OMIA 001826-9913 : Haplotype with homozygous deficiency HH4 in Bos taurus
This present OMIA entry is for HH4, which is located in chromosome BTA1, at 1.9-3.3Mb (UMD 3.1 genome assembly) (Fritz et al., 2013).Molecular basis: For eight of the nine haplotypes with a significant effect on calving rate (see Mapping section), Fritz et al. (2013) searched for causal mutations via whole-genome sequence data from 25 Holstein, 11 Montbéliarde and nine Normande bulls which had made major contributions to their breed. Specifically, they filtered "for mutations that were (a) located at+or –6 Mb from the detected haplotype (b) carried in the heterozygous state by the carrier bulls and (c) absent from the non carrier bulls from the three breeds" and then examined identified polymorphisms for their likely effect on protein structure and function. For HH4, Fritz et al. (2013) provided convincing evidence for a candidate causal mutation, namely a missense mutation (g.1277227A.C; UMD 3.1 genome assembly) in the GART gene (which encodes glycinamide ribonucleotide transformylase), leading to p.N290T. Clinical features: The effect of this haplotype is a reduction of 5.8% in heifer calving rate and of 1.74% in cow calving rate (Fritz et al., 2013). Prevalence: The HH4 haplotype occurs with a frequency of 3.6% in the 47,878 Holstein adult cattle sampled by Fritz et al. (2013), but never as a homozygote. Breed: Holstein. Associated gene:
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|GART||phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase||Bos taurus||1||NC_037328.1 (1986098..2012388)||GART||Homologene, Ensembl, NCBI gene|
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WARNING! Inclusion of a variant in this table does not automatically mean that it should be used for DNA testing. Anyone contemplating the use of any of these variants for DNA testing should examine critically the relevant evidence (especially in breeds other than the breed in which the variant was first described). If it is decided to proceed, the location and orientation of the variant sequence should be checked very carefully.
Since October 2021, OMIA includes a semiautomated lift-over pipeline to facilitate updates of genomic positions to a recent reference genome position. These changes to genomic positions are not always reflected in the ‘acknowledgements’ or ‘verbal description’ fields in this table.
|OMIA Variant ID||Breed(s)||Variant Phenotype||Gene||Allele||Type of Variant||Source of Genetic Variant||Reference Sequence||Chr.||g. or m.||c. or n.||p.||Verbal Description||EVA ID||Inferred EVA rsID||Year Published||PubMed ID(s)||Acknowledgements|
|182||Holstein||Abortion due to haplotype HH4||GART||missense||Naturally occurring variant||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)|
Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.
|2016||Cole, J.B., Null, D.J., VanRaden, P.M. :|
|Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility. J Dairy Sci 99:7274-88, 2016. Pubmed reference: 27394947. DOI: 10.3168/jds.2015-10777.|
|Segelke, D., Täubert, H., Reinhardt, F., Thaller, G. :|
|Considering genetic characteristics in German Holstein breeding programs. J Dairy Sci 99:458-67, 2016. Pubmed reference: 26601581. DOI: 10.3168/jds.2015-9764.|
|2013||Fritz, S., Capitan, A., Djari, A., Rodriguez, S.C., Barbat, A., Baur, A., Grohs, C., Weiss, B., Boussaha, M., Esquerré, D., Klopp, C., Rocha, D., Boichard, D. :|
|Detection of haplotypes associated with prenatal death in dairy cattle and identification of deleterious mutations in GART, SHBG and SLC37A2. PLoS One 8:e65550, 2013. Pubmed reference: 23762392. DOI: 10.1371/journal.pone.0065550.|
- Created by Frank Nicholas on 12 Jun 2013
- Changed by Frank Nicholas on 12 Jun 2013
- Changed by Frank Nicholas on 14 Jun 2013
- Changed by Frank Nicholas on 24 Mar 2015