 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000595-9913 | cattle | Fleckvieh Holstein-Friesian Jersey | Leukocyte adhesion deficiency, type I | ITGB2 | missense | yes | UMD3.1 | 1 | g.145114963A>G | c.383A>G | p.D128G | rs445709131 | 1992 | 1384046 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 001948-9913 | cattle | Charolais | Epidermolysis bullosa, junctionalis, ITGB4 | ITGB4 | deletion, gross (>20) | yes | "a 4.4 kb deletion involving exons 17 to 22" of the ITGB4 gene | 2015 | 25890340 | ||||||||
| OMIA 001722-9913 | cattle | Romagnola | Lethal multi-organ developmental dysplasia | KDM2B | missense | yes | UMD3.1 | 17 | g.56010031G>A | c.2503G>A | p.D835N | 2012 | 23029151 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000939-9913 | cattle | Braunvieh | Spinal muscular atrophy | KDSR | missense | yes | UMD3.1 | 24 | g.62138763G>A | c.562G>A | p.A188T | 2007 | 17420465 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000527-9913 | cattle | Charolais | Progressive ataxia | KIF1C | missense | yes | UMD3.1 | 19 | g.27041449C/T | c.608G>A | p.R203Q; p.RT203-204QStop | Duchesne et al. (2018): "Using a combination of next generation sequencing and whole genome SNP analysis, we determined that in the majority of cases with this phenotype, the disease is caused by a single substitution, c.608G>A, in the KIF1C gene. This substitution has two effects: firstly, it modifies a conserved amino acid (p.R203Q). Secondly, it causes an alternative splicing event, resulting in exon 5 skipping in most of the transcripts (p.RT203-204QStop) associated with a drastic reduction of overall mRNA expression and leading to the absence of detectable KIF1C protein in brain extracts from affected cattle." | 2018 | 30067756 | |||
| OMIA 000426-9913 | cattle | Northern Finncattle Swedish Mountain | Gonadal hypoplasia | KIT | cs(29) | complex rearrangement | yes | "gonadal hypoplasia in Northern Finncattle and Swedish Mountain cattle is associated with a complex chromosomal rearrangement including a ~500kb duplicated segment from BTA6 which is translocated to BTA29. This duplicated segment includes the entire coding sequence of the KIT gene" | 2013 | 24086604 | |||||||
| OMIA 001576-9913 | cattle | Belgian Blue British White Park Brown Swiss Galloway | Coat colour, colour-sided | KIT | Cs(29) | complex rearrangement | no | Durkin et al. (2012): "colour sidedness is determined by a first allele on chromosome 29 (Cs(29)), which results from the translocation of a 492-kilobase chromosome 6 segment encompassing KIT to chromosome 29, and a second allele on chromosome 6 (Cs(6)), derived from the first by repatriation of fused 575-kilobase chromosome 6 and 29 sequences to the KIT locus. We provide evidence that both translocation events involved circular intermediates. This is the first example, to our knowledge, of a phenotype determined by homologous yet non-syntenic alleles that result from a novel copy-number-variant-generating mechanism." | 2012 | 22297974 | |||||||
| OMIA 001576-9913 | cattle | Belgian Blue Brown Swiss | Coat colour, colour-sided | KIT | Cs(6) | complex rearrangement | no | Durkin et al. (2012): "colour sidedness is determined by a first allele on chromosome 29 (Cs(29)), which results from the translocation of a 492-kilobase chromosome 6 segment encompassing KIT to chromosome 29, and a second allele on chromosome 6 (Cs(6)), derived from the first by repatriation of fused 575-kilobase chromosome 6 and 29 sequences to the KIT locus. We provide evidence that both translocation events involved circular intermediates. This is the first example, to our knowledge, of a phenotype determined by homologous yet non-syntenic alleles that result from a novel copy-number-variant-generating mechanism." | 2012 | 22297974 | |||||||
| OMIA 001737-9913 | cattle | Brown Swiss | White spotting | KIT | deletion, gross (>20) | no | ARS1‐UCD1.2 | 6 | g.70239551_70239590del | c.1390_1429del | p.(Asn464AlafsTer50) | "NC_037333.1:g.70239551_70239590del; NM_001166484.1:c.1390_1429del; NP_001159956.1:p.(Asn464AlafsTer50)" (Häfliger et al., 2020) | 2020 | 32065668 | |||
