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245 variant records found

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

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

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 Inferred EVA rsID Year Published PubMed ID(s) Acknowledgements
1126 OMIA002238-9913 cattle Shorthorn 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 OMIA002238-9913 cattle Chianina 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 OMIA002238-9913 cattle Poll Hereford 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 rs3423092881 2020 32567073
429 OMIA001271-9913 cattle Dexter Bulldog calf ACAN BD2 regulatory Naturally occurring variant yes ARS-UCD1.2 21 g.20377856C>T c.-198C>T rs3423095877 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 OMIA001271-9913 cattle Dexter Scottish Highland Bulldog calf ACAN BD1 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 21 g.20422104_20422105insGGCA c.2266_2267insGGCA 2007 17952705 Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1060 OMIA001271-9913 cattle Miniature Zebu Bulldog calf ACAN insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 21 g.20428539_20428540insC c.5688_5689insC p.(V1897fs*9) cDNA position based on transcript NM_173981.2 2018 30305023
1419 OMIA002226-9913 cattle Brown Swiss Haplotype with homozygous deficiency BH34 ACSL5 BH34 missense Naturally occurring variant yes ARS-UCD1.2 26 32940521C>G c.528C>G p.(N176K) NM_001075650.1 2021 34915862
486 OMIA000328-9913 cattle Belgian Blue Ehlers-Danlos syndrome, type VII (Dermatosparaxis) ADAMTS2 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 7 g.2017035_2017051delinsAGC c.464_480delinsAGC 1999 10417273 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
1163 OMIA001562-9913 cattle Slovenian Cika Pulmonary hypoplasia and anasarca syndrome ADAMTS3 missense Naturally occurring variant yes ARS-UCD1.2 6 g.87462016G>A c.1222C>T p.(H408T) NM_001192797.1: c.1222C>T; NP_001179726.1: p.(His408Tyr) (Häfliger et al., 2020) 2020 32069517
935 OMIA001511-9913 cattle Angus Contractual arachnodactyly (Fawn calf syndrome) ADAMTSL3 deletion, gross (>20) Naturally occurring variant yes 21 "a large (~58 kilobase pair) deletion affecting the ADAMTSL3 gene" 2014 Reference not in PubMed; see OMIA 001511-9913 for reference details
934 OMIA002135-9913 cattle Angus Arthrogryposis multiplex congenita, AGRN-related AGRN deletion, gross (>20) Naturally occurring variant yes 16 A 23,363 bp deletion "encompasses the entirety of the ISG15 ubiquitin-like modifier (ISG15) gene . . . one or both of the 5' regulatory region of the hairy and enhancer split 4 (HES4) and of the agrin (AGRN) gene and of the first two exons of the AGRN gene" (Beever and Marron, 2011) 2011 Reference not in PubMed; see OMIA 002135-9913 for reference details
764 OMIA001009-9913 cattle Shorthorn Tibial hemimelia ALX4 deletion, gross (>20) Naturally occurring variant yes 15 Deletion of 45,694 bp including exon 1 of ALX4 2012 Reference not in PubMed; see OMIA 001009-9913 for reference details
763 OMIA001009-9913 cattle Galloway Tibial hemimelia ALX4 duplication Naturally occurring variant yes ARS-UCD1.2 15 g.74384916_74384935dup UMD3.1 position is g.75154399_75154418dup. Duplication of 20bp in exon 2 is predicted to result in a frameshift leading to a premature stop codon and truncated protein. 2015 26076463 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
927 OMIA002083-9913 cattle Japanese Black Abortion (embryonic lethality), ANXA10-related ANXA10 repeat variation Naturally occurring variant yes 8 "a "34-kb deleted-type" CNV "associated with embryonic mortality at 30-60 days after artificial insemination. The CNV harbors exon 2 to 6 of ANNEXIN A10 (ANXA10). . . . Western blot analysis showed that the CNV results in a null allele of ANXA10." 2016 27881083
286 OMIA000001-9913 cattle Friesian Holstein Abortion due to a nonsense mutation in APAF1 on haplotype HH1 APAF1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 5 g.62810245C>T c.1741C>T p.(Q581*) rs448942533 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 OMIA001965-9913 cattle Holstein Holstein cholesterol deficiency APOB insertion, gross (>20) Naturally occurring variant yes 11 "1.3kb insertion of a transposable LTR element (ERV2-1) in the coding sequence of the APOB gene, which leads to truncated transcripts and aberrant splicing [p.Gly135ValfsX10)]" 2016 26763170
780 OMIA001334-9913 cattle Swedish Red Sperm, short tail ARMC3 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 13 g.24024660del c.1442del p.(A451fs*26) rs797454424 2016 26923438 Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
712 OMIA000201-9913 cattle Normande Brindle ASIP Abr insertion, gross (>20) Naturally occurring variant no 13 "insertion of a full-length Bos taurus LINE element" 2006 16827753
289 OMIA000194-9913 cattle Holstein-Friesian Citrullinaemia ASS1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 11 g.100781668C>T c.256C>T p.(R86*) 1989 2813370 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
188 OMIA001450-9913 cattle Belgian Blue Red and White Dutch Congenital muscular dystonia 1 ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25933247G>A c.1675C>T p.(R559C) 2008 18344998 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
219 OMIA001464-9913 cattle Romagnola Pseudomyotonia, congenital ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25939141C>A c.857G>T p.(G286V) rs3423529256 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 OMIA001464-9913 cattle Romagnola Pseudomyotonia, congenital ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25939366C>A c.632G>T p.(G211V) 2012 23046865 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
205 OMIA001464-9913 cattle Chianina Pseudomyotonia, congenital ATP2A1 missense Naturally occurring variant yes ARS-UCD1.2 25 g.25940510C>T c.491G>A p.(R164H) rs3423529241 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 OMIA000627-9913 cattle Poll Hereford Maple syrup urine disease BCKDHA nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 18 g.50551011C>T c.148C>T p.(Q50*) cDNA position based on ENSBTAT00000021342.6 1990 2303405
200 OMIA000627-9913 cattle Shorthorn Maple syrup urine disease BCKDHA missense Naturally occurring variant yes ARS-UCD1.2 18 g.50560242C>T c.1380C>T p.(P372L) rs3423447991 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)
305 OMIA001079-9913 cattle Holstein Yellow fat BCO2 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 15 g.22552375G>A c.306G>A p.(W102*) UMD3.1 position is g.22877552G>A; cDNA position is based on XM_024975217.1 rs109226280 rs109226280 2009 19398771 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
981 OMIA001991-9913 cattle Nordic Red Stillbirth BTBD9 deletion, gross (>20) Naturally occurring variant yes 23 "∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8)" 2016 27091210
1087 OMIA002201-9913 cattle Normande Abortion due to haplotype NH7 CAD missense Naturally occurring variant yes ARS-UCD1.2 11 g.72409143T>C p.(Y452C) published as CAD g.72399397T>C; p.Tyr452Cys 2019 31056337 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1032 OMIA002167-9913 cattle Nordic Red Asthenospermia CCDC189 splicing Naturally occurring variant yes ARS-UCD1.2 25 g.26880841C>T Touru et al. (2019): "a variant disrupting a canonical 5’ splice donor site (GCA_000003055.3:Chr25:g.27138357C>T) in CCDC189 (transcript - ID:ENSBTAT00000045037) encoding the coiled-coil domain containing protein 189." 2019 30975085
991 OMIA001830-9913 cattle Holstein Abortion due to haplotype HH7 CENPU deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 27 g.15123637_15123640del Hozé et al. (2019): "Considering that CENPU is transcribed in the antisense orientation, this mutation is predicted to result in deletion of the nucleotides located at position +3 to + 6 bp after the splicing donor site of exon 11. Using cross-species nucleotide alignment, we observed that the nucleotide at position +3 is entirely conserved among vertebrates . . . , which suggests that it plays an important role in regulation of CENPU splicing. If modified after exon 11, the abnormal splicing of CENPU could cause mRNA decay or the production of a protein modified after residue 319 out of 409 AA. Based on these factors, we assumed that mutation g.14168130_14168133delTACT on chromosome 27 alters the splicing of CENPU and is embryonic lethal." 2020 31733857
964 OMIA001502-9913 cattle Montbeliarde Caprine-like Generalized Hypoplasia Syndrome CEP250 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 13 g.64710424C>T c.493C>T p.(Q165*) 2015 25902731 Coordinates obtained from and/or confirmed by EBI's VEP
838 OMIA002125-9913 cattle Montbeliarde Neurocristopathy CHD7 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 14 g.26402250_26402254del p.(K594Afs*29) 2017 28904385
554 OMIA002022-9913 cattle Red Danish Arthrogryposis multiplex congenita, CHRNB1-related CHRNB1 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.27122027del c.55del p.(A19Pfs47*) Published as Chr19:27757270CG > C; CHRNB1 c.55delG; (p.Ala19Profs47*) 2016 27364156 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
