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Link to this search: https://omia.org/results/?search_type=advanced&gb_species_id=9913&result_type=variant&defect=yes&singlelocus=yes&characterised=yes

247 variant records found

[show instead phene records]

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

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

Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.

OMIA Variant ID OMIA Phene-Species ID(s) Species Name Breed(s) Variant Phenotype Gene Allele Type of Variant Source of Genetic Variant Deleterious? Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
1126 OMIA:002238-9913 taurine cattle Shorthorn (Cattle) Ichthyosis, ABCA12-related ABCA12 missense Naturally occurring variant yes ARS-UCD1.2 2 g.103016791A>G c.6776T>C p.(L2259P) NM_001191294.2:c.6776T>C; NP_001178223.2:p.(Leu2259Pro) 2019 31568573
195 OMIA:002238-9913 taurine cattle Chianina (Cattle) Ichthyosis, ABCA12-related ABCA12 missense Naturally occurring variant yes ARS-UCD1.2 2 g.103025585T>C c.5804A>G p.(H1935R) 2008 18344998 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1220 OMIA:002238-9913 taurine cattle Polled Hereford (Cattle) Ichthyosis, ABCA12-related ABCA12 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 2 g.103043495_103043496insG c.5689_5690insC p.(S1784Ifs*33) BTA 2:103043495–103043496insG; ENSBTAT00000004518.6:c.5689‐5690insC; ENSBTAP00000004518.6:p.(Ser1784Ilefs*33) (Eager et al., 2020) rs3423092881 2020 32567073
1477 OMIA:002561-9913 taurine cattle Deutsche Holstein Schwarzbunt, Germany (Cattle) Infertility ABHD16B nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 13 g.53957903G>A c.652C>T p.(Q218*) ENSBTAT00000045249.4; ENSBTAP00000055253.1 rs468948776 2020 31963602
429 OMIA:001271-9913 taurine cattle Dexter (Cattle) 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)
590 OMIA:001271-9913 taurine cattle Dexter (Cattle) Highland (Cattle) Bulldog calf ACAN BD1 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 21 g.20422104_20422105insGGCA c.2266_2267insGGCA Variant initially identified in Dexter cattle and later reported in additional breeds: PMID:26885599 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)
1419 OMIA:002226-9913 taurine cattle Brown Swiss (Cattle) Haplotype with homozygous deficiency BH34 ACSL5 BH34 missense Naturally occurring variant yes ARS-UCD1.2 26 g.32940521C>G c.528C>G p.(N176K) NM_001075650.1 2021 34915862
486 OMIA:000328-9913 taurine cattle Belgian Blue (Cattle) 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
1163 OMIA:001562-9913 taurine cattle Cikasto govedo, Slovenia (Cattle) 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
935 OMIA:001511-9913 taurine cattle Angus (Cattle) 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
1435 OMIA:002535-9913 taurine cattle Original Schweizer Braunvieh, Switzerland (Cattle) Congenital cataract ADAMTSL4 missense Naturally occurring variant yes ARS-UCD1.2 3 g.20146737C>T c.2327G>A p.(R776H) NM_001101061.1; NP_001094531.1 2022 35233794
934 OMIA:002135-9913 taurine cattle Angus (Cattle) 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
1629 OMIA:002788-9913 taurine cattle Holstein Friesian (Cattle) Subfertility, AK9-related AK9 splicing Naturally occurring variant yes ARS-UCD1.2 9 g.40620329A>G rs457222030 2021 34028060
764 OMIA:001009-9913 taurine cattle Shorthorn (Cattle) 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
763 OMIA:001009-9913 taurine cattle Galloway (Cattle) Tibial hemimelia ALX4 ALX4dup-GAU 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. The same ARS-UCD1.2 location in the reverse order was included in the paper by Buitkamp et al. (2022). The allele name ALX4dup-GAU was also given by Buitkamp et al. (2022).
1516 OMIA:001009-9913 taurine cattle Galloway (Cattle) Tibial hemimelia ALX4 ALX4dup-LfL duplication Naturally occurring variant yes ARS-UCD1.2 15 g.74384938_74384919dup Buitkamp et al. (2022): "The ALX4dup-LfL duplication results in a frameshift (amino acid position 151) leading to a truncated protein of 248 nt in length, compared with 303 nt of the wild-type protein (XP_027418402.1)". 2023 36585373
927 OMIA:002083-9913 taurine cattle Japanese Black, Japan (Cattle) 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
286 OMIA:000001-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Holstein (black and white) (Cattle) 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*) Variant initially reported in Holstein Friesian cattle and later reported in additional breeds: PMID:34779908. 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)
731 OMIA:001965-9913 taurine cattle Holstein (black and white) (Cattle) 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
780 OMIA:001334-9913 taurine cattle Swedish Red (Cattle) 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
289 OMIA:000194-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Brown Swiss (Cattle) Holstein Friesian (Cattle) Citrullinaemia ASS1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 11 g.100781668C>T c.256C>T p.(R86*) Variant initially identified in Holstein Friesian and later reported in additional breeds: PMID:30014197, PMID:34779908. 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)
188 OMIA:001450-9913 OMIA:001464-9913 taurine cattle Belgian Blue (Cattle) Maas-Rijn-Ijssel (Cattle) Congenital muscular dystonia 1 ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25933247G>A c.1675C>T p.(R559C) Variant is reported to cause congenital muscular dystonia 1 in Belgian Blue cattle (OMIA 001450-9913) and congenital pseudomyotonia in a Dutch improved red and white cross-bred calf (OMIA:001464_9913). 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). 
