OMIA 002515-9913 : Haplotype with homozygous deficiency OH2, TUBGCP5-related in Bos taurus

Possibly relevant human trait(s) and/or gene(s) (MIM number): 608147 (gene)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal Recessive

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2021

Species-specific description: Häfliger et al. (2021) investigated “the two Braunvieh populations reared in Switzerland, the dairy Brown Swiss (BS) and the dual-purpose Original Braunvieh (OB). We performed a genome-wide analysis of array data of trios (sire, dam, and offspring) from the routine genomic selection to identify candidate regions showing missing homozygosity and phenotypic associations with five fertility, ten birth, and nine growth-related traits. In addition, genome-wide single SNP regression studies based on 114,890 single nucleotide polymorphisms (SNPs) for each of the two populations were performed. Furthermore, 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. …

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 OH2 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 OH2 haplotype was mapped to Chr2:1005580-1614673 (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.”

Haplotype OH2:TUBGCP5, chr2:1268426, NM_001102495.1

c.311C>A, p.Thr104Lys

Breed: Braunvieh.

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
TUBGCP5 tubulin gamma complex associated protein 5 Bos taurus 2 NC_037329.1 (1283473..1232962) TUBGCP5 Homologene, Ensembl, NCBI gene

Variants

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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
1414 Braunvieh Haplotype with homozygous deficiency OH2 TUBGCP5 missense Naturally occurring variant ARS-UCD1.2 2 g.1268426G>T c.311C>A p.(T104K) NM_001102495.1 rs720533878 2021 34915862

Reference


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.

Edit History


  • Created by Imke Tammen2 on 14 Jan 2022
  • Changed by Imke Tammen2 on 14 Jan 2022