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230 variant records found

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By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.

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

OMIA ID(s) Species Name Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Deleterious? Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Inferred EVA rsID Year Published PubMed ID(s) Acknowledgements
OMIA 002238-9913 cattle Shorthorn Ichthyosis, ABCA12-related ABCA12 missense Naturally occurring variant yes ARS-UCD1.2 2 g.103016791T>C c.6776T>C p.(L2259P) NM_001191294.2:c.6776T>C; NP_001178223.2:p.(Leu2259Pro) 2019 31568573
OMIA 002238-9913 cattle Chianina Ichthyosis, ABCA12-related ABCA12 missense Naturally occurring variant yes ARS-UCD1.2 2 g.103025585T>C c.5,804A>G p.(H1935R) 2008 18344998 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 002238-9913 cattle Poll Hereford Ichthyosis, ABCA12-related ABCA12 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 2 g.103043495_103043496insC c.5689_5690insC p.(S1784Ifs*33) BTA 2:103043495–103043496insC; ENSBTAT00000004518.6:c.5689‐5690insC; ENSBTAP00000004518.6:p.(Ser1784Ilefs*33) (Eager et al., 2020) ss7094285003 2020 32567073
OMIA 001271-9913 cattle Dexter Bulldog calf ACAN BD2 regulatory Naturally occurring variant yes ARS-UCD1.2 21 g.20377856C>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) Naturally occurring variant yes ARS-UCD1.2 21 g.20422104_20422105insGGCA 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 001271-9913 cattle Miniature Zebu Bulldog calf ACAN insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 21 g.20428539_20428540insC c.5688_5689insC p.(V1897fs*9) cDNA position based on transcript NM_173981.2 2018 30305023
OMIA 000328-9913 cattle Belgian Blue Ehlers-Danlos syndrome, type VII (Dermatosparaxis) ADAMTS2 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 7 g.2017035_2017051delinsAGC 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 Naturally occurring variant yes ARS-UCD1.2 6 g.87462016G>A c.1222C>T p.(H408T) 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) Naturally occurring variant 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) Naturally occurring variant yes 16 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) Naturally occurring variant yes 15 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 Naturally occurring variant yes ARS-UCD1.2 15 g.74384916_74384935dup UMD3.1 position is g.75154399_75154418dup. Duplication of 20bp in exon 2 is predicted to result in a frameshift leading to a premature stop codon and truncated protein. 2015 26076463 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 002083-9913 cattle Japanese Black Abortion (embryonic lethality), ANXA10-related ANXA10 repeat variation Naturally occurring variant yes 8 "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) Naturally occurring variant yes ARS-UCD1.2 5 g.62810245C>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) Naturally occurring variant yes 11 "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) Naturally occurring variant yes ARS-UCD1.2 13 g.24024660del c.1442del p.(A451fs*26) 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 Brindle ASIP Abr insertion, gross (>20) Naturally occurring variant no 13 "insertion of a full-length Bos taurus LINE element" 2006 16827753
OMIA 000194-9913 cattle Holstein-Friesian Citrullinaemia ASS1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 11 g.100781668C>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 Naturally occurring variant yes ARS-UCD1.2 25 g.25933247G>A 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 Naturally occurring variant yes ARS-UCD1.2 25 g.25939141C>A 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 Naturally occurring variant yes ARS-UCD1.2 25 g.25939366C>A 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 Naturally occurring variant yes ARS-UCD1.2 25 g.25940510C>T 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 Poll Hereford Maple syrup urine disease BCKDHA nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 18 g.50551011C>T c.148C>T p.(Q50*) cDNA position based on ENSBTAT00000021342.6 1990 2303405
OMIA 000627-9913 cattle Shorthorn Maple syrup urine disease BCKDHA missense Naturally occurring variant yes ARS-UCD1.2 18 g.50560242C>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) Naturally occurring variant yes ARS-UCD1.2 15 g.22552375G>A c.306G>A p.(W102*) UMD3.1 position is g.22877552G>A; cDNA position is based on XM_024975217.1 rs109226280 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. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001991-9913 cattle Nordic Red Stillbirth BTBD9 deletion, gross (>20) Naturally occurring variant yes 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 Naturally occurring variant yes ARS-UCD1.2 11 g.72409143T>C p.(Y452C) published as CAD g.72399397T>C; p.Tyr452Cys 2019 31056337 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 002167-9913 cattle Nordic Red Asthenospermia CCDC189 splicing Naturally occurring variant yes ARS-UCD1.2 25 g.26880841C>T Touru et al. (2019): "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) Naturally occurring variant yes ARS-UCD1.2 27 g.15123637_15123640del 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) Naturally occurring variant yes ARS-UCD1.2 13 g.64710424C>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) Naturally occurring variant yes ARS-UCD1.2 14 g.26402250_26402254del p.(K594Afs*29) 2017 28904385