| OMIA 001737-9913 | cattle | British Gloucester Eringer Evolèner Pinzgauer Slovenian Cika Spanish Berrenda en negro Tux-Zillertaler | Pinzgauer spotting | KIT | KIT^PINZ | complex rearrangement | no | ARS‐UCD1.2 | 6 | Briefly: the KIT^PINZ variant is "characterized by the fusion of a duplicated chromosome 4 segment into a deleted part of chromosome 6." (Küttel et al., 2019) In more detail: "a complex structural variant characterized by a ~9.4‐kb deletion . . . and in silico evidence for a duplication of ~1.5 kb about 34 kb farther downstream . . . . Apparently, the duplicated copy of the ~1.5‐kb segment appears inversely inserted at the upstream breakpoint of the ~9.4‐kb deletion . . . . Furthermore, we noticed at the upstream breakpoint of the inversely inserted segment chimeric read pairs in which both ends mapped to chromosome 6 and 4 . . . . The inspection of the sequence coverage of the involved genome region on chromosome 4 indicated a ~310‐kb duplication from 84 864 544 to ~85 174 000 bp". (Küttel et al., 2019) | 2019 | 31294880 | |||||
| OMIA 001216-9913 | cattle | Belgian Blue Shorthorn | Roan | KITLG | missense | no | UMD3.1 | 5 | g.18339001 | c.572C>A | p.A191N | 1999 | 10384045 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 000246-9913 | cattle | Ayrshire Fleckvieh German Angus Montbeliarde | Curly hair, karakul-type | KRT27 | missense | no | UMD3.1 | 19 | g.41636961C>G | c.276C>G | p.Asn92Lys | rs384881761 | 2014 | 25017103 | Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||
| OMIA 002081-9913 | cattle | Friesian-Jersey mosaic | Epidermolysis bullosa | KRT5 | missense | yes | UMD3.1 | 5 | g.27545478G>A | c.1432G>A | p.E478K | 2005 | 15955091 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 002114-9913 | cattle | Hereford | Hypotrichosis, KRT71-related | KRT71 | deletion, small (<=20) | yes | UMD3.1 | 5 | g.27505486delTGTGCCCA | c.334delTGTGCCCA | p.Met93AsnfsX14 | 2010 | Reference not in PubMed; see OMIA 002114-9913 for reference details | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001677-9913 | cattle | Belgian Blue | Epidermolysis bullosa, junctionalis, LAMA3-related | LAMA3 | nonsense (stop-gain) | unknown | UMD3.1 | 24 | g.33111473C>T | c.7549C>T | p.R2517* | 2015 | 26370913 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001678-9913 | cattle | Hereford | Epidermolysis bullosa, junctionalis, LAMC2 | LAMC2 | deletion, gross (>20) | yes | "2.4 kb deletion encompassing the first exon of the LAMC2 gene" | 2015 | 25888738 | ||||||||
| OMIA 001451-9913 | cattle | Belgian Blue | Congenital muscular dystonia 2 | LOC528050 | missense | yes | UMD3.1 | 29 | g.24610495T>C | c.809T>C | p.L270P | 2008 | 18344998 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000963-9913 | cattle | Angus | Syndactyly (mule foot) | LRP4 | splicing | yes | UMD3.1 | 15 | g.77667136 | c.5385+1G>A | "a G to A transition at the first nucleotide in the splice donor site of intron 37" | 2006 | 16963222 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 000963-9913 | cattle | German Simmental Holstein | Syndactyly (mule foot) | LRP4 | missense | yes | UMD3.1 | 15 | g.77675440 | c.4940C>T | p.Pro1647Leu | rs109636878 | 2007 | 17319939 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446; rsID gleaned from or confirmed by Table 1 of  Sharma et al. (2017) Animal Genetics 48(3):369-370 | ||
| OMIA 000963-9913 | cattle | Holstein | Syndactyly (mule foot) | LRP4 | indel, small (<=20) | yes | UMD3.1 | 15 | g.77675516_77675517delCGinsAT | c.4840_4841delCGinsAT | p.(Asn1614_Gly1615delinsLysCys | 2006 | 16859890 | Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000963-9913 | cattle | German Simmental Holstein | Syndactyly (mule foot) | LRP4 | missense | yes | UMD3.1 | 15 | g.77682052G>A | c.3571G>A | p.Gly1191Ser | 2007 | 17319939 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000963-9913 | cattle | German Simmental Holstein | Syndactyly (mule foot) | LRP4 | missense | yes | UMD3.1 | 15 | g.77686731G>A | c.2719G>A | p.Gly907Arg | 2007 | 17319939 | Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000185-9913 | cattle | Japanese Black | Chediak-Higashi syndrome | LYST | missense | yes | UMD3.1 | 28 | g.8508619A>G | c.6044A>G | p.H2015R | 1999 | 10594238 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000625-9913 | cattle | Galloway | Mannosidosis, alpha | MAN2B1 | missense | yes | UMD3.1 | 7 | g.13956640G>A | c.662G>A | p.R221H | 1997 | 9208932 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 000625-9913 | cattle | Angus Murray Grey | Mannosidosis, alpha | MAN2B1 | missense | yes | UMD3.1 | 7 | g.13957949T>C | c.961T>C | p.F321L | 1997 | 9208932 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000626-9913 | cattle | Salers | Mannosidosis, beta | MANBA | nonsense (stop-gain) | yes | UMD 3.1 | 6 | g.23540228G>A | c.2574G>A | p.W858* | 1999 | 10594236 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001544-9913 | cattle | Rat-tail syndrome | MC1R | E^D | missense | no | UMD3.1 | 18 | g.14,757,910T>C | c.296T>C | p.L99P | rs109688013 | 2016 | 27037038 | |||
