OMIA 001836-9913 : Haplotype with homozygous deficiency HH13 in Bos taurus
Fritz et al. (2013) named their 14 new Holstein haplotypes as HH4 to HH17, their 11 Montbéliarde haplotypes as MH1 to MH11, and their six Normande haplotypes as NH1 to NH6.
Häfliger et al. (2022) reported new Holstein haplotypes HH18-HH38.Inheritance: Häfliger et al. (2022) reported that "no single homozygous carrier of the . . . KIR2DS1 . . . [variant] was observed neither in the current population of more than 14 thousand Swiss dairy cattle nor in any other breed of cattle included in the 1000 Bull Genomes project". Mapping: By analysing Illumina Bovine 50k Beadchip genotype data from 47,878 Holstein, 16,833 Montbéliarde and 11,466 Normande cattle in the French genomic selection database, Fritz et al. (2013) identified 34 common (>1%) haplotypes that have a significant deficit (P<10^-4) of homozygotes in live animals, and which are, therefore, each likely to harbour a deleterious mutation. Three of these haplotypes, namely BY (Brachyspina; OMIA 000151-9913), HH1 (OMIA 000001-9913) and HH3 (OMIA 001824-9913), had been reported by VanRaden et al. (2011; J Dairy Sci 94:6153-61). Following the convention of naming such haplotypes with a first letter indicating breed, a second letter H for haplotype, followed by a sequential number, Fritz et al. (2013) named their 14 new Holstein haplotypes as HH4 to HH17, their 11 Montbéliarde haplotypes as MH1 to MH11, and their six Normande haplotypes as NH1 to NH6. Analyses of reproductive data indicated that nine of the 34 haplotypes have a significant effect on fertility, including six of the newly identified haplotypes, namely HH4, HH5, HH6, MH1, MH2 and NH5.
This present OMIA entry is for HH13, which is located in chromosome BTA18, at 56.4–58.4Mb (UMD 3.1 genome assembly) (Fritz et al., 2013).Molecular basis: Based on strong evidence obtained in Swiss Holsteins, Häfliger et al (2022) proposed KIR2DS1:p.Gln159* as the likely causal variant for haplotype HH13. Prevalence: The HH13 haplotype occurs with a frequency of 3.7% in the 47,878 Holstein adult cattle adult sampled by Fritz et al. (2013), but with only 16% of the expected frequency of homozygotes. Breed: Holstein. Associated gene:
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|KIR2DS1||killer cell immunoglobulin-like receptor, two domains, short cytoplasmic tail, 1||Bos taurus||18||NC_037345.1 (62766895..62754403)||KIR2DS1||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|
|1440||Swiss Holstein||Abortion due to haplotype HH13||KIR2DS1||nonsense (stop-gain)||Naturally occurring variant||ARS-UCD1.2||18||g.62758881G>A||c.475C>T||p.(Q159*)||NM_001097567.1; NP_001091036.1||rs437566778||2022||35361830|
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.
|2022||Häfliger, I.M., Spengeler, M., Seefried, F.R., Drögemüller, C. :|
|Four novel candidate causal variants for deficient homozygous haplotypes in Holstein cattle. Sci Rep 12:5435, 2022. Pubmed reference: 35361830. DOI: 10.1038/s41598-022-09403-6.|
|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.|
|2011||VanRaden, P.M., Olson, K.M., Null, D.J., Hutchison, J.L. :|
|Harmful recessive effects on fertility detected by absence of homozygous haplotypes. J Dairy Sci 94:6153-61, 2011. Pubmed reference: 22118103. DOI: 10.3168/jds.2011-4624.|
- Created by Frank Nicholas on 14 Jun 2013
- Changed by Frank Nicholas on 14 Jun 2013
- Changed by Frank Nicholas on 04 Apr 2022