OMIA 002022-9913 cattle Red Danish Arthrogryposis multiplex congenita, CHRNB1-related CHRNB1 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.27122027del c.55del p.(A19Pfs47*) Published as Chr19:27757270CG > C; CHRNB1 c.55delG; (p.Ala19Profs47*) 2016 27364156 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000685-9913 cattle Brahman Myasthenic syndrome, congenital, CHRNE-related CHRNE 470del20 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.26485848_26485867del c.470_489del Kraner et al. (2002): "a loss of 20 bp within the coding sequence of exon 5 (Fig. 2), between nucleotide 469 and 490 (nucleotide numbering referring to the cDNA sequence published under accession number X02597". These authors (and subsequent authors) call this variant "470del20". The current (2020) HGVS nomenclature is c.470_489del 200922: g. information move here (g.27119615) until standardised 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. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001887-9913 cattle Belgian Blue Osteopetrosis with gingival hamartomas CLCN7 missense Naturally occurring variant yes ARS-UCD1.2 25 g.[1139611G>T; 1139613A>G] c.[2248T>C;2250C>A] p.(Y750Q) 2014 24159188 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001135-9913 cattle Japanese Black Renal dysplasia CLDN16 Type 1 deletion, gross (>20) Naturally occurring variant yes 1 37kb deletion of exons 1-4 2000 10810088
OMIA 001135-9913 cattle Japanese Black Renal dysplasia CLDN16 Type 2 deletion, gross (>20) Naturally occurring variant yes 1 "a 56-kb deletion that eliminates exons 1-4 and 21-bp of exon 5" 200922: g. info moved to here (g.77528017_?) until can be standardised 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) Naturally occurring variant yes ARS-UCD1.2 12 g.52112732_52112733insG c.662_663insG p.(R221Gfs*6) 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) 210909: after checking the genome assembly sequence, FN changed g.52461241insG to g.52461241_52461242insG; and c.662insG to c.662_663insG
OMIA 002127-9913 cattle Red Angus Osteogenesis imperfecta, type II, COL1A1-related COL1A1 missense Naturally occurring variant yes ARS-UCD1.2 19 g.36463798G>A c.1063G>A p.(G355S) 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 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.36470764_36470767delinsT c.3145_3148delinsT p.(A1049_P1050delinsS) UMD3.1 position is g.37101299_37101302delinsT; cDNA position based on ENSBTAT00000017420.4 rs876049195 2017 28904385 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 002127-9913 cattle Holstein Osteogenesis imperfecta, type II, COL1A1-related COL1A1 missense Naturally occurring variant yes ARS-UCD1.2 19 g.36473359T>A c.3917T>A p.(V1306E) NM_001034039.2: c.3917T>A; XP_024835395.1: p.Val1306Glu (Jacinto et al., 2021) 2021 33672767
OMIA 001926-9913 cattle Charolais Salers Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32301746G>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 deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 5 g.32301911_32308589del "Sanger sequencing revealed the precise breakpoints of the heterozygous deletion from position 32 301 911 located in intron 25 to 32 308 589 located within exon 45. The 6679 bp deletion includes the entire sequence of 18 exons (26–44) plus the first 36 nucleotides of exon 45" (Jacinto et al., 2020) 2020 33316082
OMIA 001926-9913 cattle Holstein Bulldog calf COL2A1 delins, gross (>20) Naturally occurring variant yes ARS-UCD1.2 5 g.32303127_32306640delinsTCTGGGGAGC 2020 32894162
OMIA 001926-9913 cattle Holstein Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32303739G>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 Naturally occurring variant yes ARS-UCD1.2 5 g.32305226G>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 Naturally occurring variant yes ARS-UCD1.2 5 g.32307658G>A p.(G960R) 2014 25017103
OMIA 001926-9913 cattle Holstein Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32308008G>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 Naturally occurring variant yes ARS-UCD1.2 5 g.32308734G>A c.3166G>A p.(G1056S) 2019 30378686
OMIA 002295-9913 cattle Holstein Ehlers-Danlos syndrome, classic type, 2 COL5A2 missense Naturally occurring variant yes ARS-UCD1.2 2 g.7331916G>T c.2366G>T p.(G789V) XM_024979774.1: c.2366G>T; XP_024835542.1: p.Gly789Val (Jacinto et al., 2020) 2020 33143196
OMIA 002260-9913 cattle Holstein de novo mutation in an AI sire COL6A3 missense Naturally occurring variant yes ARS-UCD1.2 3 g.116826597G>A p.(T1894M) Bourneuf et al. (2017) detected COL6A3 g.117453719G>A; p.T1894M as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Holstein AI bull. No information was provided on the descendants of this bull. 2017 28904385
OMIA 000341-9913 cattle Rotes Höhenvieh Vorderwald Epidermolysis bullosa, dystrophic COL7A1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 22 g.51301158C>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 Naturally occurring variant no ARS-UCD1.2 3 g.9361962C>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) Naturally occurring variant yes ARS-UCD1.2 7 g.6073556C>T c.220C>T p.(Q74*) 2017 28683140
OMIA 002033-9913 cattle Numerous breeds A2 milk CSN2 A2 missense Naturally occurring variant no ARS-UCD1.2 6 g.85451298T>G 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 002262-9913 cattle Montbeliarde de novo mutation in an AI sire CSNK1G2 missense Naturally occurring variant yes ARS-UCD1.2 7 g.44265842G>C p.(D164H) Bourneuf et al. (2017) detected Chr7 CSNK1G2 g.45885860G>C; p.D164H as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Montbéliarde AI bull. No information was provided on the descendants of this bull. 2017 28904385
OMIA 001697-9913 cattle Jersey Abortion due to haplotype JH1 CWC15 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 15 g.15449431C>T c.163C>T p.(R55*) UMD3.1 position is g.15707169C>T, cDNA and protein positions based on XM_005215764.2 rs1115118696 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). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 002288-9913 cattle Hereford Mandibulofacial dysostosis CYP26C1 missense Naturally occurring variant yes ARS-UCD1.2 26 g.14404993T>C p.(L188P) ss7148511443 2020 33105751
