Haplotypes with homozygous deficiency HH18-HH38

Phenotype Details
Phene ID
5070
Name
Haplotypes with homozygous deficiency HH18-HH38
Phene Name
HH3 HH5 HH13 HH18 HH19 HH20 HH21 HH22 HH23 HH24 HH25 HH26 HH27 HH28 HH29 HH30 HH31 HH32 HH33 HH34 HH35 HH36 HH37 HH38
OMIA ID
2597
Species ID
9913
Characterised
No
Characterised Year
N/A
Summary

Häfliger et al. (2022) "performed haplotype screenings on almost 53 thousand genotyped [Holstein] animals including 114 k SNP data with two different approaches. We revealed significant haplotype associations to several survival, birth and fertility traits. Within haplotype regions, we mined WGS data of hundreds of bovine genomes for candidate causal variants, which were subsequently evaluated by using a custom genotyping array in several thousand breeding animals. With this approach, we confirmed the known deleterious SMC2:p.Phe1135Ser missense variant associated with Holstein haplotype (HH) 3 [see OMIA 001824-9913]. For ... previously reported deficient homozygous haplotypes that show negative associations to female fertility traits, we propose candidate causative loss-of-function .. [variant]: the HH13-related KIR2DS1:p.Gln159* nonsense variant [see OMIA 001836-9913] ... . In addition, we propose the RIOX1:p.Ala133_Glu142del deletion [see OMIA 002547-9913] as well as the PCDH15:p.Leu867Val missense variant [see OMIA 002548-9913] to explain the unexpected low number of homozygous haplotype carriers for HH25 and HH35, respectively."

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