219 OMIA:001464-9913 taurine cattle Romagnola (Cattle) Pseudomyotonia, congenital ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25939141C>A c.857G>T p.(G286V) This variant was identified as part of a haplotype with the G211V variant in Romagnola cattle. Akyürek et al. (2022; PMID: 36293223) suggest that the G286V variant is likely to be benign and that the G211V is likely to be causal. 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)
218 OMIA:001464-9913 taurine cattle Romagnola (Cattle) 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)
205 OMIA:001464-9913 taurine cattle Chianina (Cattle) Marchigiana (Cattle) Romagnola (Cattle) Pseudomyotonia, congenital ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25940510C>T c.491G>A p.(R164H) Variant initially identified in Chianina cattle and later reported in additional breeds: PMID: 35717834 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)
298 OMIA:000627-9913 taurine cattle Polled Hereford (Cattle) 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
200 OMIA:000627-9913 taurine cattle Shorthorn (Cattle) 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)
981 OMIA:001991-9913 taurine cattle Nordic Red (Cattle) 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
1660 OMIA:002819-9913 taurine cattle Holstein Friesian (Cattle) Muscle weakness CACNA1S missense Naturally occurring variant yes ARS-UCD1.2 16 g.79613592C>T c.3853G>A p.G1285S ENSBTAT00000065901.3; ENSBTAP00000054797.3 rs3423414874 2024 38246543
1087 OMIA:002201-9913 taurine cattle Normande (Cattle) 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.
1032 OMIA:002167-9913 taurine cattle Nordic Red (Cattle) 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
1528 OMIA:002626-9913 taurine cattle Japanese Black, Japan (Cattle) Haplotype with homozygous deficiency JBH17, CDC45-related CDC45 splicing Naturally occurring variant yes UMD_3.1.1 17 g.74743512G>T located in a splicing donor site at a distance of 5 bp, affecting pre-mRNA splicing 2021 33758295
991 OMIA:001830-9913 taurine cattle Holstein (black and white) (Cattle) 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
964 OMIA:001502-9913 taurine cattle Montbéliarde (Cattle) 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
838 OMIA:002125-9913 taurine cattle Montbéliarde (Cattle) Neurocristopathy CHD7 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 14 g.26402250_26402254del p.(K594Afs*29) 2017 28904385
554 OMIA:002022-9913 taurine cattle Red Dane (Cattle) 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.
210 OMIA:001887-9913 taurine cattle Belgian Blue (Cattle) 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.
648 OMIA:001135-9913 taurine cattle Japanese Black, Japan (Cattle) Renal dysplasia CLDN16 Type 1 deletion, gross (>20) Naturally occurring variant yes 1 37kb deletion of exons 1-4 2000 10810088
781 OMIA:001135-9913 taurine cattle Japanese Black, Japan (Cattle) 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
1669 OMIA:002432-9913 taurine cattle Hereford (Cattle) Retinal degeneration, CLN3-realted CLN3 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 25 g.26043843del c.1106del p.(P369Rfs*8) NM_001075174.2; NP_001068642.2 2024 38516801
593 OMIA:001482-9913 taurine cattle Devon (Cattle) 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
1400 OMIA:001365-9913 taurine cattle Brown Swiss (Cattle) Achromatopsia CNGB3 OH1 missense Naturally occurring variant yes ARS-UCD1.2 14 g.76011964G>A c.751G>A p.(D251N) XM_015474554.2: c.751G>A, XP_015330040.2: p.Asp251Asn ENSBTAT00000065296.2:c.751G>A ENSBTAP00000054173.2:p.Asp251Asn rs716218235 2021 34830323
1031 OMIA:002127-9913 taurine cattle Red Angus (Cattle) 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.) rs3423092630 2019 30788588
839 OMIA:002127-9913 taurine cattle Simmental (Cattle) 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.
1289 OMIA:002127-9913 taurine cattle Holstein (black and white) (Cattle) 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
1698 OMIA:002127-9913 taurine cattle Normande (Cattle) Osteogenesis imperfecta, type II, COL1A1-related COL1A1 missense Naturally occurring variant yes ARS-UCD1.3 19 NC_037346.1:g.36473965G>A NM_001034039.2:c.4234G>A NP_001029211.1:p.(D1412N) 2024 38773368
840 OMIA:001926-9913 taurine cattle Charolais (Cattle) Salers (Cattle) 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
1275 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) 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) 2021 33316082
1241 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) Bulldog calf COL2A1 delins, gross (>20) Naturally occurring variant yes ARS-UCD1.2 5 g.32303127_32306640delinsTCTGGGGAGC 2020 32894162
842 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) 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
414 OMIA:001926-9913 taurine cattle Danish Holstein (Cattle) 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
223 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32307658G>A p.(G960R) 2014 25017103
841 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) 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
1026 OMIA:001926-9913 taurine cattle Holstein (black and white) (Cattle) Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32308734G>A c.3166G>A p.(G1056S) 2019 30378686
1263 OMIA:002295-9913 taurine cattle Holstein (black and white) (Cattle) 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
1184 OMIA:002260-9913 taurine cattle Holstein Friesian (Cattle) 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
292 OMIA:000341-9913 taurine cattle Rotes Höhenvieh, Germany (Cattle) Vorderwälder, Germany (Cattle) 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)
358 OMIA:002111-9913 taurine cattle Holstein (red and white) (Cattle) 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
1418 OMIA:002519-9913 taurine cattle Brown Swiss (Cattle) Haplotype with homozygous deficiency BH24 CPT1C BH24 missense Naturally occurring variant yes ARS-UCD1.2 18 g.56098048G>A c.158G>A p.(G53D) XM_002695120.5 2021 34915862
1186 OMIA:002262-9913 taurine cattle Montbéliarde (Cattle) 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
287 OMIA:001697-9913 taurine cattle Jersey (Cattle) 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.
1251 OMIA:002288-9913 taurine cattle Hereford (Cattle) Mandibulofacial dysostosis CYP26C1 missense Naturally occurring variant yes ARS-UCD1.2 26 g.14404993T>C c.563T>G p.(L188P) ENSBTAT00000056396.3:c.563T>G; ENSBTAP00000050244.2:p.Leu188Arg rs431913023 2020 33105751
1411 OMIA:002508-9913 taurine cattle Simmental (Cattle) Haplotype with homozygous deficiency SH8 CYP2B6 SH8 missense Naturally occurring variant yes ARS-UCD1.2 18 g.50296371A>T c.938T>A p.(I313N) NM_001075173.1 2021 34944310
1624 OMIA:002582-9913 taurine cattle Japanese Black, Japan (Cattle) Hepatic fibrinogen storage disease DGKG missense Genome-editing (CRISPR-Cas9) yes ARS-UCD1.3 1 g.81082187C>T c.2162C>T p.T721I XM_002684869.5; XP_002684915.3 2023 37681469
1412 OMIA:002505-9913 taurine cattle Simmental (Cattle) Haplotype with homozygous deficiency SH5 DIS3 SH5 insertion, small (<=20) Naturally occurring variant unknown ARS-UCD1.2 12 g.47511687_47511687insT c.2032dup p.(I678N*2) NP_025000110.1, XM_025000110.1 2021 34944310