OMIA 002109-9913 cattle Brown Swiss Tricho-dento-osseous-like syndrome DLX3 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.36665831_36665832insGGAGCACA c.584_585insGGAGCACAGG p.(S198Rfs*99) NM_001081622 position is g.37298375_37298376insGGAGCACA 2017 28670783 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000543-9913 cattle Danish Holstein Anhidrotic ectodermal dysplasia EDA insertion, gross (>20) Naturally occurring variant yes X "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
OMIA 000543-9913 cattle German Holstein Anhidrotic ectodermal dysplasia EDA deletion, gross (>20) Naturally occurring variant yes X c.397_502del a large deletion including exon 3 in the gene for ectodysplasin (ED1; now called EDA) 200922: g. info moved to here (g.85821470) until it can be standardised 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 Naturally occurring variant yes ARS-UCD1.2 X g.77174882_80737442inv 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 000543-9913 cattle Red Angus-Simmental cross Hypohidrotic ectodermal dysplasia EDA deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 X g.80382423_80435202del GCF_002263795.1 (O'Toole et al., 2021) 2021 33801223
OMIA 000543-9913 cattle German Holstein Anhidrotic ectodermal dysplasia EDA splicing Naturally occurring variant yes ARS-UCD1.2 X g.80411671A>C c.924+2T>G c.DNA position is based on NM_001081743.2 2002 12021844 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000543-9913 cattle Holstein Friesian Anhidrotic ectodermal dysplasia EDA splicing Naturally occurring variant yes ARS-UCD1.2 X g.80411795C>A "a single nucleotide polymorphism (SNP) G/A at the 9th base of exon 8 [GenBank: AJ278907.1 position 30.549] ... Sequencing of the RT-PCR products revealed that the amplified fragment of the affected animals lacked ... exon 8. At the protein level, the exon skipping leads to a frameshift and consequently to a premature stop codon." (Gargani et al., 2011) 2011 21740563
OMIA 000543-9913 cattle Red Angus-Charolais-Simmental cross Anhidrotic ectodermal dysplasia EDA nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 X g.80415626G>A c.730C>T p.(R244*) 2007 17616058 Reference not in PubMed; see OMIA 000543-9913 for reference details The g. coordinate for the named reference genome assembly, together with the c. coordinate, were kindly provided by Tosso Leeb (22 March 2021)
OMIA 000543-9913 cattle Japanese Black Anhidrotic ectodermal dysplasia EDA insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 X g.80802800_80802801insCCCT c.280_281insAGGG p.(G94Qfs*49) 2012 22497423 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000543-9913 cattle Holstein Anhidrotic ectodermal dysplasia EDA deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 X g.80803015_80803033del c.48_66del "a 19-bp deletion at nucleotides c.48_66 in exon 1 ... . This mutation is predicted to generate a truncated 49 aa protein." 2011 21410470
OMIA 002128-9913 cattle Charolais Anhidrotic ectodermal dysplasia, EDAR-related EDAR insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 11 g.44599876_44599877insC p.(P161Rfs*97) UMD3.1 position is g.44462236_44462237insC 2017 28904385 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001716-9913 cattle Holstein Ehlers-Danlos syndrome, Holstein variant EPYC missense Naturally occurring variant yes ARS-UCD1.2 5 g.20856381C>A 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 Naturally occurring variant yes ARS-UCD1.2 6 g.103594013C>T c.1356C>T Variant creates a cryptic splice donor site in exon 11 which is leading to improper splicing at position c.1355 and resulting in the 56-base RNA deletion between 1355 and 1410. The deletion causes a frameshift and premature termination. 2002 12136126 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000187-9913 cattle Japanese Brown Chondrodysplasia EVC2 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 6 g.103609778_103609779delinsG c.2327_2328delinsG p.(A776Gfs*22) Published as c.2054_2055delCAinsG, cDNA and protein position in this table based on ENSBTAT00000005613.6 2002 12136126 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000187-9913 cattle Tyrolean Grey Chondrodysplasia EVC2 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 6 g.103651709_103651710del c.2993_2994del p.(D998Efs*13) 2014 24733244 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. 210909 FN: given that the variant is a 2bp del (AC), g.103651710_103651710del needs to be changed. BLASTing with AGAGGAGCAAGAAGAC from Fig.4 indicates that it is 719 and 710 that are deleted. THus the entry is changed to g.103651709_103651710del; and AC is removed from the c. entry.
OMIA 002042-9913 cattle Belgian Blue Abortion (embryonic lethality), EXOSC4 EXOSC4 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 14 g.755826G>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 Holstein Sahiwal Factor XI deficiency F11 insertion, gross (>20) Naturally occurring variant yes 27 a 76-bp insertion in exon 12 of the Factor XI gene 200922: g. and c. info moved here (g.15367048; c.1406ins76) until can be standardised 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 000363-9913 cattle Japanese Black Factor XI deficiency F11 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 27 g.16305660delinsATATGTGCAGAATATA c.870delinsATATGTGCAGAATATA P.(F290delinsLYVQNI) 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). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000437-9913 cattle German Fleckvieh Haemophilia A F8 missense Naturally occurring variant yes ARS-UCD1.2 X g.36017426A>T p.(H45L) ss213751737 2018 29774585
