OMIA 001908-9913 : Haplotype with homozygous deficiency HH21 in Bos taurus

Possibly relevant human trait(s) and/or gene(s) (MIM number): 600276 (gene)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal Recessive Lethal

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2022

History: This haplotype was originally named 175.5 by Van Raden et al. (2011), and was then named 07-126 by Sahana et al. (2013). It was designated HH21 by Häfliger et al. (2022).

Mapping: By genotyping each of 7,937 Nordic Holstein bulls with the BovineSNP50 BeadChip, yielding 36,387 informative autosomal SNPs, and then searching for 25-marker haplotypes that never occur as a homozygote where the minimum expectation is 6 occurrences, Sahana et al. (2013) "identified 17 homozygote deficient haplotypes which could be loosely clustered into eight genomic regions harboring possible recessive lethal alleles". One of these eight regions is haplotype 07-126 located between 6.61 and 10.91 Mb on chromosome BTA7.

Molecular basis: Based on convincing evidence from Swiss Holsteins, Häfliger et al. (2022) reported NOTCH3; c.129_131delTTG as a likely causal variant for this homozygous lethal haplotype.

Breeds: Nordic Holstein, Swiss Holstein.

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
NOTCH3 notch 3 Bos taurus 7 NC_037334.1 (7910713..7950469) NOTCH3 Homologene, Ensembl, NCBI gene

Variants

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 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
1441 Nordic Holstein Swiss Holstein Abortion due to haplotype HH21 NOTCH3 deletion, small (<=20) Naturally occurring variant ARS-UCD1.2 7 g.7913460_7913462del c.129_131del p.(C44del) XM_003586246.3; XP_003586294.1; published as c.129_131delTTG 2022 35361830

References


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 Sahana, G., Nielsen, U.S., Aamand, G.P., Lund, M.S., Guldbrandtsen, B. :
Novel harmful recessive haplotypes identified for fertility traits in nordic holstein cattle. PLoS One 8:e82909, 2013. Pubmed reference: 24376603. DOI: 10.1371/journal.pone.0082909.
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.

Edit History


  • Created by Frank Nicholas on 12 Feb 2014
  • Changed by Frank Nicholas on 12 Feb 2014
  • Changed by Frank Nicholas on 15 May 2020
  • Changed by Frank Nicholas on 04 Apr 2022