OMIA 001823-9913 : Haplotype with homozygous deficiency HH2, IFT80-related in Bos taurus
McClure et al. (2014) refined the mapping of haplotype HH2 on chromosome BTA1 to 94,860,836 to 96,553,339 (UMD3.1).Molecular basis: In an extensive study involving exome capture and next-gen sequencing, McClure et al. (2014) were not able to discover any potentially causal variant for haplotype HH2.
Yang et al. (2021): "Short- and long-read WGS was performed on four carriers and four non-carriers of HH2 to screen for variants in concordance with HH2 haplotype status.Sequence variation analysis revealed five putative functional variants of protein-coding genes, including a frameshift mutation (g.107172616delT) in intraflagellar transport protein 80 (IFT80) gene. Transcriptome analysis of whole blood indicated that no gene exhibited significantly differential expression or allele-specific expression between carriers and non-carriers in the candidate region. This evidence points to g.107172616delT as the highest priority causative mutation for HH2."Breed: Holstein. Associated gene:
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|IFT80||intraflagellar transport 80||Bos taurus||1||NC_037328.1 (107078906..107210812)||IFT80||Homologene, Ensembl, NCBI gene|
By default, variants are sorted chronologically by year of publication, to provide a historical perspective. Readers can re-sort on any column by clicking on the column header. Click it again to sort in a descending order. To create a multiple-field sort, hold down Shift while clicking on the second, third etc relevant column headers.
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|
|1396||Holstein Friesian||Haplotype with homozygous deficiency-HH2||IFT80||deletion, small (<=20)||Naturally occurring variant||ARS-UCD1.2||1||g.107172616delT||c.1140del||p.(L381Ffs*3)||g.107172616delT||rs523422030||rs523422030||2021||34873723||ENSBTAT00000044761.4:c.1140del ENSBTAP00000042227.4:p.Leu381PhefsTer3|
Note: the references are listed in reverse chronological order (from the most recent year to the earliest year), and alphabetically by first author within a year.
|2021||Yang, Y., Si, J., Lv, X., Dai, D., Liu, L., Tang, S., Wang, Y., Zhang, S., Xiao, W., Zhang, Y. :|
|Integrated analysis of whole genome and transcriptome sequencing reveals a frameshift mutation associated with recessive embryonic lethality in Holstein cattle. Anim Genet :, 2021. Pubmed reference: 34873723. DOI: 10.1111/age.13160.|
|2016||Cole, J.B., Null, D.J., VanRaden, P.M. :|
|Phenotypic and genetic effects of recessive haplotypes on yield, longevity, and fertility. J Dairy Sci 99:7274-88, 2016. Pubmed reference: 27394947. DOI: 10.3168/jds.2015-10777.|
|Segelke, D., Täubert, H., Reinhardt, F., Thaller, G. :|
|Considering genetic characteristics in German Holstein breeding programs. J Dairy Sci 99:458-67, 2016. Pubmed reference: 26601581. DOI: 10.3168/jds.2015-9764.|
|2014||McClure, M.C., Bickhart, D., Null, D., Vanraden, P., Xu, L., Wiggans, G., Liu, G., Schroeder, S., Glasscock, J., Armstrong, J., Cole, J.B., Van Tassell, C.P., Sonstegard, T.S. :|
|Bovine exome sequence analysis and targeted SNP genotyping of recessive fertility defects BH1, HH2, and HH3 reveal a putative causative mutation in SMC2 for HH3. PLoS One 9:e92769, 2014. Pubmed reference: 24667746. DOI: 10.1371/journal.pone.0092769.|
|2011||VanRaden, P.M., Olson, K.M., Null, D.J., Hutchison, J.L. :|
|Harmful recessive effects on fertility detected by absence of homozygous haplotypes. J Dairy Sci 94:6153-61, 2011. Pubmed reference: 22118103. DOI: 10.3168/jds.2011-4624.|
- Created by Frank Nicholas on 12 Jun 2013
- Changed by Frank Nicholas on 12 Jun 2013
- Changed by Frank Nicholas on 01 Apr 2014
- Changed by Frank Nicholas on 24 Mar 2015
- Changed by Imke Tammen2 on 16 Dec 2021