OMIA 000437-9913 cattle Japanese Brown Haemophilia A F8 missense Naturally occurring variant yes ARS-UCD1.2 X g.36145188T>A c.6458T>A p.(L2153H) 2009 19456318 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 002450-9913 cattle Chianina Ichthyosis congenita FA2H insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 18 g.2205625_2205626insG c.9dupC p.(A4Rfs*142) NM_001192455.1; NP_001179384.1 2021 34599683
OMIA 002259-9913 cattle Montbeliarde de novo mutation in an AI sire FAM189A1 missense Naturally occurring variant yes ARS-UCD1.2 21 g.28112913T>C p.(N192S) Bourneuf et al. (2017) detected FAM189A1 g.28644665T>C; p.N192S as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Montbéliarde AI bull. No information was provided on the descendants of this bull. 2017 28904385
OMIA 000151-9913 cattle Holstein Brachyspina FANCI deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 21 g.20773899_20777226del p.(V877Lfs*27) 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 Naturally occurring variant yes ARS-UCD1.2 10 g.61831200G>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 Naturally occurring variant yes ARS-UCD1.2 10 g.61917867G>A 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) Naturally occurring variant yes ARS-UCD1.2 24 g.56787697C>A 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 002374-9913 cattle Holstein Friesian Jersey Charcot Marie Tooth disease FGD4 splicing Naturally occurring variant yes ARS-UCD1.2 5 g.77262490C>T c.1671+1G>A Splice donor mutation based on XM_005206883.3 2021 34045765
OMIA 002090-9913 cattle Holstein Facial dysplasia syndrome FGFR2 missense Naturally occurring variant yes ARS-UCD1.2 26 g.41489034C>A c.927G>T p.(W309C) 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) Naturally occurring variant yes ARS-UCD1.2 6 g.116767863C>A c.2408G>T p.(*803Lext*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) Naturally occurring variant yes ARS-UCD1.2 16 g.38666821C>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 002318-9913 cattle Montbeliarde coat colour, dilution (milca) FZD7 missense Naturally occurring variant no ARS-UCD1.2 2 g.90572569G>C c.1241G>C p.(G414A) CDS position in transcript ENSBTAT00000002946.6 based on ENSEMBL Variant Effect Predictor 2021 33686687
OMIA 000419-9913 cattle Shorthorn Glycogen storage disease II GAA E18 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.52484973_52484974del c.2454_2455del 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. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000419-9913 cattle Brahman Glycogen storage disease II GAA E13 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 19 g.52488949G>A c1783C>T p.(R595*) UMD3.1 position is g.53105979C>T 2000 10723725 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000419-9913 cattle Brahman Droughtmaster Glycogen storage disease II GAA E7 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.52492405_52492406del c.1057_1058del p.(Y353L) UMD3.1 position is g.53109436_53109437del 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. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 002375-9913 cattle Holstein Friesian Jersey Congenital disorder of glycosylation GALNT2 splicing Naturally occurring variant yes ARS-UCD1.2 28 g.2281801G>A c.1561-1G>A Splice acceptor mutation based on NM_001193103.1. 2021 34045765
OMIA 001826-9913 cattle Holstein Abortion due to haplotype HH4 GART missense Naturally occurring variant yes ARS-UCD1.2 1 g.1997582A>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) Naturally occurring variant yes ARS-UCD1.2 26 g.36627244G>A 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 000689-9913 cattle Poll Hereford Myoclonus GLRA1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 7 g.63070074G>T 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) Naturally occurring variant yes ARS-UCD1.2 3 g.15024245del c.4286del p.(G1430Kfs*66) 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 210909: to be consistent with HGVS, FN changed g.15079217delC to g.15079217del. An examination of the information for rs723240647 indicated that c.4285_4287delCCCinsCC should be changed to c.4286del
OMIA 002230-9913 cattle Belted Galloway Hypotrichosis HEPHL1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 29 g.721234T>A c.1684A>T p.(K562*) NC_037356.1 (ARS-UCD1.2 assembly, chromosome 29): g.721234A>T; NM_001192511.2 c.1684A>T; NP_001179440.1: p.Lys562* (Kuca et al., 2021) 2021 33926013
OMIA 000317-9913 cattle Highland Ears, crop HMX1 insertion, gross (>20) Naturally occurring variant no 6 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) Naturally occurring variant 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 Naturally occurring variant yes ARS-UCD1.2 8 g.83909754C>G c.235G>C p.(V79L) 2013 23700453 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 002271-9913 cattle Holstein Immunodeficiency, IL17Ra-related IL17RA deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 5 g.108813251del c.180del p.(C61Afs*62) XM_015460734.2: c.180delC; XP_015316220.2: p.(Cys61AlafsTer62) (Häfliger et al., 2020) 2020 32448141
OMIA 002261-9913 cattle Holstein de novo mutation in an AI sire ITGA3 missense Naturally occurring variant yes ARS-UCD1.2 19 g.36586185G>A p.(T252M) Bourneuf et al. (2017) detected ITGA3 g.37219021G>A; p.T252M as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Holstein AI bull. No information was provided on the descendants of this bull. 2017 28904385
OMIA 000595-9913 cattle Fleckvieh Holstein-Friesian Jersey Leukocyte adhesion deficiency, type I ITGB2 BLAD missense Naturally occurring variant yes ARS-UCD1.2 1 g.144770078T>C 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). The genomic location on ARS-UCD1.2 was determined by Katie Eager & Shernae Woolley, EMAI, NSW Department of Primary Industries.