| OMIA 001199-9913 | cattle | Angus Holstein-Friesian Icelandic | Dominant black | MC1R | E^D | missense | no | UMD3.1 | 18 | g.14757910T>C | c.296T>C | p.L99P | rs109688013 | 1995 | 8535072 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |
| OMIA 001199-9913 | cattle | Angus Fleckvieh Red Friesian | Recessive red | MC1R | e | deletion, small (<=20) | no | UMD3.1 | 18 | g.14757924delG | c.310delG | p.Gly104ValfsX53 | rs110710422 | 1995 | 8535072 | Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |
| OMIA 002043-9913 | cattle | Belgian Blue | Abortion (embryonic lethality), MED22-related | MED22 | deletion, small (<=20) | yes | p.Leu38Argfs∗25 | 2016 | 27646536 | ||||||||
| OMIA 001106-9913 | cattle | Tyrolean Grey | Axonopathy | MFN2 | splicing | yes | UMD3.1 | 16 | g.42562057C>T | c.2229C>T | "This SNP is located within a putative exonic splice enhancer (ESE) and the variant allele leads to partial retention of the entire intron 19 and a premature stop codon in the aberrant MFN2 transcript" | 2011 | 21526202 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001565-9913 | cattle | Finnish Ayrshire | Abortion and stillbirth due to mutation in MIMT1 | MIMT1 | deletion, gross (>20) | yes | a 110 kb deletion in the MIMT1 gene | 2010 | 21152099 | ||||||||
| OMIA 001931-9913 | cattle | Holstein | Depigmentation associated with microphthalmia | MITF | deletion, gross (>20) | yes | a de novo deletion of a 19.1 Mb region of BTA22 from 28 835 247-47 983 179 | 2014 | 25199536 | ||||||||
| OMIA 001680-9913 | cattle | German Fleckvieh | Dominant white with bilateral deafness | MITF | missense | yes | UMD3.1 | 22 | g.31746502G>T | c.629G>T | p.R210I | 2011 | 22174915 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001680-9913 | cattle | Holstein | Glass-eyed albino | MITF | deletion, small (<=20) | yes | UMD3.1 | 22 | g.31746506_31746508del | p.R211del | 2017 | 28904385 | |||||
| OMIA 000214-9913 | cattle | Holstein Simmental | White spotting | MITF | regulatory | no | UMD3.1 | 22 | g.31769189A>T | c.33+112A>T | 2012 | 22486495 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||||
| OMIA 000214-9913 | cattle | Brown Swiss | White spotting | MITF | regulatory | no | UMD_3.1.1 | 22 | g.31790063G>A | c.104+53185C>T | FN 190425: The Ensembl entry for rs722765315 lists two transcripts: ENSBTAT00000067269.1:c.104+53185C>T and ENSBTAT00000076082.1:c.-53+31498C>T | rs722765315 | 2019 | 30506810 | |||
| OMIA 000031-9913 | cattle | Belgian Blue | Coat colour, cool gray | MLPH | deletion, small (<=20) | no | c.87_96del | p.Glu32Aspfs*1 | 2016 | 26582259 | |||||||
| OMIA 001819-9913 | cattle | Japanese Black | Xanthinuria, type II | MOCOS | deletion, small (<=20) | yes | c.769_771delTAC | 2000 | 10801779 | ||||||||
| OMIA 001819-9913 | cattle | Tyrolean Grey | Xanthinuria, type II | MOCOS | deletion, small (<=20) | yes | g.21222030delC | c.1881delG and c.1782delG | p.Ser628Valfs9* and p.Ser595Va | 2016 | 27919260 | ||||||
| OMIA 001541-9913 | cattle | Fleckvieh Simmental | Arachnomelia, BTA23 | MOCS1 | deletion, small (<=20) | yes | UMD3.1 | 23 | g.13833868_13833869delCA | c.1224_1225delCA | rs3835008433 | 2011 | 21255426 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 001452-9913 | cattle | Belgian Blue | Tail, crooked | MRC2 | missense | yes | UMD3.1 | 19 | g.47734925T>G | c.1906T>G | p.C636G | rs466131011 | 2012 | 22497452 | Breed and some variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 001452-9913 | cattle | Belgian Blue | Tail, crooked | MRC2 | deletion, small (<=20) | yes | UMD3.1 | 19 | g.47740473delAG | c.2904-2905delAG | p.Gly934X | 2009 | 19779552 | Breed and some variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000683-9913 | cattle | Maine Anjou | Muscular hypertrophy (double muscling) | MSTN | D182N | missense | yes | p.D182N | 2002 | Reference not in PubMed; see OMIA 000683-9913 for reference details | |||||||