615 OMIA:002109-9913 taurine cattle Brown Swiss (Cattle) 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.
1408 OMIA:002243-9913 taurine cattle Highland (Cattle) Ichthyosis, DSP-related DSP missense Naturally occurring variant yes ARS-UCD1.2 23 g.47826600G>T c.6893C>A p.(A2298D) NM_001192368.2; NP_001179297.1 2022 34996433
711 OMIA:000543-9913 taurine cattle Danish Holstein (Cattle) Anhidrotic ectodermal dysplasia EDA HED6 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 Allele id was copied from Table 1 of Capuzzello et al. (2022)
645 OMIA:000543-9913 taurine cattle Deutsche Holstein Schwarzbunt, Germany (Cattle) Anhidrotic ectodermal dysplasia EDA HED1 deletion, gross (>20) Naturally occurring variant yes X c.397_502del p.(M133Vfs*111) 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 Allele id and p. information were copied from Table 1 of Capuzzello et al. (2022)
1120 OMIA:000543-9913 taurine cattle Prim'Holstein, France (Cattle) Generalized hypohidrotic ectodermal dysplasia EDA HED8 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 Allele id was copied from Table 1 of Capuzzello et al. (2022).
1293 OMIA:000543-9913 taurine cattle Red Angus-Simmental cross Hypohidrotic ectodermal dysplasia EDA HED9 deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 X g.80382423_80435202del GCF_002263795.1 (O'Toole et al., 2021) 2021 33801223 Allele id was copied from Table 1 of Capuzzello et al. (2022).
373 OMIA:000543-9913 taurine cattle Deutsche Holstein Schwarzbunt, Germany (Cattle) Anhidrotic ectodermal dysplasia EDA HED2 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. Allele id was copied from Table 1 of Capuzzello et al. (2022)
1295 OMIA:000543-9913 taurine cattle Holstein Friesian (Cattle) Anhidrotic ectodermal dysplasia EDA HED5 splicing Naturally occurring variant yes ARS-UCD1.2 X g.80411795C>A c.802C>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 Allele id and c. information were copied from Table 1 of Capuzzello et al. (2022)
1294 OMIA:000543-9913 taurine cattle Red Angus-Charolais-Simmental cross Anhidrotic ectodermal dysplasia EDA HED3 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). Allele id was copied from Table 1 of Capuzzello et al. (2022).
1484 OMIA:000543-9913 taurine cattle British Blue x Holstein-Friesian cross Anhidrotic ectodermal dysplasia, EDA-related EDA HED10 deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 X g.80516615_80538514del c.397_502del p.(M133Vfs*111) NM_001081743.2; NP_001075212.1 2022 36068608 Allele id was copied from Table 1 of Capuzzello et al. (2022).
586 OMIA:000543-9913 taurine cattle Japanese Black, Japan (Cattle) Anhidrotic ectodermal dysplasia EDA HED7 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. Allele id was copied from Table 1 of Capuzzello et al. (2022).
482 OMIA:000543-9913 taurine cattle Holstein (black and white) (Cattle) Anhidrotic ectodermal dysplasia EDA HED4 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 X g.80803015_80803033del c.48_66del p.(A16S22fs*55) "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 Allele id and p. information were copied from Table 1 of Capuzzello et al. (2022)
1661 OMIA:000543-9913 taurine cattle Limousin (Cattle) Hypohidrotic ectodermal dysplasia, X-linked EDA HED11 missense Naturally occurring variant yes ARS-UCD1.3 X g.80411716T>C c.881A>G p.(E294G) NM_001081743.2; NP_001075212.1 rs439722471 2024 38252617
1665 OMIA:000543-9913 taurine cattle Fleckvieh-Simmental, Germany (Cattle) Hypohidrotic ectodermal dysplasia, X-linked EDA missense Naturally occurring variant yes ARS-UCD1.3 X g.80417567C>T c.679G>A p.(G227R) NM_001081743.2; NP_001075212.1; published as g.85716041G>A in ARS-UCD2.0 rs1114816375 2023 38275590
843 OMIA:002128-9913 taurine cattle Charolais (Cattle) 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.
1474 OMIA:002560-9913 taurine cattle Lidia, Spain (Cattle) Growth and respiratory lethal syndrome EDN2 missense Naturally occurring variant yes ARS-UCD1.2 3 g.104701617G>A c.149G>A p.(C50Y) ENSBTAG00000021434; ENSBTAT00000028571.3 2022 35912509
191 OMIA:001716-9913 taurine cattle Holstein (black and white) (Cattle) 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
375 OMIA:002540-9913 taurine cattle Japanese Brown, Japan (Cattle) 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.
617 OMIA:002540-9913 taurine cattle Japanese Brown, Japan (Cattle) 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.
534 OMIA:002540-9913 taurine cattle Tiroler Grauvieh (Cattle) 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.
346 OMIA:002042-9913 taurine cattle Belgian Blue (Cattle) 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
713 OMIA:000363-9913 taurine cattle Holstein (black and white) (Cattle) Sahiwal (Cattle) 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
591 OMIA:000363-9913 taurine cattle Japanese Black, Japan (Cattle) Sahiwal (Cattle) 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.
1532 OMIA:001818-9913 taurine cattle Japanese Black, Japan (Cattle) Japanese Brown, Japan (Cattle) Factor XIII deficiency F13A1 missense Naturally occurring variant yes UMD_3.1.1 23 g.48649432T>C c.248T>C p.(F83S) NM_001167894.1; NP_001161366.1; reported in Japanese Brown in PMID: 1996 Reference not in PubMed; see OMIA 001818-9913 for reference details Variant was first reported by Ogawa and Iga (1996). Variant information in this table is based on supplementary table 1 by Shibutani et al. (2023).