OMIA 001948-9913 cattle Charolais Epidermolysis bullosa, junctionalis, ITGB4 ITGB4 deletion, gross (>20) Naturally occurring variant yes 19 "a 4.4 kb deletion involving exons 17 to 22" of the ITGB4 gene 2015 25890340
OMIA 001722-9913 cattle Marchigiana Romagnola Lethal multi-organ developmental dysplasia KDM2B missense Naturally occurring variant yes ARS-UCD1.2 17 g.53761149G>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 002390-9913 cattle Braunvieh Spinal muscular atrophy KDSR missense Naturally occurring variant yes ARS-UCD1.2 24 g.61620302C>T 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 Uckermärker Progressive ataxia KIF1C missense Naturally occurring variant yes ARS-UCD1.2 19 g.26407668C>T c.608G>A p.(R203Q); p.(R203_T204delinsQ*) 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 Naturally occurring variant yes 6 "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 Naturally occurring variant no 6 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 OMIA 001737-9913 cattle British Gloucester Eringer Evolèner Pinzgauer Slovenian Cika Spanish Berrenda en negro Tux-Zillertaler Pinzgauer spotting KIT KIT^PINZ complex rearrangement Naturally occurring variant no 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 001576-9913 cattle Belgian Blue Brown Swiss Coat colour, colour-sided KIT Cs(6) complex rearrangement Naturally occurring variant no 6 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) Naturally occurring variant no ARS-UCD1.2 6 g.70239551_70239590del c.1390_1429del p.(N464Afs*50) "NC_037333.1:g.70239551_70239590del; NM_001166484.1:c.1390_1429del; NP_001159956.1:p.(Asn464AlafsTer50)" (Häfliger et al., 2020) 2020 32065668
OMIA 001216-9913 cattle Belgian Blue Shorthorn Roan KITLG missense Naturally occurring variant no ARS-UCD1.2 5 g.18273206G>T 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 Naturally occurring variant no ARS-UCD1.2 19 g.40982250G>C c.276C>G p.(N92K) 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 Belgian Blue‐Holstein cross Epidermolysis bullosa, simplex, KRT5-related` KRT5 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 5 g.27367604_27367606del c.534_536del p.(N178del) "27367604delCAA (NM_001008663.1:c.534_536delCAA), leading to a loss of an asparagine amino acid at residue 178 of the encoded KRT5 protein (NP_001008663.1:p.Asn178del)" (Jacinto et al., 2020). 2020 33135329 In an email dated 5 November 2020, Cord Drögemüller confirmed that the genomic specification for this variant is g.27367604_27367606delCAA
OMIA 002081-9913 cattle Friesian-Jersey mosaic Epidermolysis bullosa KRT5 missense Naturally occurring variant yes ARS-UCD1.2 5 g.27371128G>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) Naturally occurring variant yes ARS-UCD1.2 5 g.27331221_27331228del c.281_288del p.(M94Nfs*14) cDNA and protein positions based on NM_001075970.1 and NP_001069438.1, respectively 2021 34356054 210909: FN checked the ARS-UCD1.2 assembly, and discovered that the deletion spans 27331221 to 27331228. Thus g.27331221delTGTGCCCA was changed to g.27331221_27331228del. From NCBI's genome browser, worked out that the c. notation needs to be changed from c.281delTGTGCCCA to c.281_288del.
OMIA 001677-9913 cattle Belgian Blue Epidermolysis bullosa, junctionalis, LAMA3-related LAMA3 nonsense (stop-gain) Naturally occurring variant unknown ARS-UCD1.2 24 g.32749369G>A 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) Naturally occurring variant yes 16 "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 Naturally occurring variant yes ARS-UCD1.2 29 g.24366560A>G 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 Naturally occurring variant yes ARS-UCD1.2 15 g.76792588C>T 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 was initially 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. Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4
OMIA 000963-9913 cattle Holstein Syndactyly (mule foot) LRP4 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 15 g.76800972_76800973delinsAT c.4863_4864delinsAT p.(N1621_G1622delinsKC) 2006 16859890 Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4
OMIA 000963-9913 cattle German Simmental Syndactyly (mule foot) LRP4 missense Naturally occurring variant yes ARS-UCD1.2 15 g.76807508C>T c.3595G>A p.(G1199S) 2007 17319939 Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4
OMIA 000963-9913 cattle Simmental Charolais Cross Syndactyly (mule foot) LRP4 missense Naturally occurring variant yes ARS-UCD1.2 15 g.76812187C>T c.2719G>A p.(G907R) 2007 17319939 Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4
OMIA 000185-9913 cattle Japanese Black Chediak-Higashi syndrome LYST missense Naturally occurring variant yes ARS-UCD1.2 28 g.8464077T>C 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 Naturally occurring variant yes ARS-UCD1.2 7 g.12840983G>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 Naturally occurring variant yes ARS-UCD1.2 7 g.12842292T>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) Naturally occurring variant yes ARS-UCD1.2 6 g.22188765G>A c.2574G>A p.(W858*) 1999 10594236 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 001199-9913 cattle Angus Holstein-Friesian Icelandic Dominant black MC1R E^D missense Naturally occurring variant no ARS-UCD1.2 18 g.14705671T>C c.296T>C p.(L99P) rs109688013 1995 8535072 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 Naturally occurring variant no ARS-UCD1.2 18 g.14705671T>C c.296T>C p.(L99P) rs109688013 2016 27037038
OMIA 001199-9913 cattle Angus Fleckvieh Red Friesian Recessive red MC1R e deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 18 g.14705685del c.310del p.(G104Vfs*53) 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) Naturally occurring variant yes 11 p.(L38Rfs*25) 2016 27646536
OMIA 001106-9913 cattle Tyrolean Grey Axonopathy MFN2 splicing Naturally occurring variant yes ARS-UCD1.2 16 g.41686003G>A 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) Naturally occurring variant yes 18 a 110 kb deletion in the MIMT1 gene 2010 21152099
OMIA 001931-9913 cattle Holstein Depigmentation associated with microphthalmia MITF deletion, gross (>20) Naturally occurring variant yes 22 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 Holstein Glass-eyed albino MITF deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 22 g.31628127_31628129del p.(R211del) UMD3.1 position g.31746506_31746508del 2017 28904385 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001680-9913 cattle German Fleckvieh Dominant white with bilateral deafness MITF missense Naturally occurring variant yes ARS-UCD1.2 22 g.31628131C>A c.629G>T p.(R210I) UMD3.1 position is g.31746502 2011 22174915 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000214-9913 cattle Holstein Simmental White spotting MITF regulatory Naturally occurring variant no ARS-UCD1.2 22 g.31650821T>A c.33+112A>T UMD3.1 position is g.31769189 rs210634530 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. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000214-9913 cattle Brown Swiss White spotting MITF regulatory Naturally occurring variant no ARS-UCD1.2 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 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000031-9913 cattle Belgian Blue Coat colour, cool gray MLPH deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 3 g.116966611_116966620del c.87_96del p.(E32Dfs*1) 2016 26582259 The genomic location on ARS-UCD1.2 was determined by Katie Eager & Shernae Woolley, EMAI, NSW Department of Primary Industries.