490 OMIA000685-9913 cattle Brahman Myasthenic syndrome, congenital, CHRNE-related CHRNE 470del20 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.26485848_26485867del c.470_489del Kraner et al. (2002): "a loss of 20 bp within the coding sequence of exon 5 (Fig. 2), between nucleotide 469 and 490 (nucleotide numbering referring to the cDNA sequence published under accession number X02597". These authors (and subsequent authors) call this variant "470del20". The current (2020) HGVS nomenclature is c.470_489del 200922: g. information move here (g.27119615) until standardised 2002 12481987 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
210 OMIA001887-9913 cattle Belgian Blue Osteopetrosis with gingival hamartomas CLCN7 missense Naturally occurring variant yes ARS-UCD1.2 25 g.[1139611G>T; 1139613A>G] c.[2248T>C;2250C>A] p.(Y750Q) 2014 24159188 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
648 OMIA001135-9913 cattle Japanese Black Renal dysplasia CLDN16 Type 1 deletion, gross (>20) Naturally occurring variant yes 1 37kb deletion of exons 1-4 2000 10810088
781 OMIA001135-9913 cattle Japanese Black Renal dysplasia CLDN16 Type 2 deletion, gross (>20) Naturally occurring variant yes 1 "a 56-kb deletion that eliminates exons 1-4 and 21-bp of exon 5" 200922: g. info moved to here (g.77528017_?) until can be standardised 2002 12047224 Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
593 OMIA001482-9913 cattle Devon Neuronal ceroid lipofuscinosis, 5 CLN5 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 12 g.52112732_52112733insG c.662_663insG p.(R221Gfs*6) 2006 16935476 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) 210909: after checking the genome assembly sequence, FN changed g.52461241insG to g.52461241_52461242insG; and c.662insG to c.662_663insG
1400 OMIA001365-9913 cattle Braunvieh 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 rs716218235 2021 34830323
1031 OMIA002127-9913 cattle Red Angus Osteogenesis imperfecta, type II, COL1A1-related COL1A1 missense Naturally occurring variant yes ARS-UCD1.2 19 g.36463798G>A c.1063G>A p.(G355S) Petersen et al. (2019): "PolyPhen-2 predicted the mutation to be “probably damaging” with a score of 1.000 (sensitivity 0.00; specificity 1.00). Similarly, PROVEAN prediction classified the variant as “Deleterious” with a score of − 4.615, exceeding both the default (− 2.5) and stringent (− 4.1) thresholds for this classification." The genomic coordinate in the UMD3.1 assembly is g.37094333G>A (Petersen et al., 2019). The coding sequence coordinates are c.1063G>A (ENSBTAT00000017420.4) (Petersen, pers. comm.) rs3423092630 rs3423092630 2019 30788588
839 OMIA002127-9913 cattle Fleckvieh Osteogenesis imperfecta, type II, COL1A1-related COL1A1 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.36470764_36470767delinsT c.3145_3148delinsT p.(A1049_P1050delinsS) UMD3.1 position is g.37101299_37101302delinsT; cDNA position based on ENSBTAT00000017420.4 rs876049195 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 OMIA002127-9913 cattle Holstein Osteogenesis imperfecta, type II, COL1A1-related COL1A1 missense Naturally occurring variant yes ARS-UCD1.2 19 g.36473359T>A c.3917T>A p.(V1306E) NM_001034039.2: c.3917T>A; XP_024835395.1: p.Val1306Glu (Jacinto et al., 2021) 2021 33672767
840 OMIA001926-9913 cattle Charolais Salers Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32301746G>A c.1791G>A p.(G600D) 2017 28904385 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1275 OMIA001926-9913 cattle Holstein Bulldog calf COL2A1 deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 5 g.32301911_32308589del "Sanger sequencing revealed the precise breakpoints of the heterozygous deletion from position 32 301 911 located in intron 25 to 32 308 589 located within exon 45. The 6679 bp deletion includes the entire sequence of 18 exons (26–44) plus the first 36 nucleotides of exon 45" (Jacinto et al., 2020) 2020 33316082
1241 OMIA001926-9913 cattle Holstein Bulldog calf COL2A1 delins, gross (>20) Naturally occurring variant yes ARS-UCD1.2 5 g.32303127_32306640delinsTCTGGGGAGC 2020 32894162
842 OMIA001926-9913 cattle Holstein Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32303739G>A c.2158G>A p.(G720S) 2017 28904385 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
414 OMIA001926-9913 cattle Danish Holstein bulldog calf COL2A1 splicing Naturally occurring variant yes ARS-UCD1.2 5 g.32305226G>A c.2463+1G>A 2016 27296271 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
223 OMIA001926-9913 cattle Holstein Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32307658G>A p.(G960R) rs3423194986 2014 25017103
841 OMIA001926-9913 cattle Holstein Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32308008G>A c.2986G>A p.(G996S) rs876243579 rs876243579 2017 28904385 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1026 OMIA001926-9913 cattle Holstein Bulldog calf COL2A1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.32308734G>A c.3166G>A p.(G1056S) 2019 30378686
1263 OMIA002295-9913 cattle Holstein Ehlers-Danlos syndrome, classic type, 2 COL5A2 missense Naturally occurring variant yes ARS-UCD1.2 2 g.7331916G>T c.2366G>T p.(G789V) XM_024979774.1: c.2366G>T; XP_024835542.1: p.Gly789Val (Jacinto et al., 2020) 2020 33143196
1184 OMIA002260-9913 cattle Holstein de novo mutation in an AI sire COL6A3 missense Naturally occurring variant yes ARS-UCD1.2 3 g.116826597G>A p.(T1894M) Bourneuf et al. (2017) detected COL6A3 g.117453719G>A; p.T1894M as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Holstein AI bull. No information was provided on the descendants of this bull. 2017 28904385
292 OMIA000341-9913 cattle Rotes Höhenvieh Vorderwald Epidermolysis bullosa, dystrophic COL7A1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 22 g.51301158C>T c.4762C>T p.(R1588*) rs876174537 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)
215 OMIA001529-9913 cattle Holstein Dominant red COPA DR^DR missense Naturally occurring variant no ARS-UCD1.2 3 g.9361962C>T c.478C>T p.(R160C) rs3423151160 2017 28904385 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
358 OMIA002111-9913 cattle Red Holstein Friesian Cataract, recessive, CPAMD8-related CPAMD8 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 7 g.6073556C>T c.220C>T p.(Q74*) 2017 28683140
1418 OMIA002519-9913 cattle Brown Swiss Haplotype with homozygous deficiency BH24 CPT1C BH24 missense Naturally occurring variant yes ARS-UCD1.2 18 56098048G>A c.158G>A p.(G53D) XM_002695120.5 2021 34915862
220 OMIA002033-9913 cattle Numerous breeds A2 milk CSN2 A2 missense Naturally occurring variant no ARS-UCD1.2 6 g.85451298T>G c.245A>C p.(H82P) Note that cattle cannot be genotyped for the A2 allele solely on the basis of the c.245A>C variant because this variant is common to 4 other alleles; see Table 2 of Caroli et al. (2009) J. Dairy Sci. 92, 5335-5352 (Matt McClure, pers. comm.) rs43703011 rs43703011 2013 23102962 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1186 OMIA002262-9913 cattle Montbeliarde de novo mutation in an AI sire CSNK1G2 missense Naturally occurring variant yes ARS-UCD1.2 7 g.44265842G>C p.(D164H) Bourneuf et al. (2017) detected Chr7 CSNK1G2 g.45885860G>C; p.D164H as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Montbéliarde AI bull. No information was provided on the descendants of this bull. 2017 28904385
287 OMIA001697-9913 cattle Jersey Abortion due to haplotype JH1 CWC15 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 15 g.15449431C>T c.163C>T p.(R55*) UMD3.1 position is g.15707169C>T, cDNA and protein positions based on XM_005215764.2 rs1115118696 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 OMIA002288-9913 cattle Hereford 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 rs431913023 2020 33105751
1411 OMIA002508-9913 cattle Simmental 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
1412 OMIA002505-9913 cattle Simmental 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 OMIA002109-9913 cattle Brown Swiss Tricho-dento-osseous-like syndrome DLX3 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.36665831_36665832insGGAGCACA c.584_585insGGAGCACAGG p.(S198Rfs*99) NM_001081622 position is g.37298375_37298376insGGAGCACA 2017 28670783 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1408 OMIA002243-9913 cattle Scottish Highland 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 OMIA000543-9913 cattle Danish Holstein Anhidrotic ectodermal dysplasia EDA insertion, gross (>20) Naturally occurring variant yes X "a LINE1-derived pseudoexon between EDA exons 1 and 2. The 161-bp-long pseudoexon introduces a shift in reading frame and a premature stop codon early in EDA exon 2" 2011 22034998
645 OMIA000543-9913 cattle German Holstein Anhidrotic ectodermal dysplasia EDA deletion, gross (>20) Naturally occurring variant yes X c.397_502del a large deletion including exon 3 in the gene for ectodysplasin (ED1; now called EDA) 200922: g. info moved to here (g.85821470) until it can be standardised 2001 11591646 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