1038 OMIA:000437-9913 taurine cattle Fleckvieh-Simmental, Germany (Cattle) Haemophilia A F8 missense Naturally occurring variant yes ARS-UCD1.2 X g.36017426A>T c.134A>T p.(H45L) ENSBTAT00000036726.5:c.134A>T; ENSBTAP00000036581.4:p.His45Leu rs1117392179 2018 29774585
194 OMIA:000437-9913 taurine cattle Japanese Brown, Japan (Cattle) 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
1360 OMIA:002450-9913 taurine cattle Chianina (Cattle) 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
1183 OMIA:002259-9913 taurine cattle Montbéliarde (Cattle) 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
646 OMIA:000151-9913 taurine cattle Holstein (black and white) (Cattle) 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)
201 OMIA:000628-9913 taurine cattle Limousin (Cattle) 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
377 OMIA:000628-9913 taurine cattle Japanese Black, Japan (Cattle) 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
910 OMIA:000836-9913 taurine cattle Blonde d'Aquitaine (Cattle) Limousin (Cattle) 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)
1529 OMIA:002625-9913 taurine cattle Japanese Black, Japan (Cattle) Skeletal dysplasia, FGD3 related FGD3 delins, small (<=20) Naturally occurring variant yes UMD_3.1.1 8 g.85826989_85826990delinsTG p.(H171C) 2015 26306008
1326 OMIA:002374-9913 taurine cattle Holstein Friesian (Cattle) Jersey (Cattle) 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
787 OMIA:002090-9913 taurine cattle Holstein (black and white) (Cattle) 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
1179 OMIA:001703-9913 taurine cattle Holstein (black and white) (Cattle) 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
304 OMIA:001360-9913 taurine cattle Swedish Red and White (Cattle) 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
488 OMIA:000419-9913 taurine cattle Shorthorn (Cattle) 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.
294 OMIA:000419-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Brahman (Cattle) 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; variant initially identified in Brahman cattle and later reported in additional breeds:PMID:34779908. 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.
487 OMIA:000419-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Brahman (Cattle) Droughtmaster (Cattle) 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; variant initially identified in Brahman cattle and later reported in additional breeds: PMID:28444756, PMID:34779908. 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.
1327 OMIA:002375-9913 taurine cattle Holstein Friesian (Cattle) Jersey (Cattle) 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
182 OMIA:001826-9913 taurine cattle Holstein (black and white) (Cattle) 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)
1501 OMIA:002559-9913 taurine cattle Holstein Friesian (Cattle) Persistent truncus arteriosus GATA6 nonsense (stop-gain) Naturally occurring variant unknown ARS-UCD1.2 24 g.34187181T>A c.1249A>T p.K417X ENSBTAT00000007537.6 2022 36333145
1494 OMIA:002579-9913 taurine cattle Irish Moiled (Cattle) Perinatal mortality syndrome, GCK-related GCK splicing Naturally occurring variant yes ARS-UCD1.2 4 g.77173487A>T 2022 36105082
293 OMIA:001442-9913 taurine cattle Japanese Black, Japan (Cattle) 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
302 OMIA:000689-9913 taurine cattle Polled Hereford (Cattle) 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)
778 OMIA:001985-9913 taurine cattle Simmental (Cattle) 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
296 OMIA:002230-9913 taurine cattle Belted Galloway (Cattle) Brown Swiss (Cattle) 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); Variant initially identified in Galloway cattle and later reported in additional breeds: PMID:30014197 2021 33926013
727 OMIA:000317-9913 taurine cattle Highland (Cattle) 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
919 OMIA:001319-9913 taurine cattle Holstein Friesian (Cattle) 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
204 OMIA:001817-9913 taurine cattle Japanese Black, Japan (Cattle) 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
1396 OMIA:001823-9913 taurine cattle Holstein Friesian (Cattle) Haplotype with homozygous deficiency-HH2 IFT80 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 1 g.107172616delT c.1140del p.(L381Ffs*3) g.107172616delT rs523422030 2021 34873723 ENSBTAT00000044761.4:c.1140del ENSBTAP00000042227.4:p.Leu381PhefsTer3
1202 OMIA:002271-9913 taurine cattle Holstein (black and white) (Cattle) 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
1185 OMIA:002261-9913 taurine cattle Holstein (black and white) (Cattle) 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
1577 OMIA:002718-9913 taurine cattle Charolais (Cattle) Epidermolysis bullosa, junctional, ITGA6-related ITGA6 splicing Naturally occurring variant yes ARS-UCD1.2 2 g.24112740C>A c.2160+1G>T p.(I657Mfs) NM_001109981.1 2023 37308849
197 OMIA:000595-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Holstein Friesian (Cattle) Jersey (Cattle) Simmental (Cattle) Leukocyte adhesion deficiency, type I ITGB2 BLAD missense Naturally occurring variant yes ARS-UCD1.2 1 g.144770078T>C c.383A>G p.(D128G) Variant initially identified in Holstein Friesian cattle and later reported in additional breeds. 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.