| OMIA 000683-9913 | cattle | Angus Limousin | Muscular hypertrophy (double muscling) | MSTN | missense | yes | UMD 3.1 | 2 | g.6213980A>C | c.282C>A | p.Phe94Leu | rs110065568 | 1998 | 9501304 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 000683-9913 | cattle | Blonde d'Aquitaine Charolais Limousin | Muscular hypertrophy (double muscling) | MSTN | nonsense (stop-gain) | yes | UMD 3.1 | 2 | g.6216138C>T | c.610C>T | p.Q204* | rs110344317 | 1998 | 9501304 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 000683-9913 | cattle | Maine Anjou Marchigiana | Muscular hypertrophy (double muscling) | MSTN | nonsense (stop-gain) | yes | UMD 3.1 | 2 | g.6216204G>T | c.676G>T | p.E226* | 1998 | 9501304 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000683-9913 | cattle | Maine Anjou Marchigiana | Muscular hypertrophy (double muscling) | MSTN | nonsense (stop-gain) | yes | UMD 3.1 | 2 | g.6218432G>T | c.1004G>T | p.E291* | 2013 | 22497537 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000683-9913 | cattle | Gelbvieh | Muscular hypertrophy (double muscling) | MSTN | missense | yes | UMD3.1 | 2 | g.6213889T>C | c.191T>C | p.L64P | rs449270213 | 2015 | 25515003 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 000683-9913 | cattle | Parthenaise | Muscular hypertrophy (double muscling) | MSTN | missense | yes | UMD3.1 | 2 | g.6214012C>G | c.314C>G | p.Ser105Cys | 2002 | Reference not in PubMed; see OMIA 000683-9913 for reference details | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000683-9913 | cattle | Maine Anjou | Muscular hypertrophy (double muscling) | MSTN | nt419(del7-ins10) | indel, small (<=20) | yes | UMD3.1 | 2 | g.6215947 | c.419_425del7, c418_426ins10 | an insertion/deletion in which 10 unrelated bases are inserted in the place a 7 bases that have been deleted at nucleotide 418 | 1998 | 9501304 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||
| OMIA 000683-9913 | cattle | Angus Asturiana Belgian Blue Blonde d'Aquitaine Braford Limousin Murray Grey Parthenaise Santa Gertrudis South Devon | Muscular hypertrophy (double muscling) | MSTN | deletion, small (<=20) | yes | UMD3.1 | 2 | g.6218379delATGAACACTCC | c.821-831delTGAACACTCCA | p.Glu275ArgfsX14 | 1997 | 9288100 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000683-9913 | cattle | Gasconne Parthenaise Piedmontese | Muscular hypertrophy (double muscling) | MSTN | missense | yes | UMD3.1 | 2 | g.6218499G>A | c.938G>A | p.C313Y | 1997 | 9314496 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001978-9913 | cattle | Swiss Holstein | Arthrogryposis, distal, type 1B | MYBPC1 | missense | yes | UMD3.1 | 5 | g.65787153T>G | c.884T>G | p.L295R | 2015 | 26289121 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 002039-9913 | cattle | Belgian Blue | Abortion (embryonic lethality), MYH6-related | MYH6 | deletion, small (<=20) | yes | p.Lys1730del | 2016 | 27646536 | ||||||||
| OMIA 001342-9913 | cattle | Mucopolysaccharidosis IIIB | NAGLU | missense | yes | UMD3.1 | 19 | g.43264699G>A | c.1354G>A | p.E452K | 2007 | 17458708 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||||
| OMIA 002103-9913 | cattle | Angus | Developmental duplications | NHLRC2 | missense | yes | UMD3.1 | 26 | g.34618072T>C | c.932T>C | p.V311A | 2014 | Reference not in PubMed; see OMIA 002103-9913 for reference details | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001936-9913 | cattle | Romagnola | Cataract, recessive, Romagnola | NID1 | deletion, gross (>20) | yes | "an 855 bp deletion across the exon 19/intron 19 border of the bovine nidogen 1 (NID1) gene (c.3579_3604+829del)" | 2014 | 25347398 | ||||||||
| OMIA 002035-9913 | cattle | Jersey | Abortion (embryonic lethality), OBFC1-related | OBFC1 | deletion, small (<=20) | yes | 26 | g.24720155_24720156delAA | c.379_380delAA | p.Lys127Valfs∗28 | 2016 | 27646536 | |||||
| OMIA 000162-9913 | cattle | Red Holstein | Cardiomyopathy, dilated | OPA3 | nonsense (stop-gain) | yes | UMD 3.1 | 18 | g.53546443C>T | c.343C>T | p.Q115* | 2011 | 20923700 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001437-9913 | cattle | Brown Swiss | Beta-lactoglobulin, aberrant low expression | PAEP | regulatory | yes | UMD3.1 | 11 | g.103301704 | c.-215C>A | "C to A transversion at position 215 bp upstream of the translation initiation site" | 2006 | 17033029 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 001827-9913 | cattle | Montbeliarde Vorderwald | Abortion due to haplotype MH1 | PFAS | missense | yes | UMD3.1 | 19 | g.28511199C>T | c.3613C>T | p.R1205C | rs455876205 | 2017 | 28803020 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 001953-9913 | cattle | Belgian Blue | Arthrogryposis, lethal syndrome | PIGH | splicing | yes | UMD3.1.1 | 10 | g.79814520C>G | c.211-10C>G | rs451004237 | 2015 | 25895751 | Variant information gleaned from or confirmed by Table 1 of  Sharma et al. (2017) Animal Genetics 48(3):369-370 | |||