1120 OMIA000543-9913 cattle French Holstein Generalized hypohidrotic ectodermal dysplasia EDA inversion Naturally occurring variant yes ARS-UCD1.2 X g.77174882_80737442inv Escouflaire et al. (2019): The "first breakpoint . . . [is] between positions 82,271,052 and 82,271,053 bp on chromosome X . . . The second breakpoint is situated at position 86,034,441 bp within the EDA intron 1" 2019 31533624
1293 OMIA000543-9913 cattle Red Angus-Simmental cross Hypohidrotic ectodermal dysplasia EDA deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 X g.80382423_80435202del GCF_002263795.1 (O'Toole et al., 2021) 2021 33801223
373 OMIA000543-9913 cattle German Holstein Anhidrotic ectodermal dysplasia EDA splicing Naturally occurring variant yes ARS-UCD1.2 X g.80411671A>C c.924+2T>G c.DNA position is based on NM_001081743.2 2002 12021844 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1295 OMIA000543-9913 cattle Holstein Friesian Anhidrotic ectodermal dysplasia EDA splicing Naturally occurring variant yes ARS-UCD1.2 X g.80411795C>A "a single nucleotide polymorphism (SNP) G/A at the 9th base of exon 8 [GenBank: AJ278907.1 position 30.549] ... Sequencing of the RT-PCR products revealed that the amplified fragment of the affected animals lacked ... exon 8. At the protein level, the exon skipping leads to a frameshift and consequently to a premature stop codon." (Gargani et al., 2011) 2011 21740563
1294 OMIA000543-9913 cattle Red Angus-Charolais-Simmental cross Anhidrotic ectodermal dysplasia EDA nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 X g.80415626G>A c.730C>T p.(R244*) 2007 17616058 Reference not in PubMed; see OMIA 000543-9913 for reference details The g. coordinate for the named reference genome assembly, together with the c. coordinate, were kindly provided by Tosso Leeb (22 March 2021)
586 OMIA000543-9913 cattle Japanese Black Anhidrotic ectodermal dysplasia EDA insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 X g.80802800_80802801insCCCT c.280_281insAGGG p.(G94Qfs*49) 2012 22497423 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
482 OMIA000543-9913 cattle Holstein Anhidrotic ectodermal dysplasia EDA deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 X g.80803015_80803033del c.48_66del "a 19-bp deletion at nucleotides c.48_66 in exon 1 ... . This mutation is predicted to generate a truncated 49 aa protein." 2011 21410470
843 OMIA002128-9913 cattle Charolais Anhidrotic ectodermal dysplasia, EDAR-related EDAR insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 11 g.44599876_44599877insC p.(P161Rfs*97) UMD3.1 position is g.44462236_44462237insC 2017 28904385 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
191 OMIA001716-9913 cattle Holstein Ehlers-Danlos syndrome, Holstein variant EPYC missense Naturally occurring variant yes ARS-UCD1.2 5 g.20856381C>A c.258G>T p.(S87N) 1999 10357109 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
375 OMIA000187-9913 cattle Japanese Brown Chondrodysplasia EVC2 splicing Naturally occurring variant yes ARS-UCD1.2 6 g.103594013C>T c.1356C>T Variant creates a cryptic splice donor site in exon 11 which is leading to improper splicing at position c.1355 and resulting in the 56-base RNA deletion between 1355 and 1410. The deletion causes a frameshift and premature termination. 2002 12136126 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
617 OMIA000187-9913 cattle Japanese Brown Chondrodysplasia EVC2 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 6 g.103609778_103609779delinsG c.2327_2328delinsG p.(A776Gfs*22) Published as c.2054_2055delCAinsG, cDNA and protein position in this table based on ENSBTAT00000005613.6 2002 12136126 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
534 OMIA000187-9913 cattle Tyrolean Grey Chondrodysplasia EVC2 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 6 g.103651709_103651710del c.2993_2994del p.(D998Efs*13) 2014 24733244 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. 210909 FN: given that the variant is a 2bp del (AC), g.103651710_103651710del needs to be changed. BLASTing with AGAGGAGCAAGAAGAC from Fig.4 indicates that it is 719 and 710 that are deleted. THus the entry is changed to g.103651709_103651710del; and AC is removed from the c. entry.
346 OMIA002042-9913 cattle Belgian Blue Abortion (embryonic lethality), EXOSC4 EXOSC4 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 14 g.755826G>A c.190G>A p.(R64*) rs3423357300 2016 27646536 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
713 OMIA000363-9913 cattle Holstein Sahiwal Factor XI deficiency F11 insertion, gross (>20) Naturally occurring variant yes 27 a 76-bp insertion in exon 12 of the Factor XI gene 200922: g. and c. info moved here (g.15367048; c.1406ins76) until can be standardised 2004 15566468 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
591 OMIA000363-9913 cattle Japanese Black Factor XI deficiency F11 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 27 g.16305660delinsATATGTGCAGAATATA c.870delinsATATGTGCAGAATATA P.(F290delinsLYVQNI) 2005 16104386 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1038 OMIA000437-9913 cattle German Fleckvieh 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 rs1117392179 2018 29774585
194 OMIA000437-9913 cattle Japanese Brown Haemophilia A F8 missense Naturally occurring variant yes ARS-UCD1.2 X g.36145188T>A c.6458T>A p.(L2153H) 2009 19456318 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1360 OMIA002450-9913 cattle Chianina Ichthyosis congenita FA2H insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 18 g.2205625_2205626insG c.9dupC p.(A4Rfs*142) NM_001192455.1; NP_001179384.1 2021 34599683
1183 OMIA002259-9913 cattle Montbeliarde de novo mutation in an AI sire FAM189A1 missense Naturally occurring variant yes ARS-UCD1.2 21 g.28112913T>C p.(N192S) Bourneuf et al. (2017) detected FAM189A1 g.28644665T>C; p.N192S as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Montbéliarde AI bull. No information was provided on the descendants of this bull. 2017 28904385
646 OMIA000151-9913 cattle Holstein Brachyspina FANCI deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 21 g.20773899_20777226del p.(V877Lfs*27) 2012 22952632 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
201 OMIA000628-9913 cattle Limousin Marfan syndrome FBN1 missense Naturally occurring variant yes ARS-UCD1.2 10 g.61831200G>A c.3598G>A p.(E1200K) 2005 15776436 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
377 OMIA000628-9913 cattle Japanese Black Marfan syndrome FBN1 splicing Naturally occurring variant yes ARS-UCD1.2 10 g.61917867G>A c.8227-1G>A 2012 22221020 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
910 OMIA000836-9913 cattle Blonde d'Aquitaine Limousin Protoporphyria FECH extension (stop-lost) Naturally occurring variant yes ARS-UCD1.2 24 g.56787697C>A c.1250G>T p.(*417Lext*27) 1998 9784594 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1326 OMIA002374-9913 cattle Holstein Friesian Jersey Charcot Marie Tooth disease FGD4 splicing Naturally occurring variant yes ARS-UCD1.2 5 g.77262490C>T c.1671+1G>A Splice donor mutation based on XM_005206883.3 2021 34045765
787 OMIA002090-9913 cattle Holstein Facial dysplasia syndrome FGFR2 missense Naturally occurring variant yes ARS-UCD1.2 26 g.41489034C>A c.927G>T p.(W309C) 2017 28768473 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1179 OMIA001703-9913 cattle Holstein Chondrodysplasia, disproportionate FGFR3 extension (stop-lost) Naturally occurring variant yes ARS-UCD1.2 6 g.116767863C>A c.2408G>T p.(*803Lext*93) NM_174318.3: c.2408G>T; [XM_024992994.1: p.(Ter803Leuext*93) 2020 32239744
304 OMIA001360-9913 cattle Swedish Red and White Trimethylaminuria (fishy taint) FMO3 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 16 g.38666821C>T c.712C>T p.(R238*) rs797790546 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
1299 OMIA002318-9913 cattle Montbeliarde coat colour, dilution (milca) FZD7 missense Naturally occurring variant no ARS-UCD1.2 2 g.90572569G>C c.1241G>C p.(G414A) CDS position in transcript ENSBTAT00000002946.6 based on ENSEMBL Variant Effect Predictor 2021 33686687
488 OMIA000419-9913 cattle Shorthorn Glycogen storage disease II GAA E18 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.52484973_52484974del c.2454_2455del p.(T819R) 2000 10723725 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
294 OMIA000419-9913 cattle Brahman Glycogen storage disease II GAA E13 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 19 g.52488949G>A c1783C>T p.(R595*) UMD3.1 position is g.53105979C>T 2000 10723725 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
487 OMIA000419-9913 cattle Brahman Droughtmaster Glycogen storage disease II GAA E7 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.52492405_52492406del c.1057_1058del p.(Y353L) UMD3.1 position is g.53109436_53109437del 2000 10723725 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1327 OMIA002375-9913 cattle Holstein Friesian Jersey Congenital disorder of glycosylation GALNT2 splicing Naturally occurring variant yes ARS-UCD1.2 28 g.2281801G>A c.1561-1G>A Splice acceptor mutation based on NM_001193103.1. 2021 34045765