684 OMIA:001948-9913 taurine cattle Charolais (Cattle) 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
1390 OMIA:002483-9913 taurine cattle Neuromuscular channelopathy KCNG1 missense Naturally occurring variant yes ARS-UCD1.2 13 g.78918850C>A c.1248G>T p.(W416C) NM_001205719.1; NP_001192648.1 2021 34828398
196 OMIA:001722-9913 taurine cattle Marchigiana (Cattle) Romagnola (Cattle) 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)
207 OMIA:002390-9913 taurine cattle Brown Swiss (Cattle) 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
1005 OMIA:000527-9913 taurine cattle Angus (Cattle) Charolais (Cattle) Uckermärker, Germany (Cattle) Progressive ataxia KIF1C missense Naturally occurring variant yes ARS-UCD1.2 19 g.26407668C>T c.608G>A p.(R203Q); p.(R203_T204delinsQ*) ENSBTAT00000081136.1:c.608G>A ENSBTAP00000062635.1:p.Arg203Gln Duchesne et al. (2018): "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." The variant was initially reported in Charolais cattle and later reported in additional breeds (see PMIDs 38338009 and 32281115). rs800926237 2018 30067756
1440 OMIA:001836-9913 taurine cattle Holstein-Friesian, Switzerland (Cattle) Abortion due to haplotype HH13 KIR2DS1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 18 g.62758881G>A c.475C>T p.(Q159*) NM_001097567.1; NP_001091036.1 2022 35361830
748 OMIA:000426-9913 taurine cattle Fjällnära boskap, Sweden (Cattle) Pohjoissuomenkarja, Finland (Cattle) 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
1265 OMIA:002081-9913 taurine cattle Belgian Blue (Cattle) 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
192 OMIA:002081-9913 taurine cattle Friesian cross (Cattle) Jersey cross 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
1337 OMIA:002114-9913 taurine cattle Hereford (Cattle) 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.
909 OMIA:001677-9913 taurine cattle Belgian Blue (Cattle) 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
1387 OMIA:002479-9913 taurine cattle Romagnola (Cattle) Hemifacial microsomia LAMB1 HFM missense Naturally occurring variant unknown ARS-UCD1.2 4 g.49019693G>A c.2002C>T p.(R668C) NM_001206519.1; NP_001193448.1; 2022 34796979
682 OMIA:001678-9913 taurine cattle Hereford (Cattle) 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
1415 OMIA:002516-9913 taurine cattle Brown Swiss (Cattle) Haplotype with homozygous deficiency OH4 LIG3 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.15080336_15080341del c.2483_2484+4delAGGTG p.K828fs NM_001038107.2 2021 34915862
378 OMIA:000963-9913 taurine cattle Angus (Cattle) 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
627 OMIA:000963-9913 taurine cattle Holstein Friesian (Cattle) Syndactyly (mule foot) LRP4 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 15 g.76800972_76800973delinsAT c.4863_4864delinsAT p.(N1621_G1622delinsKC) Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4 2006 16859890
769 OMIA:000963-9913 taurine cattle Simmental (Cattle) 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
768 OMIA:000963-9913 taurine 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
183 OMIA:000185-9913 taurine cattle Japanese Black, Japan (Cattle) 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)
199 OMIA:000625-9913 taurine cattle Galloway (Cattle) 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
198 OMIA:000625-9913 taurine cattle Angus (Cattle) Murray Grey (Cattle) 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)
297 OMIA:000626-9913 taurine cattle Salers (Cattle) 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
1473 OMIA:002381-9913 taurine cattle Romagnola (Cattle) Skeletal-cardio-enteric dysplasia MAP2K2 missense Naturally occurring variant yes ARS-UCD1.2 7 g.19923991C>T c.535G>A p.(R179W) NM_001038071.2; NP_001033160.2; possible de-novo causal variant 2021 34209498
1416 OMIA:002517-9913 taurine cattle Brown Swiss (Cattle) Haplotype with homozygous deficiency BH6 MARS2 BH6 missense Naturally occurring variant yes ARS-UCD1.2 2 g.86191230G>A c.1553G>A p.(R518Q) NM_001098971.1 2021 34915862
1167 OMIA:001544-9913 taurine 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
558 OMIA:002043-9913 taurine cattle Belgian Blue (Cattle) Abortion (embryonic lethality), MED22-related MED22 deletion, small (<=20) Naturally occurring variant yes 11 p.(L38Rfs*25) 2016 27646536
374 OMIA:001106-9913 taurine cattle Blanco Orejinegro, Colombia (Cattle) Tiroler Grauvieh (Cattle) 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". Variant initially identified in Tiroler Grauvieh and later reported in additional breeds: PMID:34779908 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)
644 OMIA:001565-9913 taurine cattle Ayrshire (Cattle) 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
678 OMIA:001931-9913 taurine cattle Holstein (black and white) (Cattle) 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
837 OMIA:001680-9913 taurine cattle Holstein (black and white) (Cattle) 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.
189 OMIA:001680-9913 taurine cattle Fleckvieh-Simmental, Germany (Cattle) 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.
492 OMIA:001819-9913 taurine cattle Brown Swiss (Cattle) Tiroler Grauvieh (Cattle) 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*). Variant was initially described in Tyrolean Grey cattle and later reported in Brown Swiss cattle (PMID: 37675885) 2016 27919260 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
446 OMIA:001819-9913 taurine cattle Japanese Black, Japan (Cattle) 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.
483 OMIA:001541-9913 taurine cattle Simmental (Cattle) Arachnomelia, BTA23 MOCS1 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 23 g.13837657_13837658del c.1224_1225del p.(H408Qfs*51) 220110: changed g.13837654_13837655del to g.13837657_13837658del based on HGVS 3'rule. ENSBTAT00000013792.6:c.1224_1225del ENSBTAP00000013792.5:p.His408GlnfsTer51 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.
208 OMIA:001452-9913 taurine cattle Belgian Blue (Cattle) 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)
491 OMIA:001452-9913 taurine cattle Belgian Blue (Cattle) 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
1417 OMIA:002518-9913 taurine cattle Brown Swiss (Cattle) Haplotype with homozygous deficiency BH14 MRPL55 BH14 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 7 g.2996436C>T c.169C>T p.(R57*) NM_001303490.1 2021 34915862
212 OMIA:000683-9913 taurine cattle Gelbvieh (Cattle) 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.
771 OMIA:000683-9913 taurine cattle Angus (Cattle) Limousin (Cattle) 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.
772 OMIA:000683-9913 taurine cattle Parthenais (Cattle) 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.
618 OMIA:000683-9913 taurine cattle Maine-Anjou (Cattle) 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)
773 OMIA:000683-9913 taurine cattle Maine-Anjou (Cattle) 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.
299 OMIA:000683-9913 taurine cattle Blonde d'Aquitaine (Cattle) Charolais (Cattle) Limousin (Cattle) 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.
