OMIA 002597-9913 : Haplotypes with homozygous deficiency HH18-HH38 in Bos taurus

Mendelian trait/disorder: unknown

Considered a defect: yes

Species-specific 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

Species-specific description: 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."

Mapping: Häfliger et al. (2022) identified several haplotypes with homozygous deficiency, some of these had been previously reported. Likely causal variants have been confirmed for haplotype HH3 and identified for haplotypes HH13, 25 and 35 (see haplptype specific OMIA entries for these haplotypes). A reported variant in the NOTCH3 gene was later identified to not be causal for HH21 (Cord Drögemüller, pers. communication).

Detail of chromosomal location of all identified haplotypes are listed below:

Name chr:Pos in Mb in ARS-UCD1.2 (Comment)

HH3 8:90.959–92.085 (see OMIA 001824-9913, haplotype previously described)

HH5 9:90.928–91.824 (haplotype previously described)

HH13 18:60.932–62.101 and 62.070–63.045 (see OMIA 001836-9913, haplotype previously described)

HH18 1:10.302–104.376

HH19 1:139.874–140.643 (haplotype co-localises with previously described haplotype)

HH20 2:134.477–135.148

HH21 7:7.872–10.433 (haplotype previously described, reported NOTCH3 variant is not causal)

HH22 7:93.582–94.642

HH23 8:15.562–16.863

HH24 8:66.699–68.006

HH25 10:86.876–87.773 (see OMIA 002547-9913)

HH26 11:4.531–5.362

HH27 13:7.083–8.297

HH28 14:24.591–24.827

HH29 14:58.128–59.238

HH30 21:7.844–8.671

HH31 22:59.811–60.704

HH32 23:32.773–33.726 and 33.545–34.948

HH33 24:44.693–45.678

HH34 25:36.162–37.330

HH35 26:3.359–4.235 (see OMIA 002548-9913)

HH36 28:28.541–29.736 and 29.731–30.877

HH37 28:40.348–41.271

HH38 29:14.243–15.317

Breed: Holstein-Friesian.


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.

Edit History

  • Created by Imke Tammen2 on 16 Nov 2022
  • Changed by Imke Tammen2 on 16 Nov 2022
  • Changed by Imke Tammen2 on 17 Nov 2022