182 OMIA001826-9913 cattle Holstein Abortion due to haplotype HH4 GART missense Naturally occurring variant yes ARS-UCD1.2 1 g.1997582A>C c.869A>C p.(N290T) rs465495560 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)
293 OMIA001442-9913 cattle Japanese Black Forelimb-girdle muscular anomaly GFRA1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 26 g.36627244G>A c.430C>T p.(Q144*) 2013 Reference not in PubMed; see OMIA 001442-9913 for reference details Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
302 OMIA000689-9913 cattle Poll Hereford Myoclonus GLRA1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 7 g.63070074G>T c.156C>A p.(Y52*) 2001 11178872 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
778 OMIA001985-9913 cattle Fleckvieh Dwarfism, Fleckvieh GON4L deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 3 g.15024245del c.4286del p.(G1430Kfs*66) rs723240647 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 OMIA002230-9913 cattle Belted Galloway Hypotrichosis HEPHL1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 29 g.721234T>A c.1684A>T p.(K562*) NC_037356.1 (ARS-UCD1.2 assembly, chromosome 29): g.721234A>T; NM_001192511.2 c.1684A>T; NP_001179440.1: p.Lys562* (Kuca et al., 2021) 2021 33926013
727 OMIA000317-9913 cattle Highland Ears, crop HMX1 insertion, gross (>20) Naturally occurring variant no 6 76bp duplication of 106,720058 to 106,720,133 on BTA6; UMD3 reference assembly 2013 24194898
919 OMIA001319-9913 cattle Holstein-Friesian Myopathy of the diaphragmatic muscles HSPA1A deletion, gross (>20) Naturally occurring variant yes 23 Deletion of one of two HSP70 (heat-shock protein) genes in the bovine major histocompatibility complex 2003 12755819
204 OMIA001817-9913 cattle Japanese Black Perinatal weak calf syndrome IARS missense Naturally occurring variant yes ARS-UCD1.2 8 g.83909754C>G c.235G>C p.(V79L) 2013 23700453 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1396 OMIA001823-9913 cattle Holstein Friesian 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 rs523422030 2021 34873723 ENSBTAT00000044761.4:c.1140del ENSBTAP00000042227.4:p.Leu381PhefsTer3
1202 OMIA002271-9913 cattle Holstein Immunodeficiency, IL17Ra-related IL17RA deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 5 g.108813251del c.180del p.(C61Afs*62) XM_015460734.2: c.180delC; XP_015316220.2: p.(Cys61AlafsTer62) (Häfliger et al., 2020) 2020 32448141
1185 OMIA002261-9913 cattle Holstein de novo mutation in an AI sire ITGA3 missense Naturally occurring variant yes ARS-UCD1.2 19 g.36586185G>A p.(T252M) Bourneuf et al. (2017) detected ITGA3 g.37219021G>A; p.T252M as a de novo recessive potentially lethal mutation from an analysis of whole-genome-sequence of a Holstein AI bull. No information was provided on the descendants of this bull. 2017 28904385
197 OMIA000595-9913 cattle Fleckvieh Holstein-Friesian Jersey Leukocyte adhesion deficiency, type I ITGB2 BLAD missense Naturally occurring variant yes ARS-UCD1.2 1 g.144770078T>C c.383A>G p.(D128G) rs445709131 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 OMIA001948-9913 cattle Charolais Epidermolysis bullosa, junctionalis, ITGB4 ITGB4 deletion, gross (>20) Naturally occurring variant yes 19 "a 4.4 kb deletion involving exons 17 to 22" of the ITGB4 gene 2015 25890340
1390 OMIA002483-9913 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 rs3423356335 2021 34828398
196 OMIA001722-9913 cattle Marchigiana Romagnola Lethal multi-organ developmental dysplasia KDM2B missense Naturally occurring variant yes ARS-UCD1.2 17 g.53761149G>A c.2503G>A p.(D835N) 2012 23029151 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
207 OMIA002390-9913 cattle Braunvieh Spinal muscular atrophy KDSR missense Naturally occurring variant yes ARS-UCD1.2 24 g.61620302C>T c.562G>A p.(A188T) 2007 17420465 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1005 OMIA000527-9913 cattle Charolais Uckermärker Progressive ataxia KIF1C missense Naturally occurring variant yes ARS-UCD1.2 19 g.26407668C>T c.608G>A p.(R203Q); p.(R203_T204delinsQ*) 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." rs800926237 rs800926237 2018 30067756
748 OMIA000426-9913 cattle Northern Finncattle Swedish Mountain Gonadal hypoplasia KIT cs(29) complex rearrangement Naturally occurring variant yes 6 "gonadal hypoplasia in Northern Finncattle and Swedish Mountain cattle is associated with a complex chromosomal rearrangement including a ~500kb duplicated segment from BTA6 which is translocated to BTA29. This duplicated segment includes the entire coding sequence of the KIT gene" 2013 24086604
749 OMIA001576-9913 cattle Belgian Blue British White Park Brown Swiss Galloway Coat colour, colour-sided KIT Cs(29) complex rearrangement Naturally occurring variant no 6 Durkin et al. (2012): "colour sidedness is determined by a first allele on chromosome 29 (Cs(29)), which results from the translocation of a 492-kilobase chromosome 6 segment encompassing KIT to chromosome 29, and a second allele on chromosome 6 (Cs(6)), derived from the first by repatriation of fused 575-kilobase chromosome 6 and 29 sequences to the KIT locus. We provide evidence that both translocation events involved circular intermediates. This is the first example, to our knowledge, of a phenotype determined by homologous yet non-syntenic alleles that result from a novel copy-number-variant-generating mechanism." 2012 22297974
1116 OMIA001576-9913 OMIA001737-9913 cattle British Gloucester Eringer Evolèner Pinzgauer Slovenian Cika Spanish Berrenda en negro Tux-Zillertaler Pinzgauer spotting KIT KIT^PINZ complex rearrangement Naturally occurring variant no 6 Briefly: the KIT^PINZ variant is "characterized by the fusion of a duplicated chromosome 4 segment into a deleted part of chromosome 6." (Küttel et al., 2019) In more detail: "a complex structural variant characterized by a ~9.4-kb deletion . . . and in silico evidence for a duplication of ~1.5 kb about 34 kb farther downstream . . . . Apparently, the duplicated copy of the ~1.5-kb segment appears inversely inserted at the upstream breakpoint of the ~9.4-kb deletion . . . . Furthermore, we noticed at the upstream breakpoint of the inversely inserted segment chimeric read pairs in which both ends mapped to chromosome 6 and 4 . . . . The inspection of the sequence coverage of the involved genome region on chromosome 4 indicated a ~310-kb duplication from 84 864 544 to ~85 174 000 bp". (Küttel et al., 2019) 2019 31294880
1133 OMIA001576-9913 cattle Belgian Blue Brown Swiss Coat colour, colour-sided KIT Cs(6) complex rearrangement Naturally occurring variant no 6 Durkin et al. (2012): "colour sidedness is determined by a first allele on chromosome 29 (Cs(29)), which results from the translocation of a 492-kilobase chromosome 6 segment encompassing KIT to chromosome 29, and a second allele on chromosome 6 (Cs(6)), derived from the first by repatriation of fused 575-kilobase chromosome 6 and 29 sequences to the KIT locus. We provide evidence that both translocation events involved circular intermediates. This is the first example, to our knowledge, of a phenotype determined by homologous yet non-syntenic alleles that result from a novel copy-number-variant-generating mechanism." 2012 22297974
1165 OMIA001737-9913 cattle Brown Swiss White spotting KIT deletion, gross (>20) Naturally occurring variant no ARS-UCD1.2 6 g.70239551_70239590del c.1390_1429del p.(N464Afs*50) "NC_037333.1:g.70239551_70239590del; NM_001166484.1:c.1390_1429del; NP_001159956.1:p.(Asn464AlafsTer50)" (Häfliger et al., 2020) 2020 32065668
186 OMIA001216-9913 cattle Belgian Blue Shorthorn Roan KITLG missense Naturally occurring variant no ARS-UCD1.2 5 g.18273206G>T c.572C>A p.(A191N) 1999 10384045 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
777 OMIA000246-9913 cattle Ayrshire Fleckvieh German Angus Montbeliarde Curly hair, karakul-type KRT27 missense Naturally occurring variant no ARS-UCD1.2 19 g.40982250G>C c.276C>G p.(N92K) rs384881761 rs384881761 2014 25017103 Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
1265 OMIA002081-9913 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 OMIA002081-9913 cattle Friesian-Jersey mosaic Epidermolysis bullosa KRT5 missense Naturally occurring variant yes ARS-UCD1.2 5 g.27371128G>A c.1432G>A p.(E478K) 2005 15955091 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1337 OMIA002114-9913 cattle Hereford Hypotrichosis, KRT71-related KRT71 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 5 g.27331221_27331228del c.281_288del p.(M94Nfs*14) cDNA and protein positions based on NM_001075970.1 and NP_001069438.1, respectively 2021 34356054 210909: FN checked the ARS-UCD1.2 assembly, and discovered that the deletion spans 27331221 to 27331228. Thus g.27331221delTGTGCCCA was changed to g.27331221_27331228del. From NCBI's genome browser, worked out that the c. notation needs to be changed from c.281delTGTGCCCA to c.281_288del.