300 OMIA:000683-9913 taurine cattle Maine-Anjou (Cattle) Marchigiana (Cattle) 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.
489 OMIA:000683-9913 taurine cattle Angus (Cattle) Asturian Valley (Cattle) Belgian Blue (Cattle) Blonde d'Aquitaine (Cattle) Braford (Cattle) Limousin (Cattle) Murray Grey (Cattle) Parthenais (Cattle) Santa Gertrudis (Cattle) South Devon (Cattle) 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).
301 OMIA:000683-9913 taurine cattle Maine-Anjou (Cattle) Marchigiana (Cattle) 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.
203 OMIA:000683-9913 taurine cattle Gascon (Cattle) Parthenais (Cattle) Piedmont (Cattle) 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.
217 OMIA:001978-9913 taurine cattle Holstein Friesian (Cattle) 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
1500 OMIA:002590-9913 taurine cattle Limousin (Cattle) Cleft palate MYH3 deletion, small (<=20) Naturally occurring variant unknown ARS-UCD1.2 19 g.[29609605-29609615del;29609623A>G] c.[2864T>C;2872_2882del] c.[I955T; p.L958Tfs*5] NM_001101835.1 2022 36309651
556 OMIA:002039-9913 taurine cattle Belgian Blue (Cattle) 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.
202 OMIA:001342-9913 taurine cattle Santa Gertrudis (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
1469 OMIA:002557-9913 taurine cattle Cikasto govedo, Slovenia (Cattle) Leber optic neuropathy ND4L missense Naturally occurring variant yes m.10432T>C Novosel et al. (2022): "two “mutant” Cika cattle animals (GenBank acc. Nos. MZ901663 and MZ MZ901663)" 2019 Reference not in PubMed; see OMIA 002557-9913 for reference details
766 OMIA:002103-9913 taurine cattle Angus (Cattle) 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)
679 OMIA:001936-9913 taurine cattle Romagnola (Cattle) 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
1244 OMIA:000725-9913 taurine cattle Angus (Cattle) 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 rs482882512 2020 32970694
1410 OMIA:002509-9913 taurine cattle Simmental (Cattle) Haplotype with homozygous deficiency SH9 NUBPL SH9 missense Naturally occurring variant yes ARS-UCD1.2 21 g.42154344C>A c.428C>A p.(S143Y) NM_001193042.1 2021 34944310
1468 OMIA:002556-9913 taurine cattle Chianina (Cattle) Double-outlet right ventricle NUMB missense Naturally occurring variant yes ARS-UCD1.2 10 g.84751870G>A c.416C>T p.(T139M) NM_001101951.1; NP_001095421.1 2022 35748177
555 OMIA:002035-9913 taurine cattle Jersey (Cattle) Abortion (embryonic lethality), OBFC1-related OBFC1 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 26 g.24461804_24461805del c.379_380del p.(K127Vfs*29) rs455647476 2016 27646536 220110: Changed from g.24461803_24461804del to g.24461804_24461805del to adhere to HGVS 3'rule ENSBTAT00000019995.6:c.379_380del ENSBTAP00000019995.5:p.Lys127ValfsTer29 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
288 OMIA:000162-9913 taurine cattle Holstein Friesian (Cattle) Red Holstein, Switzerland (Cattle) 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.
428 OMIA:001437-9913 taurine cattle Brown Swiss (Cattle) 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
1443 OMIA:002548-9913 taurine cattle Holstein Friesian (Cattle) Deficiency of haplotype HH35 PCDH15 missense Naturally occurring variant yes ARS-UCD1.2 26 g.5325675C>G c.2599C>G p.(L867V) XM_015460562.2; XP_015316048.2 2022 35361830
820 OMIA:001827-9913 taurine cattle Montbéliarde (Cattle) Vorderwälder, Germany (Cattle) 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
406 OMIA:001953-9913 taurine cattle Belgian Blue (Cattle) 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
339 OMIA:001935-9913 taurine cattle Simmental (Cattle) 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.
1493 OMIA:002578-9913 taurine cattle Holstein (black and white) (Cattle) Mast cell tumour, congenital PLP2 missense Naturally occurring variant yes ARS-UCD1.2 X g.87216480C>T c.50C>T p.(T17I) NM_203363.1; XP_005642144.1 2022 36139188
1166 OMIA:001544-9913 taurine 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
765 OMIA:000827-9913 taurine cattle Brown Swiss (Cattle) Carora, Venezuela (Bolivarian Republic of) (Cattle) 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)
588 OMIA:000161-9913 taurine cattle Polled Hereford (Cattle) 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)
291 OMIA:001485-9913 taurine cattle Angus (Cattle) 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
352 OMIA:001485-9913 taurine cattle Angus (Cattle) Dwarfism, Angus PRKG2 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 6 g.95896205G>A c.2032C>T p.(R678*) ENSBTAT00000003877.4:c.2032C>T ENSBTAP00000003877.4:p.Arg678Ter rs109639251 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
1447 OMIA:001372-9913 taurine cattle Slick hair PRLR SLICK4 nonsense (stop-gain) Naturally occurring variant no ARS-UCD1.2 20 g.39099113C>G c.1281C>G p.(Y427*) NM_001039726.2; NP_001034815.1 2021 33259090
