OMIA 002505-9913 : Haplotype with homozygous deficiency SH5, DIS3-related in Bos taurus
The SH5 haplotype was mapped to ARS-UCD1.2 Chr12:46.828–47.837 MB using the trio approach and Chr:12: 46.831–47.843 MB using the pgp approach (depletion of homozygosity =100%, allele frequency = 0.062).Molecular basis: Häfliger et al. (2021): “With the selected haplotypes, we predicted individual diplotypes that represent if an animal carries one, two, or no copies of the haplotype. Based on these diplotypes, we selected three carrier animals for whole-genome sequencing (WGS) for each haplotype region. … For three deficient homozygous haplotypes (SH5, SH8, and SH9), by linkage disequilibrium analysis, we found perfectly linked (r2 = 1) candidate causal variants. … None of these variants occurred in homozygous state in any of more than 5200 sequenced cattle of various breeds. Selection against these alleles in order to reduce reproductive failure and animal loss is recommended.”
SH5: DIS3 c.2032dupA, p.Ile678AsnTer2 (XM_025000110.1)Breed: Simmental. Associated gene:
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|DIS3||DIS3 homolog, exosome endoribonuclease and 3'-5' exoribonuclease||Bos taurus||12||NC_037339.1 (47532768..47504541)||DIS3||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|
|1412||Simmental||Haplotype with homozygous deficiency SH5||DIS3||SH5||insertion, small (<=20)||Naturally occurring variant||ARS-UCD1.2||12||g.47511687_47511687insT||c.2032dup||p.(I678N*2)||NP_025000110.1, XM_025000110.1||2021||34944310|
|2021||Häfliger, I.M., Seefried, F.R., Drögemüller, C. :|
|Reverse genetic screen for deleterious recessive variants in the local Simmental cattle population of Switzerland. Animals (Basel) 11:3535, 2021. Pubmed reference: 34944310. DOI: 10.3390/ani11123535.|
- Created by Imke Tammen2 on 13 Jan 2022