909 OMIA001677-9913 cattle Belgian Blue Epidermolysis bullosa, junctionalis, LAMA3-related LAMA3 nonsense (stop-gain) Naturally occurring variant unknown ARS-UCD1.2 24 g.32749369G>A c.7549C>T p.(R2517*) 2015 26370913 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1387 OMIA002479-9913 cattle Romagnola 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; 2021 34796979
682 OMIA001678-9913 cattle Hereford Epidermolysis bullosa, junctionalis, LAMC2 LAMC2 deletion, gross (>20) Naturally occurring variant yes 16 "2.4 kb deletion encompassing the first exon of the LAMC2 gene" 2015 25888738
1415 OMIA002516-9913 cattle Braunvieh 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
904 OMIA001451-9913 cattle Belgian Blue Congenital muscular dystonia 2 LOC528050 missense Naturally occurring variant yes ARS-UCD1.2 29 g.24366560A>G c.809T>C p.(L270P) rs3423560860 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)
378 OMIA000963-9913 cattle Angus Syndactyly (mule foot) LRP4 splicing Naturally occurring variant yes ARS-UCD1.2 15 g.76792588C>T c.5385+1G>A "a G to A transition at the first nucleotide in the splice donor site of intron 37" 2006 16963222 Variant information was initially kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4
627 OMIA000963-9913 cattle Holstein Syndactyly (mule foot) LRP4 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 15 g.76800972_76800973delinsAT c.4863_4864delinsAT p.(N1621_G1622delinsKC) 2006 16859890 Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4
769 OMIA000963-9913 cattle German Simmental Syndactyly (mule foot) LRP4 missense Naturally occurring variant yes ARS-UCD1.2 15 g.76807508C>T c.3595G>A p.(G1199S) rs3423411024 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 OMIA000963-9913 cattle Simmental Charolais Cross Syndactyly (mule foot) LRP4 missense Naturally occurring variant yes ARS-UCD1.2 15 g.76812187C>T c.2719G>A p.(G907R) 2007 17319939 Variant information updated to ARS-UCD1.2 and variant effect predicted using Ensembl Variant Effect Predictor (VEP) based on transcript ENSBTAT00000043997.4
183 OMIA000185-9913 cattle Japanese Black Chediak-Higashi syndrome LYST missense Naturally occurring variant yes ARS-UCD1.2 28 g.8464077T>C c.6044A>G p.(H2015R) 1999 10594238 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
199 OMIA000625-9913 cattle Galloway Mannosidosis, alpha MAN2B1 missense Naturally occurring variant yes ARS-UCD1.2 7 g.12840983G>A c.662G>A p.(R221H) 1997 9208932 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
198 OMIA000625-9913 cattle Angus Murray Grey Mannosidosis, alpha MAN2B1 missense Naturally occurring variant yes ARS-UCD1.2 7 g.12842292T>C c.961T>C p.(F321L) 1997 9208932 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
297 OMIA000626-9913 cattle Salers Mannosidosis, beta MANBA nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 6 g.22188765G>A c.2574G>A p.(W858*) 1999 10594236 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1416 OMIA002517-9913 cattle Brown Swiss 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
185 OMIA001199-9913 cattle Angus Holstein-Friesian Icelandic Dominant black MC1R E^D missense Naturally occurring variant no ARS-UCD1.2 18 g.14705671T>C c.296T>C p.(L99P) rs109688013 rs109688013 1995 8535072 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1167 OMIA001544-9913 cattle Rat-tail syndrome MC1R E^D missense Naturally occurring variant no ARS-UCD1.2 18 g.14705671T>C c.296T>C p.(L99P) rs109688013 rs109688013 2016 27037038
485 OMIA001199-9913 cattle Angus Fleckvieh Red Friesian Recessive red MC1R e deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 18 g.14705685del c.310del p.(G104Vfs*53) rs110710422 rs110710422 1995 8535072 Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
558 OMIA002043-9913 cattle Belgian Blue Abortion (embryonic lethality), MED22-related MED22 deletion, small (<=20) Naturally occurring variant yes 11 p.(L38Rfs*25) 2016 27646536
374 OMIA001106-9913 cattle Tyrolean Grey Axonopathy MFN2 splicing Naturally occurring variant yes ARS-UCD1.2 16 g.41686003G>A c.2229C>T "This SNP is located within a putative exonic splice enhancer (ESE) and the variant allele leads to partial retention of the entire intron 19 and a premature stop codon in the aberrant MFN2 transcript" 2011 21526202 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
644 OMIA001565-9913 cattle Finnish Ayrshire Abortion and stillbirth due to mutation in MIMT1 MIMT1 deletion, gross (>20) Naturally occurring variant yes 18 a 110 kb deletion in the MIMT1 gene 2010 21152099
678 OMIA001931-9913 cattle Holstein Depigmentation associated with microphthalmia MITF deletion, gross (>20) Naturally occurring variant yes 22 a de novo deletion of a 19.1 Mb region of BTA22 from 28 835 247-47 983 179 2014 25199536
837 OMIA001680-9913 cattle Holstein Glass-eyed albino MITF deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 22 g.31628127_31628129del p.(R211del) UMD3.1 position g.31746506_31746508del 2017 28904385 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
189 OMIA001680-9913 cattle German Fleckvieh Dominant white with bilateral deafness MITF missense Naturally occurring variant yes ARS-UCD1.2 22 g.31628131C>A c.629G>T p.(R210I) UMD3.1 position is g.31746502 2011 22174915 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
782 OMIA000214-9913 cattle Holstein Simmental White spotting MITF regulatory Naturally occurring variant no ARS-UCD1.2 22 g.31650821T>A c.33+112A>T UMD3.1 position is g.31769189 rs210634530 rs210634530 2012 22486495 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
1018 OMIA000214-9913 cattle Brown Swiss White spotting MITF regulatory Naturally occurring variant no ARS-UCD1.2 22 g.31790063G>A c.104+53185C>T FN 190425: The Ensembl entry for rs722765315 lists two transcripts: ENSBTAT00000067269.1:c.104+53185C>T and ENSBTAT00000076082.1:c.-53+31498C>T rs722765315 rs722765315 2019 30506810 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
553 OMIA000031-9913 cattle Belgian Blue Coat colour, cool gray MLPH deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 3 g.116966611_116966620del c.87_96del p.(E32Dfs*1) 2016 26582259 The genomic location on ARS-UCD1.2 was determined by Katie Eager & Shernae Woolley, EMAI, NSW Department of Primary Industries.