OMIA 001819-9913 cattle Tyrolean Grey Xanthinuria, type II MOCOS deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 24 g.20911933del c.1881del p.(S628Vfs9*) Published using UMD3.1 position: g.21222030delC; cDNA and protein positions are given transcript: ENSBTAT00000048768. Positions for a second transcript (ENSBTAT00000065375) were given in the paper: c.1782del and p.(S595Vfs9*). 2016 27919260 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001819-9913 cattle Japanese Black Xanthinuria, type II MOCOS deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 24 g.20936257_20936259del c.769_771del p.(Y257del) published as c.769_771delTAC 2000 10801779 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001541-9913 cattle Fleckvieh Simmental Arachnomelia, BTA23 MOCS1 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 23 g.13837654_13837655del c.1224_1225del UMD3.1 position is g.13833868_13833869del rs383500843 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. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001452-9913 cattle Belgian Blue Tail, crooked MRC2 missense Naturally occurring variant yes ARS-UCD1.2 19 g.47089627T>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) Naturally occurring variant yes ARS-UCD1.2 19 g.47095176_47095177del c.2904_2905del p.(G934*) 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) 210908 the entry g.47740473delAG can't be correct because if two bases have been deleted, the g. notation must include the two relevant base positions. FN BLASTED the sequence CCAGACCTGCCGCCCACAG obtained from Fig 3 against UMD3.1.1, and determined that the entry should be g.47740474_47740475del
OMIA 000683-9913 cattle Gelbvieh Muscular hypertrophy (double muscling) MSTN missense Naturally occurring variant yes ARS-UCD1.2 2 g.6279187T>C c.191T>C p.(L64P) UMD3.1 position is g.6213889T>C rs449270213 2015 25515003 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000683-9913 cattle Angus Limousin Muscular hypertrophy (double muscling) MSTN missense Naturally occurring variant yes ARS-UCD1.2 2 g.6279278C>A c.282C>A p.(F94L) UMD3.1 position is g.6213980A>C 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). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000683-9913 cattle Parthenaise Muscular hypertrophy (double muscling) MSTN missense Naturally occurring variant yes ARS-UCD1.2 2 g.6279310C>G c.314C>G p.(S105C) UMD3.1 position is g.6214012C>G 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). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000683-9913 cattle Maine Anjou Muscular hypertrophy (double muscling) MSTN nt419(del7-ins10) delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 2 g.6281243_6281249delinsAAGCATACAA c.419_425delinsAAGCATACAA p.(F140*) cDNA and protein positions based on NM_001001525.3 and NP_001001525.1, retrospectively 1998 9501304 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. Variant coordinates updated based on Johnsson and Jungnickel (2021)
OMIA 000683-9913 cattle Maine Anjou Muscular hypertrophy (double muscling) MSTN D182N missense Naturally occurring variant yes ARS-UCD1.2 2 g.6281368G>A c.544G>A p.(D182N) 2002 Reference not in PubMed; see OMIA 000683-9913 for reference details The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000683-9913 cattle Blonde d'Aquitaine Charolais Limousin Muscular hypertrophy (double muscling) MSTN nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 2 g.6281434C>T c.610C>T p.(Q204*) UMD3.1 position is g.6216138C>T rs110344317 1998 9501304 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000683-9913 cattle Maine Anjou Marchigiana Muscular hypertrophy (double muscling) MSTN nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 2 g.6281500G>T c.676G>T p.(E226*) UMD3.1 position is g.6216204G>T 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). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
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) Naturally occurring variant yes ARS-UCD1.2 2 g.6283674_6283684del c.821_831del p.(D273RfsX14) UMD3.1 position is g.6218379delATGAACACTCC rs382669990 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). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. Protein coordinates updated based on Johnsson and Jungnickel (2021).
OMIA 000683-9913 cattle Maine Anjou Marchigiana Muscular hypertrophy (double muscling) MSTN nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 2 g.6283727G>T c.1004G>T p.(E291*) UMD3.1 position is g.6218432G>T 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). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 000683-9913 cattle Gasconne Parthenaise Piedmontese Muscular hypertrophy (double muscling) MSTN missense Naturally occurring variant yes ARS-UCD1.2 2 g.6283794G>A c.938G>A p.(C313Y) UMD3.1 position is g.6218499G>A 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). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001978-9913 cattle Swiss Holstein Arthrogryposis, distal, type 1B MYBPC1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.65446598T>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) Naturally occurring variant yes ARS-UCD1.2 10 g.21538917_21538919del p.(K1730del) 2016 27646536 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001342-9913 cattle Mucopolysaccharidosis IIIB NAGLU missense Naturally occurring variant yes ARS-UCD1.2 19 g.42624367G>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 Naturally occurring variant yes ARS-UCD1.2 26 g.34340886T>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) Naturally occurring variant yes 28 "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 000725-9913 cattle Angus Niemann-Pick type C1 NPC1 missense Naturally occurring variant yes ARS-UCD1.2 24 g.33099467C>G c.2969C>G p.(P990R) NM_174758.2:c.2969C>G ss7148491913 2020 32970694
OMIA 002035-9913 cattle Jersey Abortion (embryonic lethality), OBFC1-related OBFC1 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 26 g.24461803_24461804del c.379_380del p.(K127Vfs*28) 2016 27646536 210909: FN changed c.379_380delAA to c.379_380del. He also added the ref sequence, based on the words in the text "Sequence reads were aligned to the bosTau6 reference genome". FN also checked the g. location against Suppl Material S2, which lists the location as 24720154. However, a search of the UMD assembly confirms that the AA del is actually as given, i.e. g.24720155_24720156del
