OMIA:002547-9913 : Haplotype with homozygous deficiency HH25, RIOX1-related in Bos taurus (taurine cattle)
Categories: Mortality / aging (incl. embryonic lethal)
Possibly relevant human trait(s) and/or gene(s) (MIM number): 611919 (gene)
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Mode of inheritance: Autosomal recessive
Considered a defect: yes
Key variant known: yes
Year key variant first reported: 2022
Inheritance: Häfliger et al. (2022) reported a 75% deficiency of homozygotes for this haplotype in Swiss Holsteins.
Markers: Based on strong evidence from Swiss Holsteins, Häfliger et al. (2022) reported RIOX1; c.396_425delGGC GCA GAC CCC GGC GGC ACG CTT GGT GGA as a likely causal variant for haplotype H25.
Have human generated variants been created, e.g. through genetic engineering and gene editing
Holstein-Friesian, Switzerland (Cattle) (VBO_0003139).
Breeds in which the phene has been documented. For breeds in which a likely causal variant has been documented, see the variant table below
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|RIOX1||Bos taurus||10||NC_037337.1 (84937977..84940480)||RIOX1||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|
|1442||Holstein-Friesian, Switzerland (Cattle)||Haplotype HH25 deficiency||RIOX1||deletion, gross (>20)||Naturally occurring variant||ARS-UCD1.2||10||g.84938408_84938437del||c.396_425del||p.(A133_E142del)||NM_001099702.1; NP_001093172.1; published as c.396_425delGGCGCAGACCCCGGCGGCACGCTTGGTGGA||2022||35361830|
Cite this entry
|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.|
- Created by Frank Nicholas on 04 Apr 2022
- Changed by Frank Nicholas on 04 Apr 2022