492 OMIA001819-9913 cattle Tyrolean Grey Xanthinuria, type II MOCOS deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 24 g.20911933del c.1881del p.(S628Vfs9*) Published using UMD3.1 position: g.21222030delC; cDNA and protein positions are given transcript: ENSBTAT00000048768. Positions for a second transcript (ENSBTAT00000065375) were given in the paper: c.1782del and p.(S595Vfs9*). 2016 27919260 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
446 OMIA001819-9913 cattle Japanese Black Xanthinuria, type II MOCOS deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 24 g.20936257_20936259del c.769_771del p.(Y257del) published as c.769_771delTAC 2000 10801779 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
483 OMIA001541-9913 cattle Fleckvieh Simmental 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 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 OMIA001452-9913 cattle Belgian Blue Tail, crooked MRC2 missense Naturally occurring variant yes ARS-UCD1.2 19 g.47089627T>G c.1906T>G p.(C636G) rs466131011 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 OMIA001452-9913 cattle Belgian Blue Tail, crooked MRC2 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 19 g.47095176_47095177del c.2904_2905del p.(G934*) 2009 19779552 Breed and some variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) 210908 the entry g.47740473delAG can't be correct because if two bases have been deleted, the g. notation must include the two relevant base positions. FN BLASTED the sequence CCAGACCTGCCGCCCACAG obtained from Fig 3 against UMD3.1.1, and determined that the entry should be g.47740474_47740475del
1417 OMIA002518-9913 cattle Brown Swiss Haplotype with homozygous deficiency BH14 MRPL55 BH14 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 7 g.2996436 c.169C>T p.(R57*) NM_001303490.1 2021 34915862
212 OMIA000683-9913 cattle Gelbvieh Muscular hypertrophy (double muscling) MSTN missense Naturally occurring variant yes ARS-UCD1.2 2 g.6279187T>C c.191T>C p.(L64P) UMD3.1 position is g.6213889T>C rs449270213 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 OMIA000683-9913 cattle Angus Limousin Muscular hypertrophy (double muscling) MSTN missense Naturally occurring variant yes ARS-UCD1.2 2 g.6279278C>A c.282C>A p.(F94L) UMD3.1 position is g.6213980A>C rs110065568 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 OMIA000683-9913 cattle Parthenaise Muscular hypertrophy (double muscling) MSTN missense Naturally occurring variant yes ARS-UCD1.2 2 g.6279310C>G c.314C>G p.(S105C) UMD3.1 position is g.6214012C>G 2002 Reference not in PubMed; see OMIA 000683-9913 for reference details Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
618 OMIA000683-9913 cattle Maine Anjou Muscular hypertrophy (double muscling) MSTN nt419(del7-ins10) delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 2 g.6281243_6281249delinsAAGCATACAA c.419_425delinsAAGCATACAA p.(F140*) cDNA and protein positions based on NM_001001525.3 and NP_001001525.1, retrospectively 1998 9501304 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. Variant coordinates updated based on Johnsson and Jungnickel (2021)
773 OMIA000683-9913 cattle Maine Anjou Muscular hypertrophy (double muscling) MSTN D182N missense Naturally occurring variant yes ARS-UCD1.2 2 g.6281368G>A c.544G>A p.(D182N) 2002 Reference not in PubMed; see OMIA 000683-9913 for reference details The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
299 OMIA000683-9913 cattle Blonde d'Aquitaine Charolais Limousin Muscular hypertrophy (double muscling) MSTN nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 2 g.6281434C>T c.610C>T p.(Q204*) UMD3.1 position is g.6216138C>T rs110344317 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 OMIA000683-9913 cattle Maine Anjou Marchigiana Muscular hypertrophy (double muscling) MSTN nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 2 g.6281500G>T c.676G>T p.(E226*) UMD3.1 position is g.6216204G>T 1998 9501304 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
489 OMIA000683-9913 cattle Angus Asturiana Belgian Blue Blonde d'Aquitaine Braford Limousin Murray Grey Parthenaise Santa Gertrudis South Devon Muscular hypertrophy (double muscling) MSTN deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 2 g.6283674_6283684del c.821_831del p.(D273RfsX14) UMD3.1 position is g.6218379delATGAACACTCC rs382669990 1997 9288100 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. Protein coordinates updated based on Johnsson and Jungnickel (2021).
301 OMIA000683-9913 cattle Maine Anjou Marchigiana Muscular hypertrophy (double muscling) MSTN nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 2 g.6283727G>T c.1004G>T p.(E291*) UMD3.1 position is g.6218432G>T 2013 22497537 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
203 OMIA000683-9913 cattle Gasconne Parthenaise Piedmontese Muscular hypertrophy (double muscling) MSTN missense Naturally occurring variant yes ARS-UCD1.2 2 g.6283794G>A c.938G>A p.(C313Y) UMD3.1 position is g.6218499G>A 1997 9314496 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
217 OMIA001978-9913 cattle Swiss Holstein Arthrogryposis, distal, type 1B MYBPC1 missense Naturally occurring variant yes ARS-UCD1.2 5 g.65446598T>G c.884T>G p.(L295R) 2015 26289121 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
556 OMIA002039-9913 cattle Belgian Blue Abortion (embryonic lethality), MYH6-related MYH6 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 10 g.21538917_21538919del p.(K1730del) 2016 27646536 The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
202 OMIA001342-9913 cattle Mucopolysaccharidosis IIIB NAGLU missense Naturally occurring variant yes ARS-UCD1.2 19 g.42624367G>A c.1354G>A p.(E452K) 2007 17458708 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
766 OMIA002103-9913 cattle Angus Developmental duplications NHLRC2 missense Naturally occurring variant yes ARS-UCD1.2 26 g.34340886T>C c.932T>C p.(V311A) 2014 Reference not in PubMed; see OMIA 002103-9913 for reference details Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
679 OMIA001936-9913 cattle Romagnola Cataract, recessive, Romagnola NID1 deletion, gross (>20) Naturally occurring variant yes 28 "an 855 bp deletion across the exon 19/intron 19 border of the bovine nidogen 1 (NID1) gene (c.3579_3604+829del)" 2014 25347398
1244 OMIA000725-9913 cattle Angus Niemann-Pick type C1 NPC1 missense Naturally occurring variant yes ARS-UCD1.2 24 g.33099467C>G c.2969C>G p.(P990R) NM_174758.2:c.2969C>G rs482882512 rs482882512 2020 32970694
1410 OMIA002509-9913 cattle Simmental 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
555 OMIA002035-9913 cattle Jersey 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 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 OMIA000162-9913 cattle Red Holstein Cardiomyopathy, dilated OPA3 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 18 g.53152213G>A c.343C>T p.(Q115*) UMD3.1 position is g.53546443C>T; cDNA position based on ENSBTAT00000064088.2 rs479222100 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 OMIA001437-9913 cattle Brown Swiss Beta-lactoglobulin, aberrant low expression PAEP regulatory Naturally occurring variant yes ARS-UCD1.2 11 g.103255964C>A c.-215C>A "C to A transversion at position 215 bp upstream of the translation initiation site" 2006 17033029 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
820 OMIA001827-9913 cattle Montbeliarde Vorderwald Abortion due to haplotype MH1 PFAS missense Naturally occurring variant yes ARS-UCD1.2 19 g.27895397C>T c.3613C>T p.(R1205C) rs455876205 rs455876205 2017 28803020 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
406 OMIA001953-9913 cattle Belgian Blue Arthrogryposis, lethal syndrome PIGH splicing Naturally occurring variant yes ARS-UCD1.2 10 g.79469727G>C c.211-10C>G rs451004237 rs451004237 2015 25895751 Variant information gleaned from or confirmed by Table 1 of  Sharma et al. (2017) Animal Genetics 48(3):369-370
339 OMIA001935-9913 cattle Fleckvieh Zinc deficiency-like syndrome PLD4 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 21 g.69352995G>A c.702G>A p.(W234*) UMD3.1 position is g.71001232G>A rs378824791 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.