544 OMIA:001372-9913 taurine cattle Carora, Venezuela (Bolivarian Republic of) (Cattle) Romosinuano, Venezuela (Bolivarian Republic of) (Cattle) Senepol (Cattle) Slick hair PRLR SLICK1 deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 20 g.39099214del c.1382del p.(A461Vfs*2) NM_001039726.2; NP_001034815.1 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
974 OMIA:001372-9913 taurine cattle Limonero, Venezuela (Bolivarian Republic of) (Cattle) Slick hair PRLR SLICK3 nonsense (stop-gain) Naturally occurring variant no ARS-UCD1.2 20 g.39099226C>A c.1394C>A p.(S465*) NM_001039726.2; NP_001034815.1 2018 29527221
1448 OMIA:001372-9913 taurine cattle Carora, Venezuela (Bolivarian Republic of) (Cattle) Romosinuano, Venezuela (Bolivarian Republic of) (Cattle) Slick hair PRLR SLICK5 nonsense (stop-gain) Naturally occurring variant no ARS-UCD1.2 20 g.39099228A>T c.1396A>T p.(K466*) NM_001039726.2; NP_001034815.1 2021 33259090
1449 OMIA:001372-9913 taurine cattle Carora, Venezuela (Bolivarian Republic of) (Cattle) Romosinuano, Venezuela (Bolivarian Republic of) (Cattle) Slick hair PRLR SLICK6 nonsense (stop-gain) Naturally occurring variant no ARS-UCD1.2 20 g.39099267C>T c.1435C>T p.(Q479*) NM_001039726.2; NP_001034815.1 2021 33259090
975 OMIA:001372-9913 taurine cattle Carora, Venezuela (Bolivarian Republic of) (Cattle) Limonero, Venezuela (Bolivarian Republic of) (Cattle) Romosinuano, Venezuela (Bolivarian Republic of) (Cattle) Slick hair PRLR SLICK2 nonsense (stop-gain) Naturally occurring variant no ARS-UCD1.2 20 g.39099321C>T c.1489C>T p.(R497*) NM_001039726.2; NP_001034815.1 2018 29527221
193 OMIA:001139-9913 taurine cattle Charolais (Cattle) 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
1688 OMIA:001139-9913 taurine cattle Red Angus (Cattle) Glycogen storage disease V PYGM nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.3 29 NC_037356.1:g.42989581G>A NM_175786.2 c.1948C>T NP_786980.1:p.(R650*) published as c.2257C>T in ARS-UCD1.2 2024 38678201
1689 OMIA:002848-9913 taurine cattle Brown Swiss (Cattle) Spermatogenic failure, QRICH2-related QRICH2 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.3 19 NC_037346.1:g.55436710del XM_002696205.5:c.4929del XP_002696251.3:C1644Afs*52 Coordinates in this table consider 3' rule of HGVS recommendation 2022 35255804
221 OMIA:002037-9913 taurine cattle Holstein Friesian (Cattle) Abortion (embryonic lethality), RABGGTB RABGGTB missense Naturally occurring variant yes ARS-UCD1.2 3 g.69060748T>C c.584A>G p.(Y195C) ENSBTAT00000024551.6:c.584A>G ENSBTAP00000024551.6:p.Tyr195Cys rs1118263722 2016 27646536 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
209 OMIA:002433-9913 taurine cattle Simmental (Cattle) 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)
1442 OMIA:002547-9913 taurine cattle Holstein-Friesian, Switzerland (Cattle) Haplotype HH25 deficiency RIOX1 deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 10 g.84938408_84938437del c.396_425del p.(A133_E142del) NM_001099702.1; NP_001093172.1; published as c.396_425delGGCGCAGACCCCGGCGGCACGCTTGGTGGA 2022 35361830
676 OMIA:001901-9913 taurine cattle Nordic Red (Cattle) Abortion due to deletion of RNASEH2B RNASEH2B deletion, gross (>20) Naturally occurring variant yes UMD3.1 12 g.20100648_20763119del A 662kb deletion encompases the gene RNASEH2B, lack of which creates embryonic lethality. 2014 24391517 Genomic position gained from Mesbah-Uddin et al. (2021) - structural variant id esv4015629 (Database of Genomic Variants archive extracted from Ensembl release 94 - http://ftp.ensembl.org/pub/release-94/).
376 OMIA:001686-9913 taurine cattle Belgian Blue (Cattle) 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)
344 OMIA:002038-9913 taurine cattle Holstein Friesian (Cattle) 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
611 OMIA:002029-9913 taurine cattle Angus (Cattle) Belgian Blue (Cattle) Charolais (Cattle) Gelbvieh (Cattle) Holstein (black and white) (Cattle) Maine-Anjou (Cattle) Normande (Cattle) Red Angus (Cattle) Retinitis pigmentosa 1 RP1 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 14 g.22340665_22340666insA p.(R791Kfs*13) 2016 27510606
858 OMIA:002134-9913 taurine cattle Ayrshire (Cattle) 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
416 OMIA:002041-9913 taurine cattle Belgian Blue (Cattle) 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
1269 OMIA:002297-9913 taurine cattle Holstein Friesian (Cattle) 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
990 OMIA:002149-9913 taurine cattle Holstein (black and white) (Cattle) Abortion due to haplotype HH6 SDE2 start-lost Naturally occurring variant yes ARS-UCD1.2 16 g.29020700A>G c.2T>C p.(M1?) ENSBTAT00000016992.6:c.2T>C ENSBTAP00000016992.5:p.Met1? "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
222 OMIA:002444-9913 taurine cattle Japanese Black, Japan (Cattle) Hydrallantois SLC12A1 missense Naturally occurring variant yes ARS-UCD1.2 10 g.62157819G>A p.(P372L) 2016 27613513
992 OMIA:002150-9913 taurine cattle Rouge des prés, France (Cattle) 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
626 OMIA:000366-9913 taurine cattle Brown Swiss (Cattle) Simmental (Cattle) 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.