OMIA 000162-9913 cattle Red Holstein Cardiomyopathy, dilated OPA3 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 18 g.53152213G>A c.343C>T p.(Q115*) UMD3.1 position is g.53546443C>T; cDNA position based on ENSBTAT00000064088.2 rs479222100 2011 20923700 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001437-9913 cattle Brown Swiss Beta-lactoglobulin, aberrant low expression PAEP regulatory Naturally occurring variant yes ARS-UCD1.2 11 g.103255964C>A 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 Naturally occurring variant yes ARS-UCD1.2 19 g.27895397C>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 Naturally occurring variant yes ARS-UCD1.2 10 g.79469727G>C 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) Naturally occurring variant yes ARS-UCD1.2 21 g.69352995G>A c.702G>A p.(W234*) UMD3.1 position is g.71001232G>A 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. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001545-9913 cattle Charolais Galloway Hereford Highland Simmental Coat colour, dilution PMEL deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 5 g.57345302_57345304del c.50_52del p.(L19del) 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 001544-9913 cattle Rat-tail syndrome PMEL deletion, small (<=20) Naturally occurring variant unknown ARS-UCD1.2 5 g.57345302_57345304del c.50_52del p.(L19del) rs385468954 2016 27037038
OMIA 001545-9913 cattle Charolais Coat colour, dilution PMEL missense Naturally occurring variant no ARS-UCD1.2 5 g.57345315G>A c.64G>A p.(G22R) 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 Naturally occurring variant yes ARS-UCD1.2 4 g.49600585C>T 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 Naturally occurring variant 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 Naturally occurring variant 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 Brahman Polled, Celtic POLLED P[sub]C OR P[sub]202ID complex rearrangement Naturally occurring variant 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 Naturally occurring variant 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 Poll Hereford Cardiomyopathy and woolly haircoat syndrome PPP1R13L duplication Naturally occurring variant yes ARS-UCD1.2 18 g.53013747_53013753dup c.956-962dupACAGGCG p.(G335Efs*36) 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) Naturally occurring variant yes ARS-UCD1.2 6 g.95896205G>A 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) Naturally occurring variant yes ARS-UCD1.2 6 g.95896205G>A 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 Naturally occurring variant no ARS-UCD1.2 23 g.35332871A>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 SLICK1 deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 20 g.39099214del c.1382del p.(A461Vfs*2) rs517047387 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) Naturally occurring variant no ARS-UCD1.2 20 g.39099226C>A p.(S465*) 2018 29527221
OMIA 001372-9913 cattle Carora Limonero Slick hair PRLR nonsense (stop-gain) Naturally occurring variant no ARS-UCD1.2 20 g.39099321C>T p.(R497*) 2018 29527221
OMIA 000944-9913 cattle Numerous breeds Spongiform encephalopathy (mad cow disease) PRNP missense Naturally occurring variant yes ARS-UCD1.2 13 g.47056730G>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 Naturally occurring variant yes ARS-UCD1.2 29 g.42991370G>A 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 Naturally occurring variant yes ARS-UCD1.2 3 g.69060748T>C c.584A>G p.(Y195C) 2016 27646536 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 002433-9913 cattle Fleckvieh Simmental Thrombopathia RASGRP2 missense Naturally occurring variant yes ARS-UCD1.2 29 g.42978791A>G 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) Naturally occurring variant yes 12 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 Naturally occurring variant yes ARS-UCD1.2 3 g.95015373T>C c.124-2A>G NM_001077953.1 2012 22438830 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 002038-9913 cattle Holstein-Friesian Abortion (embryonic lethality), RNF20 RNF20 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 8 g.91297797A>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 Naturally occurring variant yes ARS-UCD1.2 8 g.85905534T>A p.(W9R) 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) Naturally occurring variant yes ARS-UCD1.2 14 g.22340665_22340666insA p.(R791Kfs*13) 2016 27510606
OMIA 002134-9913 cattle Ayrshire Abortion due to haplotype AH2 RPAP2 splicing Naturally occurring variant yes 3 a splice acceptor variant at 51,267,548 bp [reference sequence not specified] in RPAP2 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 Naturally occurring variant yes ARS-UCD1.2 11 g.47355110C>T c.826+1G>A 2016 27646536 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
OMIA 002297-9913 cattle Holstein Friesian Tetradysmelia RSPO2 delins, gross (>20) Naturally occurring variant yes ARS-UCD1.2 14 g.56451029_56501201delinsTGACAA a 50-kb deletion spanning three exons of the R-spondin 2 (RSPO2) gene 2020 33176673
OMIA 002149-9913 cattle Holstein Abortion due to haplotype HH6 SDE2 start-lost Naturally occurring variant yes ARS-UCD1.2 16 g.29020700A>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 002444-9913 cattle Japanese Black Hydrallantois SLC12A1 missense Naturally occurring variant yes ARS-UCD1.2 10 g.62157819G>A p.(P372L) 2016 27613513
OMIA 002150-9913 cattle Rouge-des-Prés Syndrome des veaux tourneurs (Turning calves syndrome) SLC25A46 missense Naturally occurring variant yes ARS-UCD1.2 7 g.109742796C>T c.376C>T p.(R126C) 2017 28376083
OMIA 000366-9913 cattle Braunvieh Fleckvieh Fanconi syndrome SLC2A2 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 1 g.96472797_96472804delinsCATC c.771_778delinsCATC p.(L258fs16) 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 210909: FN changed c.771_778delTTGAAAAGinsCATC to c.771_778delinsCATC. Also, since the del is of 8 bp, the g. designation has been changed from g.97239973_97239976delTTGAAAAG (which encompasses a deletion of only 4bp) to g.97239973_97239980delinsCATC.