484 OMIA001545-9913 cattle Charolais Galloway Hereford Highland Simmental Coat colour, dilution PMEL deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 5 g.57345302_57345304del c.50_52del p.(L19del) rs385468954 2008 18408794 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
1166 OMIA001544-9913 cattle Rat-tail syndrome PMEL deletion, small (<=20) Naturally occurring variant unknown ARS-UCD1.2 5 g.57345302_57345304del c.50_52del p.(L19del) rs385468954 2016 27037038
774 OMIA001545-9913 cattle Charolais Coat colour, dilution PMEL missense Naturally occurring variant no ARS-UCD1.2 5 g.57345315G>A c.64G>A p.(G22R) rs718553050 rs718553050 2007 17705851 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
765 OMIA000827-9913 cattle Brown Swiss Carora Progressive degenerative myeloencephalopathy (Weaver syndrome) PNPLA8 missense Naturally occurring variant yes ARS-UCD1.2 4 g.49600585C>T c.1703G>A p.(S568N) rs800397662 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)
1070 OMIA000483-9913 cattle Nellore Polled, Guarani POLLED P[sub]G duplication Naturally occurring variant no ARS-UCD1.2 1 g.2614828_2724315dup "a novel duplication variant" in the region BTA1:1,893,790–2,004,553 (Utsunomiya et al., (2019) 2019 30644114 Randhawa et al. (2019): ARS-UCD1.2 g.2614828_2724315dup
867 OMIA000483-9913 cattle Friesian Polled, Friesian POLLED P[sub]F OR P(sub)80kbID duplication Naturally occurring variant no ARS-UCD1.2 1 g.2629113_2709240dup 2013 23717440 In relation to assembly UMD v3.1.1, Utsunomiya et al. (2019) described this variant as "a duplication of CHR1:1,909,352–1,989,480". Randhawa et al. (2019): ARS-UCD1.2 g.2629113_2709240dup
866 OMIA000483-9913 cattle Brahman Polled, Celtic POLLED P[sub]C OR P[sub]202ID complex rearrangement Naturally occurring variant no ARS-UCD1.2 1 g.[22429326_2429335del;2429109_2429320dupins] UMD3.1: g.1706051_1706060 delins170583 2012 22737241 Randhawa et al. (2019) ARS-UCD1.2 g.[22429326_2429335del;2429109_2429320dupins]
844 OMIA000483-9913 cattle Mongolian Turano Polled, Mongolian POLLED P[sub]M OR P[sub]219ID complex rearrangement Naturally occurring variant no ARS-UCD1.2 1 g.[2695261_2695267delinsTCTGAA;2695889_2696047dupins] "a complex 219-bp duplication-insertion (P219ID) beginning at 1,976,128 bp and a 7-bp deletion and 6-bp insertion (P1ID) located 621 bp upstream of this position . . . . This rearrangement results in duplication of an 11-bp motif (5'-AAAGAAGCAAA-3') that is entirely conserved among Bovidae . . . and that is also duplicated in the 80-kb duplication responsible for Friesian polledness" In relation to assembly UMD v3.1.1, Utsunomiya et al. (2019) described this variant as "a complex duplication starting at CHR1:1,976,128". 2017 28135247 Randhawa et al. (2019): ARS-UCD1.2 g.[2695261_2695267delinsTCTGAA;2695889_2696047dupins]
588 OMIA000161-9913 cattle Poll Hereford Cardiomyopathy and woolly haircoat syndrome PPP1R13L duplication Naturally occurring variant yes ARS-UCD1.2 18 g.53013747_53013753dup c.956-962dupACAGGCG p.(G335Efs*36) 2009 19016676 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
291 OMIA001485-9913 cattle Angus Dwarfism, Angus PRKG2 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 6 g.95896205G>A c.1573C>T p.(R525*) rs109639251 rs109639251 2009 19887637 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
352 OMIA001485-9913 cattle Angus Dwarfism, Angus PRKG2 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 6 g.95896205G>A c.2032C>T p.(R678*) ENSBTAT00000003877.4:c.2032C>T ENSBTAP00000003877.4:p.Arg678Ter rs109639251 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
216 OMIA000441-9913 cattle Fleckvieh Holstein-Friesian Jersey Hairy PRL missense Naturally occurring variant no ARS-UCD1.2 23 g.35332871A>C c.661A>C p.(C221G) ENSBTAT00000020313.4:c.661T>G ENSBTAP00000020313.3:p.Cys221Gly rs520582588 rs520582588 2014 25519203 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
544 OMIA001372-9913 cattle Carora Romosinuano Senepol Slick hair PRLR SLICK1 deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 20 g.39099214del c.1382del p.(A461Vfs*2) rs517047387 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 OMIA001372-9913 cattle Limonero Slick hair PRLR nonsense (stop-gain) Naturally occurring variant no ARS-UCD1.2 20 g.39099226C>A p.(S465*) 2018 29527221
975 OMIA001372-9913 cattle Carora Limonero Slick hair PRLR nonsense (stop-gain) Naturally occurring variant no ARS-UCD1.2 20 g.39099321C>T p.(R497*) 2018 29527221
834 OMIA000944-9913 cattle Numerous breeds Spongiform encephalopathy (mad cow disease) PRNP missense Naturally occurring variant yes ARS-UCD1.2 13 g.47056730G>A c.631G>A p.(E211K) 2008 18787697 Genomic coordinates obtained from EBI's VEP
193 OMIA001139-9913 cattle Charolais Glycogen storage disease V PYGM missense Naturally occurring variant yes ARS-UCD1.2 29 g.42991370G>A c.1468C>T p.(R490W) 1996 8845714 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
221 OMIA002037-9913 cattle Holstein-Friesian Abortion (embryonic lethality), RABGGTB RABGGTB missense Naturally occurring variant yes ARS-UCD1.2 3 g.69060748T>C c.584A>G p.(Y195C) ENSBTAT00000024551.6:c.584A>G ENSBTAP00000024551.6:p.Tyr195Cys rs1118263722 rs1118263722 2016 27646536 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
209 OMIA002433-9913 cattle Fleckvieh Simmental Thrombopathia RASGRP2 missense Naturally occurring variant yes ARS-UCD1.2 29 g.42978791A>G c.701T>C p.(L234P) rs385444696 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)
676 OMIA001901-9913 cattle Nordic Red Abortion due to deletion of RNASEH2B RNASEH2B deletion, gross (>20) Naturally occurring variant yes 12 A 662kb deletion encompases the gene RNASEH2B, lack of which creates embryonic lethality 2014 24391517
376 OMIA001686-9913 cattle Belgian Blue Dwarfism, proportionate, with inflammatory lesions RNF11 splicing Naturally occurring variant yes ARS-UCD1.2 3 g.95015373T>C c.124-2A>G NM_001077953.1 rs3423159409 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 OMIA002038-9913 cattle Holstein-Friesian Abortion (embryonic lethality), RNF20 RNF20 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 8 g.91297797A>T c.2077A>T p.(K693*) 2016 27646536 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1139 OMIA002223-9913 cattle Holstein Interdigital hyperplasia ROR2 missense Naturally occurring variant yes ARS-UCD1.2 8 g.85905534T>A c.25T>A p.(W9R) ENSBTAT00000061589.3:c.25T>A ENSBTAP00000053765.2:p.Trp9Arg rs377953295 rs377953295 2019 31798639
611 OMIA002029-9913 cattle Angus Belgian Blue Charolais Gelbvieh Holstein Maine Anjou Normande Red Angus Retinitis pigmentosa 1 RP1 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 14 g.22340665_22340666insA p.(R791Kfs*13) 2016 27510606
858 OMIA002134-9913 cattle Ayrshire Abortion due to haplotype AH2 RPAP2 splicing Naturally occurring variant yes 3 a splice acceptor variant at 51,267,548 bp [reference sequence not specified] in RPAP2 2017 Reference not in PubMed; see OMIA 002134-9913 for reference details
416 OMIA002041-9913 cattle Belgian Blue Abortion (embryonic lethality), RPIA-related RPIA splicing Naturally occurring variant yes ARS-UCD1.2 11 g.47355110C>T c.826+1G>A 2016 27646536 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
1269 OMIA002297-9913 cattle Holstein Friesian Tetradysmelia RSPO2 delins, gross (>20) Naturally occurring variant yes ARS-UCD1.2 14 g.56451029_56501201delinsTGACAA a 50-kb deletion spanning three exons of the R-spondin 2 (RSPO2) gene 2020 33176673
990 OMIA002149-9913 cattle Holstein 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 rs434666183 2018 29680649
222 OMIA002444-9913 cattle Japanese Black Hydrallantois SLC12A1 missense Naturally occurring variant yes ARS-UCD1.2 10 g.62157819G>A p.(P372L) 2016 27613513
992 OMIA002150-9913 cattle Rouge-des-Prés Syndrome des veaux tourneurs (Turning calves syndrome) SLC25A46 missense Naturally occurring variant yes ARS-UCD1.2 7 g.109742796C>T c.376C>T p.(R126C) 2017 28376083
626 OMIA000366-9913 cattle Braunvieh Fleckvieh Fanconi syndrome SLC2A2 delins, small (<=20) Naturally occurring variant yes ARS-UCD1.2 1 g.96472797_96472804delinsCATC c.771_778delinsCATC p.(L258fs16) rs379675307 2016 27169150 Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446 210909: FN changed c.771_778delTTGAAAAGinsCATC to c.771_778delinsCATC. Also, since the del is of 8 bp, the g. designation has been changed from g.97239973_97239976delTTGAAAAG (which encompasses a deletion of only 4bp) to g.97239973_97239980delinsCATC.