187 OMIA:001340-9913 taurine cattle Holstein Friesian (Cattle) 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)
1181 OMIA:001340-9913 taurine cattle Montbéliarde (Cattle) 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
263 OMIA:001828-9913 taurine cattle Montbéliarde (Cattle) Vorderwälder, Germany (Cattle) 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*) 2013 23762392 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
372 OMIA:000593-9913 taurine cattle Holstein (black and white) (Cattle) 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
847 OMIA:001821-9913 taurine cattle Brown Swiss (Cattle) 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
848 OMIA:001821-9913 taurine cattle Brown Swiss (Cattle) 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
303 OMIA:001228-9913 taurine cattle Japanese Black, Japan (Cattle) 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
647 OMIA:002443-9913 taurine cattle Angus (Cattle) Hereford (Cattle) Holstein (black and white) (Cattle) Simmental (Cattle) 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)
904 OMIA:001451-9913 taurine cattle Belgian Blue (Cattle) Congenital muscular dystonia 2 SLC6A5 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)
211 OMIA:001824-9913 taurine cattle Holstein (black and white) (Cattle) Abortion due to haplotype HH3 SMC2 missense Naturally occurring variant yes ARS-UCD1.2 8 g.93753358T>C c.3404T>C p.(F1135S) XM_015472668.2; XP_015328154.1 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)
557 OMIA:002040-9913 taurine cattle Belgian Blue (Cattle) Abortion (embryonic lethality), SNAPC4-related SNAPC4 deletion, small (<=20) Naturally occurring variant yes 11 p.(L1227Afs*134) 2016 27646536
1182 OMIA:002258-9913 taurine cattle Charolais (Cattle) 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
206 OMIA:001247-9913 taurine cattle Brown Swiss (Cattle) 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
920 OMIA:001230-9913 taurine cattle Holstein Friesian (Cattle) Japanese Black, Japan (Cattle) Jersey (Cattle) Ovotesticular DSD (Disorder of Sexual Development) SRY deletion, gross (>20) Naturally occurring variant yes Y A deletion of the SRY gene 1996 8978769
214 OMIA:001960-9913 taurine cattle Simmental (Cattle) 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
587 OMIA:000059-9913 taurine cattle Brown Swiss (Cattle) 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)
213 OMIA:001951-9913 taurine cattle Holstein (black and white) (Cattle) Vertebral and spinal dysplasia TBXT 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
963 OMIA:001941-9913 taurine cattle Holstein (black and white) (Cattle) 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
295 OMIA:000424-9913 taurine cattle Africander (Cattle) 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
779 OMIA:001902-9913 taurine cattle Simmental (Cattle) 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
410 OMIA:000542-9913 taurine cattle Pezzata Rossa Italiana, Italy (Cattle) 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)
345 OMIA:002036-9913 taurine cattle Holstein Friesian (Cattle) 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
776 OMIA:001939-9913 taurine cattle Brown Swiss (Cattle) Simmental (Cattle) Haplotype with homozygous deficiency 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
1414 OMIA:002515-9913 taurine cattle Brown Swiss (Cattle) Haplotype with homozygous deficiency OH2 TUBGCP5 missense Naturally occurring variant yes ARS-UCD1.2 2 g.1268426G>T c.311C>A p.(T104K) NM_001102495.1 2021 34915862
589 OMIA:000202-9913 taurine cattle Brown Swiss (Cattle) 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.
404 OMIA:001934-9913 taurine cattle Ayrshire, Finland (Cattle) Ptosis, intellectual disability, retarded growth and mortality (PIRM) syndrome UBE3B splicing Naturally occurring variant yes ARS-UCD1.2 17 g.63668380C>T c.2076G>A p.(E692E) ENSBTAT00000003493.5:c.2076G>A ENSBTAP00000003493.4:p.Glu692= 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
1409 OMIA:002298-9913 taurine cattle Jersey (Cattle) Neuropathy with splayed forelimbs UCHL1 JNS missense Naturally occurring variant yes ARS-UCD1.2 6 g.60158901G>A c.979G>A p.(E327K) Several transcripts are reported: ENSBTAT00000046823.2:c.718G>A ENSBTAP00000044075.1:p.Glu240Lys ENSBTAT00000066434.1:c.931G>A ENSBTAP00000063885.1:p.Glu311Lys ENSBTAT00000072800.1:c.979G>A ENSBTAP00000059848.1:p.Glu327Lys ENSBTAT00000074165.1:c.706G>A ENSBTAP00000057432.1:p.Glu236Lys rs1116058914 2022 34955244
290 OMIA:000262-9913 taurine cattle Holstein (black and white) (Cattle) Holstein Friesian (Cattle) Red Holstein, Switzerland (Cattle) Wagyu (Cattle) 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)
592 OMIA:002423-9913 taurine cattle Japanese Black, Japan (Cattle) 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.
1618 OMIA:002759-9913 taurine cattle Brown Swiss (Cattle) Brachygnathia WNT10B duplication Naturally occurring variant unknown ARS-UCD1.2 5 g.30846510dup c.910dup p.R304Pfs*14 XM_010805029.3; XP_010803331.1; published as g.30,846,510dupC; c.910dupC; variant is associated with increased risk of brachygnathia rs525007739 2023 37641348
921 OMIA:001736-9913 taurine cattle Charolais (Cattle) 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
1246 OMIA:001736-9913 taurine cattle Simmental (Cattle) 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
1283 OMIA:002307-9913 taurine cattle Limousin (Cattle) Frontonasal dysplasia ZIC2 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 12 g.76742067del c.1596del p.(S453X) 2021 33388042
Overall Statistics
Total number of variants 247
Variants with genomic location 221 (89.5% )
Variants in a variant database, i.e. with rs ID 55 (22.3%)
Variant Type Count Percent
complex rearrangement 2 0.8%
deletion, gross (>20) 22 8.9%
deletion, small (<=20) 30 12.1%
delins, gross (>20) 2 0.8%
delins, small (<=20) 9 3.6%
duplication 4 1.6%
extension (stop-lost) 2 0.8%
insertion, gross (>20) 4 1.6%
insertion, small (<=20) 12 4.9%
inversion 1 0.4%
missense 94 38.1%
nonsense (stop-gain) 40 16.2%
regulatory 2 0.8%
repeat variation 1 0.4%
splicing 21 8.5%
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 0 0.0%
1996 4 1.6%
1997 4 1.6%
1998 5 2.0%
1999 5 2.0%
2000 5 2.0%
2001 2 0.8%
2002 7 2.8%
2003 1 0.4%
2004 2 0.8%
2005 3 1.2%
2006 7 2.8%
2007 7 2.8%
2008 4 1.6%
2009 6 2.4%
2010 4 1.6%
2011 8 3.2%
2012 11 4.5%
2013 8 3.2%
2014 13 5.3%
2015 12 4.9%
2016 26 10.5%
2017 21 8.5%
2018 5 2.0%
2019 7 2.8%
2020 13 5.3%
2021 27 10.9%
2022 15 6.1%
2023 5 2.0%
2024 5 2.0%