| OMIA 001935-9913 | cattle | Fleckvieh | Zinc deficiency-like syndrome | PLD4 | nonsense (stop-gain) | yes | UMD3.1 | 21 | g.71001232G>A | c.702G>A | p.W234* | rs378824791 | 2014 | 25052073 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; rsID gleaned from or confirmed by Table 1 of  Sharma et al. (2017) Animal Genetics 48(3):369-370 | ||
| OMIA 001544-9913 | cattle | Rat-tail syndrome | PMEL | deletion, small (<=20) | unknown | UMD3.1 | 5 | g.57,669,913_57,669,915delTTC | c.50_52delTTC | p.Leu19del | rs385468954 | 2016 | 27037038 | ||||
| OMIA 001545-9913 | cattle | Charolais Galloway Hereford Highland Simmental | Coat colour, dilution | PMEL | deletion, small (<=20) | no | UMD3.1 | 5 | g.57669913_57669915delTTC | c.50_52delTTC | p.Leu19del | rs385468954 | 2008 | 18408794 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 001545-9913 | cattle | Charolais | Coat colour, dilution | PMEL | missense | no | UMD3.1 | 5 | g.57669926G>A | c.64G>A | p.Gly22Arg | rs718553050 | 2007 | 17705851 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 000827-9913 | cattle | Brown Swiss Carora | Progressive degenerative myeloencephalopathy (Weaver syndrome) | PNPLA8 | missense | yes | UMD3.1 | 4 | g.49878773G>A | c.1703G>A | p.S568N | rs800397662 | 2016 | 26992691 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 000483-9913 | cattle | Nellore | Polled, Guarani | POLLED | P[sub]G | duplication | no | ARS-UCD1.2 | 1 | g.2614828_2724315dup | "a novel duplication variant" in the region BTA1:1,893,790–2,004,553 (Utsunomiya et al., (2019) | 2019 | 30644114 | Randhawa et al. (2019): ARS-UCD1.2 g.2614828_2724315dup | |||
| OMIA 000483-9913 | cattle | Friesian | Polled, Friesian | POLLED | P[sub]F OR P(sub)80kbID | duplication | no | ARS-UCD1.2 | 1 | g.2629113_2709240dup | 2013 | 23717440 | In relation to assembly UMD v3.1.1, Utsunomiya et al. (2019) described this variant as "a duplication of CHR1:1,909,352–1,989,480". Randhawa et al. (2019): ARS-UCD1.2 g.2629113_2709240dup | ||||
| OMIA 000483-9913 | cattle | Polled, Celtic | POLLED | P[sub]C OR P[sub]202ID | complex rearrangement | no | ARS-UCD1.2 | 1 | g.[22429326_2429335del;2429109_2429320dupins] | UMD3.1: g.1706051_1706060 delins170583 | 2012 | 22737241 | Randhawa et al. (2019) ARS-UCD1.2 g.[22429326_2429335del;2429109_2429320dupins] | ||||
| OMIA 000483-9913 | cattle | Mongolian Turano | Polled, Mongolian | POLLED | P[sub]M OR P[sub]219ID | complex rearrangement | no | ARS-UCD1.2 | 1 | g.[2695261_2695267delinsTCTGAA;2695889_2696047dupins] | "a complex 219-bp duplication-insertion (P219ID) beginning at 1,976,128 bp and a 7-bp deletion and 6-bp insertion (P1ID) located 621 bp upstream of this position . . . . This rearrangement results in duplication of an 11-bp motif (5'-AAAGAAGCAAA-3') that is entirely conserved among Bovidae . . . and that is also duplicated in the 80-kb duplication responsible for Friesian polledness" In relation to assembly UMD v3.1.1, Utsunomiya et al. (2019) described this variant as "a complex duplication starting at CHR1:1,976,128". | 2017 | 28135247 | Randhawa et al. (2019): ARS-UCD1.2 g.[2695261_2695267delinsTCTGAA;2695889_2696047dupins] | |||
| OMIA 000161-9913 | cattle | Polled Hereford | Cardiomyopathy and woolly haircoat syndrome | PPP1R13L | insertion, small (<=20) | yes | UMD3.1 | 18 | g.53440861-53440867dupACAGGCG | c.956-962dupACAGGCG | p.Gly335GlufsX36 | 2009 | 19016676 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001485-9913 | cattle | Angus | Dwarfism, Angus | PRKG2 | nonsense (stop-gain) | yes | UMD 3.1 | 6 | g.97667351C>T | c.1573C>T | p.R525* | rs109639251 | 2009 | 19887637 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 001485-9913 | cattle | Angus | Dwarfism, Angus | PRKG2 | nonsense (stop-gain) | yes | UMD3.1 | 6 | g.97667351 | c.2032C>T | p.R678* | 2009 | 19887637 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 000441-9913 | cattle | Fleckvieh Holstein-Friesian Jersey | Hairy | PRL | missense | no | UMD3.1 | 23 | g.35105313A>C | c.661A>C | p.C221G | 2014 | 25519203 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001372-9913 | cattle | Carora Romosinuano Senepol | Slick hair | PRLR | deletion, small (<=20) | no | UMD3.1 | 20 | g.39136559delC | p.Leu462* | ss1067289408 | 2014 | 25519203 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; some variant information gleaned from or confirmed by Table 1 of  Sharma et al. (2017) Animal Genetics 48(3):369-370 | |||