187 OMIA001340-9913 cattle Friesian Holstein Complex vertebral malformation SLC35A3 missense Naturally occurring variant yes ARS-UCD1.2 3 g.43261945C>A c.538G>T p.(V180F) rs438228855 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 OMIA001340-9913 cattle Montbeliarde de novo mutation in an AI sire SLC35A3 missense Naturally occurring variant yes ARS-UCD1.2 3 g.43268369G>T p.(R25S) This variant was detected by Bourneuf et al. (2017) as a de novo mutation from an analysis of whole-genome-sequence of an AI Montbéliarde bull. No information was provided on the descendants of this bull. 2017 28904385
263 OMIA001828-9913 cattle Montbeliarde Vorderwald Abortion due to haplotype MH2 SLC37A2 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 29 g.28510651C>T c.34C>T p.(R12*) 2013 23762392 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
372 OMIA000593-9913 cattle Holstein Acrodermatitis enteropathica SLC39A4 splicing Naturally occurring variant yes ARS-UCD1.2 14 g.537516G>A c.1645+1G>A "a single nucleotide mutation of the splice donor site in intron 10" 2006 16714095 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
847 OMIA001821-9913 cattle Braunvieh Coat colour, albinism, oculocutaneous type IV SLC45A2 missense Naturally occurring variant yes ARS-UCD1.2 20 g.39790069G>A c.134G>A p.(R45Q) Important note by Rothammer et al. (2017): "To determine which of the two mutations or even if the combination of both is causal for oculocutaneous albinism in Braunvieh, it would be necessary to produce additional cases and investigate them more precisely" 2017 28982372 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
848 OMIA001821-9913 cattle Braunvieh Coat colour, albinism, oculocutaneous type IV SLC45A2 missense Naturally occurring variant yes ARS-UCD1.2 20 g.39824417C>T c.1331C>T p.(T444I) Important note by Rothammer et al. 92017): "To determine which of the two mutations or even if the combination of both is causal for oculocutaneous albinism in Braunvieh, it would be necessary to produce additional cases and investigate them more precisely" 2017 28982372 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
303 OMIA001228-9913 cattle Japanese Black Spherocytosis SLC4A1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 19 g.44069903G>A c.1990C>T p.(R664*) 1996 8621763 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446
647 OMIA002443-9913 cattle Angus Friesian Hereford Holstein Simmental Osteopetrosis SLC4A2 deletion, gross (>20) Naturally occurring variant yes ARS-UCD1.2 4 g.113638011_113640784del "approximately 2.8-kb deletion mutation in affected calves that encompasses exon 2 and nearly half of exon 3" 2010 20507629 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
211 OMIA001824-9913 cattle Friesian Holstein Abortion due to haplotype HH3 SMC2 missense Naturally occurring variant yes ARS-UCD1.2 8 g.93753358T>C c.3404T>C p.(F1135S) rs456206907 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 OMIA002040-9913 cattle Belgian Blue Abortion (embryonic lethality), SNAPC4-related SNAPC4 deletion, small (<=20) Naturally occurring variant yes 11 p.(L1227Afs*134) 2016 27646536
1182 OMIA002258-9913 cattle Charolais Lethality, SOWAHB-related SOWAHB missense Naturally occurring variant yes ARS-UCD1.2 6 g.91735816G>T p.(Q379K) This variant was detected by Bourneuf et al. (2017) as a de novo mutation from an analysis of whole-genome-sequence of a Charolais AI bull. No information was provided on the descendants of this bull. 2017 28904385
206 OMIA001247-9913 cattle American Brown Swiss Spinal dysmyelination SPAST missense Naturally occurring variant yes ARS-UCD1.2 11 g.14742184G>A c.1964G>A p.(R560Q) rs445770480 rs445770480 2010 19714378 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
920 OMIA001230-9913 cattle Japanese Black Ovotesticular DSD (Disorder of Sexual Development) SRY deletion, gross (>20) Naturally occurring variant yes Y A deletion of the SRY gene 1996 8978769
214 OMIA001960-9913 cattle Fleckvieh Abortion due to haplotype FH4 SUGT1 missense Naturally occurring variant yes ARS-UCD1.2 12 g.11102143A>G c.949T>C p.(W317R) rs110793536 rs110793536 2015 25927203 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
587 OMIA000059-9913 cattle Brown Swiss Arachnomelia, BTA5 SUOX insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 5 g.57316723_57316724insG c.363_364insG p.(A124Gfs*42) 2010 20865119 Variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
213 OMIA001951-9913 cattle Holstein Vertebral and spinal dysplasia T missense Naturally occurring variant yes ARS-UCD1.2 9 g.101160274T>C c.196A>G p.(K66E) 2015 25614605 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
963 OMIA001941-9913 cattle Holstein Abortion due to haplotype HH5 TFB1M complex rearrangement Naturally occurring variant yes 9 "a deletion of 138kbp, spanning position 93,233kb to 93,371kb on chromosome 9 (BTA9), harboring only dimethyl-adenosine transferase 1 (TFB1M). The deletion breakpoints are flanked by bovine long interspersed nuclear elements Bov-B (upstream) and L1ME3 (downstream), suggesting a homologous recombination/deletion event." 2016 27128314
295 OMIA000424-9913 cattle Afrikander Goitre, familial TG nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 14 g.8432343G>A c.1963C>T p.(R655*) rs480120030 rs480120030 1987 3472203 Variant coordinates obtained from or confirmed by EBI's Variant Effect Predictor (VEP) tool
779 OMIA001902-9913 cattle Fleckvieh Male subfertility TMEM95 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 19 g.27056843C>A c.483C>A p.(C161*) rs378652941 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 OMIA000542-9913 cattle Pezzata Rossa Hypotrichosis, streaked TSR2 splicing Naturally occurring variant yes ARS-UCD1.2 X g.91964644A>G c.441+226A>G 2015 26203908 Breed and variant information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
345 OMIA002036-9913 cattle Holstein-Friesian Abortion (embryonic lethality), TTF1 TTF1 nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 11 g.102463944G>A c.1579G>A p.(R527*) rs715966442 rs715966442 2016 27646536 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
776 OMIA001939-9913 cattle Brown Swiss Haplotype with homozygous deficiency BH2 TUBD1 missense Naturally occurring variant yes ARS-UCD1.2 19 g.10833921T>C c.757T>C p.(H210R) rs383232842 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 OMIA002515-9913 cattle Braunvieh 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
594 OMIA001593-9913 cattle Charolais Scurs, type 2 TWIST1 duplication Naturally occurring variant no ARS-UCD1.2 4 g.27819577_27819586dup c.148_157dup p.(A56Rfs*87) c.DNA position based on NM_001191145.1 2011 21814570 Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446.
761 OMIA001469-9913 cattle Belted Galloway Brown Swiss Dutch Belted Gurtenvieh Lakenvelder Yakutian Coat colour, white belt TWIST2 repeat variation Naturally occurring variant no 3 "The belt-associated variant was a copy number variant (CNV) involving the quadruplication of a 6 kb non-coding sequence located approximately 16 kb upstream of the TWIST2 gene" (Awasthi Mishra et al., 2017) 200922: g. info moved to here (g.118,607,715-118,614,131) until it can be standardised "a quadruplication on bovine chromosome 3 between positions 118,608,362 and 118,614,132 bp" (UMD3.1) (Rothammer et al., 2018) 2017 28658273
589 OMIA000202-9913 cattle Braunvieh Coat colour, albinism TYR insertion, small (<=20) Naturally occurring variant no ARS-UCD1.2 29 g.6424971_6424972insG c.925_926insC Insertion causes a frameshift that resulted in a premature stop codon at residue 316, whereas normal sequence contains 517 amino acids. 2004 14727143 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
184 OMIA001249-9913 cattle Dexter Dun brown TYRP1 missense Naturally occurring variant no ARS-UCD1.2 8 g.31633328G>A c.1300C>T p.(H434Y) rs3423268465 2003 12755816 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool
404 OMIA001934-9913 cattle Finnish Ayrshire Ptosis, intellectual disability, retarded growth and mortality (PIRM) syndrome UBE3B splicing Naturally occurring variant yes ARS-UCD1.2 17 g.63668380C>T c.2076G>A p.(E692E) ENSBTAT00000003493.5:c.2076G>A ENSBTAP00000003493.4:p.Glu692= rs475678587 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 OMIA002298-9913 cattle Jersey 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 2021 34955244
290 OMIA000262-9913 cattle Friesian Holstein Holstein-Friesian Red Holstein Wagyu Deficiency of uridine monophosphate synthase UMPS nonsense (stop-gain) Naturally occurring variant yes ARS-UCD1.2 1 g.69151931C>T c.1213C>T p.(R405*) 1993 8486364 Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170)
592 OMIA002423-9913 cattle Japanese Black Multiple ocular defects WFDC1 insertion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 18 g.10567100_10567101insC c.321insC insertion of a single base causes a frame shift mutation and a premature termination codon appeared at codon 126 2009 19374945 Variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446. The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries.
921 OMIA001736-9913 cattle Charolais Polled and multisystemic syndrome ZEB2 deletion, gross (>20) Naturally occurring variant yes 2 A 3.7Mb deletion encompassing the genes ARHGAP15, GTDC1 and ZEB2 2012 23152852
1246 OMIA001736-9913 cattle Fleckvieh Polledness, abnormal skull shape, small body stature and subfertility ZEB2 Del11 deletion, small (<=20) Naturally occurring variant no ARS-UCD1.2 2 g.52263360_52263370del 2020 33046754
1283 OMIA002307-9913 cattle Limousin Frontonasal dysplasia ZIC2 deletion, small (<=20) Naturally occurring variant yes ARS-UCD1.2 12 g.76742067del rs3423095151 2021 33388042
Overall Statistics
Total number of variants 245
Variants with genomic location 214 (87.3% )
Variants in a variant database, i.e. with rs ID 60 (24.5%)
Variant Type Count Percent
complex rearrangement 7 2.9%
deletion, gross (>20) 21 8.6%
deletion, small (<=20) 32 13.1%
delins, gross (>20) 2 0.8%
delins, small (<=20) 7 2.9%
duplication 5 2.0%
extension (stop-lost) 2 0.8%
insertion, gross (>20) 5 2.0%
insertion, small (<=20) 13 5.3%
inversion 1 0.4%
missense 92 37.6%
nonsense (stop-gain) 34 13.9%
regulatory 4 1.6%
repeat variation 2 0.8%
splicing 17 6.9%
start-lost 1 0.4%
Year First Reported Count Percent
1987 1 0.4%
1988 0 0.0%
1989 1 0.4%
1990 1 0.4%
1991 0 0.0%
1992 1 0.4%
1993 1 0.4%
1994 0 0.0%
1995 2 0.8%
1996 3 1.2%
1997 4 1.6%
1998 5 2.0%
1999 6 2.4%
2000 5 2.0%
2001 2 0.8%
2002 8 3.3%
2003 2 0.8%
2004 2 0.8%
2005 3 1.2%
2006 8 3.3%
2007 8 3.3%
2008 6 2.4%
2009 7 2.9%
2010 4 1.6%
2011 9 3.7%
2012 15 6.1%
2013 10 4.1%
2014 15 6.1%
2015 11 4.5%
2016 27 11.0%
2017 24 9.8%
2018 6 2.4%
2019 10 4.1%
2020 14 5.7%
2021 23 9.4%
2022 1 0.4%