OMIA 001340-9913 cattle Friesian Holstein Complex vertebral malformation SLC35A3 missense Naturally occurring variant yes ARS-UCD1.2 3 g.43261945C>A 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 001340-9913 cattle Montbeliarde de novo mutation in an AI sire SLC35A3 missense Naturally occurring variant yes ARS-UCD1.2 3 g.43268369G>T p.(R25S) This variant was detected by Bourneuf et al. (2017) as a de novo mutation from an analysis of whole-genome-sequence of an AI Montbéliarde bull. No information was provided on the descendants of this bull. 2017 28904385
OMIA 001828-9913 cattle Montbeliarde Vorderwald Abortion due to haplotype MH2 SLC37A2 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 29 g.28510651C>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 Naturally occurring variant yes ARS-UCD1.2 14 g.537516G>A 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 Naturally occurring variant yes ARS-UCD1.2 20 g.39790069G>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 Naturally occurring variant yes ARS-UCD1.2 20 g.39824417C>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) Naturally occurring variant yes ARS-UCD1.2 19 g.44069903G>A 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 002443-9913 cattle Angus Friesian Hereford Holstein Simmental Osteopetrosis SLC4A2 deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 4 g.113638011_113640784del "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 Naturally occurring variant yes ARS-UCD1.2 8 g.93753358T>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) Naturally occurring variant yes 11 p.(L1227Afs*134) 2016 27646536
OMIA 002258-9913 cattle Charolais Lethality, SOWAHB-related SOWAHB missense Naturally occurring variant yes ARS-UCD1.2 6 g.91735816G>T p.(Q379K) This variant was detected by Bourneuf et al. (2017) as a de novo mutation from an analysis of whole-genome-sequence of a Charolais AI bull. No information was provided on the descendants of this bull. 2017 28904385
OMIA 001247-9913 cattle American Brown Swiss Spinal dysmyelination SPAST missense Naturally occurring variant yes ARS-UCD1.2 11 g.14742184G>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) Naturally occurring variant yes Y A deletion of the SRY gene 1996 8978769
OMIA 001960-9913 cattle Fleckvieh Abortion due to haplotype FH4 SUGT1 missense Naturally occurring variant yes ARS-UCD1.2 12 g.11102143A>G 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) Naturally occurring variant yes ARS-UCD1.2 5 g.57316723_57316724insG c.363_364insG p.(A124Gfs*42) 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 Naturally occurring variant yes ARS-UCD1.2 9 g.101160274T>C 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 Naturally occurring variant yes 9 "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) Naturally occurring variant yes ARS-UCD1.2 14 g.8432343G>A c.1963C>T p.(R655*) rs480120030 1987 3472203 Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
OMIA 001902-9913 cattle Fleckvieh Male subfertility TMEM95 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 19 g.27056843C>A c.483C>A p.(C161*) 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 Naturally occurring variant yes ARS-UCD1.2 X g.91964644A>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) Naturally occurring variant yes ARS-UCD1.2 11 g.102463944G>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 Naturally occurring variant yes ARS-UCD1.2 19 g.10833921T>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 duplication Naturally occurring variant no ARS-UCD1.2 4 g.27819577_27819586dup c.148_157dup p.(A56Rfs*87) c.DNA position based on NM_001191145.1 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 Naturally occurring variant no 3 "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) 200922: g. info moved to here (g.118,607,715-118,614,131) until it can be standardised "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) Naturally occurring variant no ARS-UCD1.2 29 g.6424971_6424972insG c.925_926insC Insertion causes a frameshift that resulted in a premature stop codon at residue 316, whereas normal sequence contains 517 amino acids. 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. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001249-9913 cattle Dexter Dun brown TYRP1 missense Naturally occurring variant no ARS-UCD1.2 8 g.31633328G>A 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 Naturally occurring variant yes ARS-UCD1.2 17 g.63668380C>T 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 Wagyu Deficiency of uridine monophosphate synthase UMPS nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 1 g.69151931C>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 002423-9913 cattle Japanese Black Multiple ocular defects WFDC1 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 18 g.10567100_10567101insC c.321insC insertion of a single base causes a frame shift mutation and a premature termination codon appeared at codon 126 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. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
OMIA 001736-9913 cattle Charolais Polled and multisystemic syndrome ZEB2 deletion, gross (>20) Naturally occurring variant yes 2 A 3.7Mb deletion encompassing the genes ARHGAP15, GTDC1 and ZEB2 2012 23152852
OMIA 001736-9913 cattle Fleckvieh Polledness, abnormal skull shape, small body stature and subfertility ZEB2 Del11 deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 2 g.52263360_52263370del 2020 33046754
OMIA 002307-9913 cattle Limousin Frontonasal dysplasia ZIC2 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 12 g.76742067del 2021 33388042
Overall Statistics
Total number of variants 230
Variants with genomic location 199 (86.5% )
Variants in a variant database, i.e. with rs ID 53 (23.0%)
Variant Type Count Percent
complex rearrangement 7 3.0%
deletion, gross (>20) 21 9.1%
deletion, small (<=20) 30 13.0%
delins, gross (>20) 2 0.9%
delins, small (<=20) 7 3.0%
duplication 5 2.2%
extension (stop-lost) 2 0.9%
insertion, gross (>20) 5 2.2%
insertion, small (<=20) 12 5.2%
inversion 1 0.4%
missense 81 35.2%
nonsense (stop-gain) 33 14.3%
regulatory 4 1.7%
repeat variation 2 0.9%
splicing 17 7.4%
start-lost 1 0.4%
Year First Reported Count Percent
1987 1 0.4%
1988 0 0.0%
1989 1 0.4%
1990 1 0.4%
1991 0 0.0%
1992 1 0.4%
1993 1 0.4%
1994 0 0.0%
1995 2 0.9%
1996 3 1.3%
1997 4 1.7%
1998 5 2.2%
1999 6 2.6%
2000 5 2.2%
2001 2 0.9%
2002 8 3.5%
2003 2 0.9%
2004 2 0.9%
2005 3 1.3%
2006 8 3.5%
2007 8 3.5%
2008 6 2.6%
2009 7 3.0%
2010 4 1.7%
2011 9 3.9%
2012 15 6.5%
2013 10 4.3%
2014 15 6.5%
2015 11 4.8%
2016 27 11.7%
2017 24 10.4%
2018 6 2.6%
2019 10 4.3%
2020 14 6.1%
2021 9 3.9%