| OMIA 001372-9913 | cattle | Limonero | Slick hair | PRLR | nonsense (stop-gain) | no | UMD3.1 | 20 | g.39136571C>A | p.Ser465∗ | 2018 | 29527221 | |||||
| OMIA 001372-9913 | cattle | Carora Limonero | Slick hair | PRLR | nonsense (stop-gain) | no | UMD3.1 | 20 | g.39136666C>T | p.Arg497∗ | 2018 | 29527221 | |||||
| OMIA 000944-9913 | cattle | Numerous breeds | Spongiform encephalopathy (mad cow disease) | PRNP | missense | yes | UMD3.1 | 13 | g.47415059G>A | c.631G>A | p.E211K | 2008 | 18787697 | Genomic coordinates obtained from EBI's VEP | |||
| OMIA 001139-9913 | cattle | Charolais | Glycogen storage disease V | PYGM | missense | yes | UMD3.1 | 29 | g.43611783 | c.1468C>T | p.R490W | 1996 | 8845714 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 002037-9913 | cattle | Holstein-Friesian | Abortion (embryonic lethality), RABGGTB | RABGGTB | missense | yes | UMD3.1 | 3 | g.69318970A>G | c.584A>G | p.Y195C | 2016 | 27646536 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001003-9913 | cattle | Fleckvieh Simmental | Thrombopathia | RASGRP2 | missense | yes | UMD3.1 | 29 | g.43599204T>C | c.701T>C | p.L234P | rs385444696 | 2007 | 18039909 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 001901-9913 | cattle | Nordic Red | Abortion due to deletion of RNASEH2B | RNASEH2B | deletion, gross (>20) | yes | A 662kb deletion encompases the gene RNASEH2B, lack of which creates embryonic lethality | 2014 | 24391517 | ||||||||
| OMIA 001686-9913 | cattle | Belgian Blue | Dwarfism, proportionate, with inflammatory lesions | RNF11 | splicing | yes | UMD3.1 | 3 | g.95601696A>G | c.124-2A>G | 2012 | 22438830 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||||
| OMIA 002038-9913 | cattle | Holstein-Friesian | Abortion (embryonic lethality), RNF20 | RNF20 | nonsense (stop-gain) | yes | UMD3.1 | 8 | g.92930920A>T | c.2077A>T | p.K693* | 2016 | 27646536 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 002223-9913 | cattle | Holstein | Interdigital hyperplasia | ROR2 | missense | yes | ARS-UCD1.2 | 8 | g.85,905,534T>A | p.(Trp9Arg) | Zhang et al. (2019): "NC_037335.1:g.85,905,534T>A, ARS-UCD1.2; ENSBTAP00000053765.2:p.Trp9Arg; rs377953295" | rs377953295 | 2019 | 31798639 | |||
| OMIA 002029-9913 | cattle | Angus Beef Booster Composite Belgian Blue Charolais Gelbvieh Holstein Maine Anjou Normande Red Angus | Retinitis pigmentosa 1 | RP1 | insertion, small (<=20) | yes | UMD3.1 | 14 | g.23995411_23995412insA | p. R791KfsX13 | 2016 | 27510606 | |||||
| OMIA 002134-9913 | cattle | Ayrshire | Abortion due to haplotype AH2 | RPAP2 | splicing | yes | 3 | g.51267548 | 2017 | Reference not in PubMed; see OMIA 002134-9913 for reference details | |||||||
| OMIA 002041-9913 | cattle | Belgian Blue | Abortion (embryonic lethality), RPIA-related | RPIA | splicing | yes | UMD3.1 | 11 | g.47223666 | c.826+1G>A | 2016 | 27646536 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||||
| OMIA 002149-9913 | cattle | Holstein | Abortion due to haplotype HH6 | SDE2 | start-lost | yes | UMD3.1 | 16 | g.29773628A>G | "This A-to-G transition changes the initiator ATG (methionine) codon to ACG because the gene is transcribed on the reverse strand. . . . Initiation of translation at the closest in-frame Met codon would truncate SDE2 by 83 amino acids, including an 8-amino acid motif conserved among eukaryotes" | rs434666183 | 2018 | 29680649 | ||||
| OMIA 002053-9913 | cattle | Japanese Black | Hydrallantois | SLC12A1 | missense | yes | UMD3.1 | 10 | g.62382825G > A | p.P386L | 2016 | 27613513 | |||||
| OMIA 002150-9913 | cattle | Rouge-des-Prés | Syndrome des veaux tourneurs (Turning calves syndrome) | SLC25A46 | missense | yes | UMD3.1 | 7 | g.112337413C>T | c.376C>T | p.Arg126Cys | 2017 | 28376083 | ||||
| OMIA 000366-9913 | cattle | Braunvieh Fleckvieh | Fanconi syndrome | SLC2A2 | indel, small (<=20) | yes | UMD3.1 | 1 | g.97239973_97239976delTTGAAAAG | c.771_778delTTGAAAAGinsCATC | rs379675307 | 2016 | 27169150 | Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 001958-9913 | cattle | Fleckvieh | Abortion due to haplotype FH2 | SLC2A2 | indel, small (<=20) | yes | UMD3.1 | 1 | g.97239973_97239976delTTGAAAAG | c.771_778delTTGAAAAGinsCATC | rs379675307 | 2015 | 25927203 | Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 001340-9913 | cattle | Friesian Holstein | Complex vertebral malformation | SLC35A3 | missense | yes | UMD3.1 | 3 | g.43412427G>T | c.538G>T | p.V180F | rs438228855 | 2006 | 16344554 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 001828-9913 | cattle | Montbeliarde Vorderwald | Abortion due to haplotype MH2 | SLC37A2 | nonsense (stop-gain) | yes | UMD 3.1 | 29 | g.28879810C>T | c.34C>T | p.R12* | ss2019324563 | 2013 | 23762392 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 000593-9913 | cattle | Holstein | Acrodermatitis enteropathica | SLC39A4 | splicing | yes | UMD3.1 | 14 | g.1723330 | c.1645+1G>A | "a single nucleotide mutation of the splice donor site in intron 10" | 2006 | 16714095 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 001821-9913 | cattle | Braunvieh | Coat colour, albinism, oculocutaneous type IV | SLC45A2 | missense | yes | UMD3.1 | 20 | g.39829806G>A | c.134G>A | p.R45Q | Important note by Rothammer et al. (2017): "To determine which of the two mutations or even if the combination of both is causal for oculocutaneous albinism in Braunvieh, it would be necessary to produce additional cases and investigate them more precisely" | 2017 | 28982372 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 001821-9913 | cattle | Braunvieh | Coat colour, albinism, oculocutaneous type IV | SLC45A2 | missense | yes | UMD3.1 | 20 | g.39864148C>T | c.1331C>T | p.T444I | Important note by Rothammer et al. 92017): "To determine which of the two mutations or even if the combination of both is causal for oculocutaneous albinism in Braunvieh, it would be necessary to produce additional cases and investigate them more precisely" | 2017 | 28982372 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 001228-9913 | cattle | Japanese Black | Spherocytosis | SLC4A1 | nonsense (stop-gain) | yes | UMD3.1 | 19 | g.44695843 | c.1990C>T | p.R664* | 1996 | 8621763 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 000755-9913 | cattle | Angus Friesian Hereford Holstein Simmental | Osteopetrosis | SLC4A2 | deletion, gross (>20) | yes | UMD3.1 | 4 | g.114437192_114439942del | "approximately 2.8-kb deletion mutation in affected calves that encompasses exon 2 and nearly half of exon 3" | 2010 | 20507629 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||||
| OMIA 001824-9913 | cattle | Friesian Holstein | Abortion due to haplotype HH3 | SMC2 | missense | yes | UMD3.1 | 8 | g.95410507T>C | c.3404T>C | p.F1135S | rs456206907 | 2014 | 24667746 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||
| OMIA 002040-9913 | cattle | Belgian Blue | Abortion (embryonic lethality), SNAPC4-related | SNAPC4 | deletion, small (<=20) | yes | p.Leu1227Alafs*134 | 2016 | 27646536 | ||||||||
| OMIA 001247-9913 | cattle | American Brown Swiss | Spinal dysmyelination | SPAST | missense | yes | UMD3.1 | 11 | g.14760164G>A | c.1964G>A | p.R560Q | rs445770480 | 2010 | 19714378 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 001230-9913 | cattle | Japanese Black | Ovotesticular DSD (Disorder of Sexual Development) | SRY | deletion, gross (>20) | yes | Y | A deletion of the SRY gene | 1996 | 8978769 | |||||||
| OMIA 001960-9913 | cattle | Fleckvieh | Abortion due to haplotype FH4 | SUGT1 | missense | yes | UMD3.1 | 12 | g.11131497T>C | c.949T>C | p.W317R | rs110793536 | 2015 | 25927203 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 000059-9913 | cattle | Brown Swiss | Arachnomelia, BTA5 | SUOX | insertion, small (<=20) | yes | UMD3.1 | 5 | g.57641332-57641333insG | c.363-364insG | p.Ala124GlyfsX42 | 2010 | 20865119 | Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 001951-9913 | cattle | Holstein | Vertebral and spinal dysplasia | T | missense | yes | UMD3.1 | 9 | g.102675827A>G | c.196A>G | p.K66E | 2015 | 25614605 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001941-9913 | cattle | Holstein | Abortion due to haplotype HH5 | TFB1M | complex rearrangement | yes | "a deletion of 138kbp, spanning position 93,233kb to 93,371kb on chromosome 9 (BTA9), harboring only dimethyl-adenosine transferase 1 (TFB1M). The deletion breakpoints are flanked by bovine long interspersed nuclear elements Bov-B (upstream) and L1ME3 (downstream), suggesting a homologous recombination/deletion event." | 2016 | 27128314 | ||||||||
| OMIA 000424-9913 | cattle | Afrikander | Goitre, familial | TG | nonsense (stop-gain) | yes | UMD 3.1 | 14 | g. 9487845C>T | c.1963C>T | p.R655* | rs480120030 | 1987 | 3472203 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 001902-9913 | cattle | Fleckvieh | Male subfertility | TMEM95 | nonsense (stop-gain) | yes | UMD3.1 | 19 | g.27689622C>A | c.483C>A | p.Cys161* | rs378652941 | 2014 | 24391514 | Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||
