OMIA 002516-9913 : Haplotype with homozygous deficiency OH4, LIG3-related in Bos taurus
Using a trio-based approach, we identified 38 haplotype regions for BS and five for OB … . For the BS population, we confirmed two known haplotypes, BH1 and BH2 [OMIA 001825-9913 and OMIA 001939-9913]. Twenty-four variants that potentially explained the missing homozygosity and associated traits were detected …. We propose a list of six protein-changing variants as potentially causing missing homozygosity. These variants need to be functionally validated and incorporated in the breeding program.”
Information about the OH4 haplotype is described in this entry.Mapping: Häfliger et al. (2021) “The OB dataset included 10,085 genotyped animals, … [with] 3287 trios (trio: sire, dam, and offspring)." The OH4 haplotype was mapped to Chr19:14336760-15222429 (ARSUCD1.2) Molecular basis: Häfliger et al. (2021) “Whole-genome sequencing data of 430 cattle including 70 putative haplotype carriers were mined to identify potential candidate variants that were validated by genotyping the current population using a custom array.”
The likely causal variant for the OH4 haplotype was identified as LIG3: chr19:15080335, NM_001038107.2, c.2483_2484 + 4delAGGTGBreed: Braunvieh. Associated gene:
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|LIG3||ligase III, DNA, ATP-dependent||Bos taurus||19||NC_037346.1 (15098477..15077269)||LIG3||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|
|1415||Braunvieh||Haplotype with homozygous deficiency OH4||LIG3||deletion, small (<=20)||Naturally occurring variant||ARS-UCD1.2||19||g.15080336_15080341del||c.2483_2484+4delAGGTG||p.K828fs||NM_001038107.2||2021||34915862|
|2021||Häfliger, I.M., Seefried, F.R., Spengeler, M., Drögemüller, C. :|
|Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success. Genet Sel Evol 53:95, 2021. Pubmed reference: 34915862. DOI: 10.1186/s12711-021-00686-3.|
- Created by Imke Tammen2 on 14 Jan 2022