| OMIA 000542-9913 | cattle | Pezzata Rossa | Hypotrichosis, streaked | TSR2 | splicing | yes | UMD3.1 | X | g.97363937A>G | c.441+226A>G | 2015 | 26203908 | Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | ||||
| OMIA 002036-9913 | cattle | Holstein-Friesian | Abortion (embryonic lethality), TTF1 | TTF1 | nonsense (stop-gain) | yes | UMD3.1 | 11 | g.102498942G>A | c.1579G>A | p.R527* | rs715966442 | 2016 | 27646536 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | ||
| OMIA 001939-9913 | cattle | Brown Swiss | Abortion due to haplotype BH2 | TUBD1 | missense | yes | UMD3.1 | 19 | g.11063520T>C | c.757T>C | p.H210R | rs383232842 | 2016 | 27225349 | Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||
| OMIA 001593-9913 | cattle | Charolais | Scurs, type 2 | TWIST1 | insertion, small (<=20) | no | UMD3.1 | 4 | g.27855023 | c.148_157dup | p.A56RfsX87 | 2011 | 21814570 | Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 001469-9913 | cattle | Belted Galloway Brown Swiss Dutch Belted Gurtenvieh Lakenvelder Yakutian | Coat colour, white belt | TWIST2 | repeat variation | no | UMD3.1 | 3 | g.118,607,715-118,614,131 | "The belt-associated variant was a copy number variant (CNV) involving the quadruplication of a 6 kb non-coding sequence located approximately 16 kb upstream of the TWIST2 gene" (Awasthi Mishra et al., 2017) "a quadruplication on bovine chromosome 3 between positions 118,608,362 and 118,614,132 bp" (UMD3.1) (Rothammer et al., 2018) | 2017 | 28658273 | |||||
| OMIA 000202-9913 | cattle | Braunvieh | Coat colour, albinism | TYR | insertion, small (<=20) | no | UMD3.1 | 29 | g.6451725 | c.925_926insC | 2004 | 14727143 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | ||||
| OMIA 001249-9913 | cattle | Dexter | Dun brown | TYRP1 | missense | no | UMD3.1 | 8 | g.31711945C>T | c.1300C>T | p.H434Y | 2003 | 12755816 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool | |||
| OMIA 001934-9913 | cattle | Finnish Ayrshire | Ptosis, intellectual disability, retarded growth and mortality (PIRM) syndrome | UBE3B | splicing | yes | UMD3.1.1 | 17 | g.65921497G>A | p.E692E | rs475678587 | 2014 | 25306138 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Variant rsID kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 000262-9913 | cattle | Friesian Holstein Holstein-Friesian Red Holstein Waygu | Deficiency of uridine monophosphate synthase | UMPS | nonsense (stop-gain) | yes | UMD 3.1 | 1 | g.69756880C>T | c.1213C>T | p.R405* | 1993 | 8486364 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) | |||
| OMIA 000733-9913 | cattle | Japanese Black | Multiple ocular defects | WFDC1 | insertion, small (<=20) | yes | UMD3.1 | 18 | g.10570493 | c.321insC | insertion of a single base in the gene for WFDC1 | 2009 | 19374945 | Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 | |||
| OMIA 001736-9913 | cattle | Charolais | Polled and multisystemic syndrome | ZEB2 | deletion, gross (>20) | yes | A 3.7Mb deletion encompassing the genes ARHGAP15, GTDC1 and ZEB2 | 2012 | 23152852 |
| Overall Statistics | |
|---|---|
| Total number of variants | 208 |
| Variants with genomic location | 170 (81.7% ) |
| Variants in a variant database, i.e. with rs ID | 47 (22.6%) |
| Variant Type | Count | Percent |
|---|---|---|
| complex rearrangement | 7 | 3.4% |
| deletion, gross (>20) | 19 | 9.1% |
| deletion, small (<=20) | 26 | 12.5% |
| duplication | 3 | 1.4% |
| extension (stop-lost) | 2 | 1.0% |
| indel, small (<=20) | 7 | 3.4% |
| insertion, gross (>20) | 5 | 2.4% |
| insertion, small (<=20) | 13 | 6.2% |
| inversion | 1 | 0.5% |
| missense | 72 | 34.6% |
| nonsense (stop-gain) | 32 | 15.4% |
| regulatory | 4 | 1.9% |
| repeat variation | 2 | 1.0% |
| splicing | 14 | 6.7% |
| start-lost | 1 | 0.5% |
| Year First Reported | Count | Percent |
|---|---|---|
| 1987 | 1 | 0.5% |
| 1988 | 0 | 0.0% |
| 1989 | 1 | 0.5% |
| 1990 | 1 | 0.5% |
| 1991 | 0 | 0.0% |
| 1992 | 1 | 0.5% |
| 1993 | 1 | 0.5% |
| 1994 | 0 | 0.0% |
| 1995 | 2 | 1.0% |
| 1996 | 3 | 1.4% |
| 1997 | 4 | 1.9% |
| 1998 | 5 | 2.4% |
| 1999 | 6 | 2.9% |
| 2000 | 5 | 2.4% |
| 2001 | 2 | 1.0% |
| 2002 | 8 | 3.8% |
| 2003 | 2 | 1.0% |
| 2004 | 2 | 1.0% |
| 2005 | 3 | 1.4% |
| 2006 | 7 | 3.4% |
| 2007 | 9 | 4.3% |
| 2008 | 6 | 2.9% |
| 2009 | 8 | 3.8% |
| 2010 | 5 | 2.4% |
| 2011 | 8 | 3.8% |
| 2012 | 16 | 7.7% |
| 2013 | 10 | 4.8% |
| 2014 | 15 | 7.2% |
| 2015 | 12 | 5.8% |
| 2016 | 27 | 13.0% |
| 2017 | 18 | 8.7% |
| 2018 | 6 | 2.9% |
| 2019 | 10 | 4.8% |
| 2020 | 4 | 1.9% |