OMIA 001939-9913 : Haplotype with homozygous deficiency BH2, TUBD1-related in Bos taurus
In a preprint posted on the Cold Spring Harbor bioRxiv preprint server on 1st March 2016, Schwarzenbacher et al. (2016) documented the quite marked effects of this haplotype on mortality, and reported the discovery of its causal mutation as "a missense mutation in TUBD1 (rs383232842[T>C], p.H210R)". This is the first result from a preprint to be included in OMIA. A refereed version of this paper was published three months later in BMC Genomics (see reference list).
Häfliger et al. (2021) identified the same haplotype and same likely causal variant in Brown Swiss cattle in their investigation of Brown Swiss and Original Braunvieh populations reared in Switzerland - see OMIA002513-9913 for more detail.Clinical features: As reported by Schwarzenbacher et al. (2016),"Homozygous calves suffer from chronic airway disease resulting in poor growth performance and high juvenile mortality. The respiratory manifestations resemble key features of diseases resulting from impaired function of airway cilia." As pointed out carefully by Schwarzenbacher et al. (2016), not all homozygotes die, i.e. the lethal allele has incomplete penetrance. Prevalence: Wu et al. (2020) reported the frequency for this lethal haplotype as 4.4% in 19,309 Nordic Red Dairy cattle. Noting an inconsistency in this breed between the occurrence of the lethal haplotype and the likely causal variant (p.H210R) in Brown Swiss reported by Schwarzenbacher et al. (2016), Wu et al. (2020) noted that "it is highly likely that an additional recessive lethal mutation is segregating in this region in" Nordic Red Dairy cattle. Breeds: Brown Swiss, Nordic Red. Associated gene:
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|TUBD1||tubulin delta 1||Bos taurus||19||NC_037346.1 (10840880..10816976)||TUBD1||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|
|776||Brown Swiss||Haplotype with homozygous deficiency BH2||TUBD1||missense||Naturally occurring variant||ARS-UCD1.2||19||g.10833921T>C||c.757T>C||p.(H210R)||rs383232842||rs383232842||2016||27225349||Some variant information kindly provided or confirmed by Hubert Pausch, including information from Additional Table 6 of Jansen et al. (2013) BMC Genomics201314:446 https://doi.org/10.1186/1471-2164-14-446|
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||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.|
|2020||Wu, X., Mesbah-Uddin, M., Guldbrandtsen, B., Lund, M.S., Sahana, G. :|
|Novel haplotypes responsible for prenatal death in Nordic Red and Danish Jersey cattle. J Dairy Sci 103:4570-4578, 2020. Pubmed reference: 32197842. DOI: 10.3168/jds.2019-17831.|
|2016||Biscarini, F., Schwarzenbacher, H., Pausch, H., Nicolazzi, E.L., Pirola, Y., Biffani, S. :|
|Use of SNP genotypes to identify carriers of harmful recessive mutations in cattle populations. BMC Genomics 17:857, 2016. Pubmed reference: 27809787. DOI: 10.1186/s12864-016-3218-9.|
|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.|
|Schwarzenbacher, H., Burgstaller, J., Seefried, F.R., Wurmser, C., Hilbe, M., Jung, S., Fuerst, C., Dinhopl, N., Weissenböck, H., Fuerst-Waltl, B., Dolezal, M., Winkler, R., Grueter, O., Bleul, U., Wittek, T., Fries, R., Pausch, H. :|
|A missense mutation in TUBD1 is associated with high juvenile mortality in Braunvieh and Fleckvieh cattle. BMC Genomics 17:400, 2016. Pubmed reference: 27225349. DOI: 10.1186/s12864-016-2742-y.|
|Schwarzenbacher, H. et al. :|
|A missense mutation in TUBD1 is associated with high juvenile mortality in Braunvieh and Fleckvieh cattle BioRchiv :, 2016. DOI: 10.1101/041921 .|
|2014||Cole, J.B., VanRaden, P.M., Null, D.J., Hutchison, J.L., Cooper, T.A., Hubbard, S.M. :|
|Haplotype tests for recessive disorders that affect fertility and other traits. AIP RESEARCH REPORT GENOMIC3 (09-13); http://aipl.arsusda.gov/reference/recessive_haplotypes_ARR-G3.html :, 2014.|
|2013||VanRaden, P., Null, D., Hutchison, J., Cooper, T. :|
|New fertility and stillbirth haplotypes and changes in haplotype status Website of the Council on Dairy Cattle Breeding: https://www.cdcb.us/reference/changes/eval1308.htm :, 2013.|
|2012||Schwarzenbacher, H., Fuerst, C., Fuerst-Waltl, B., Dolezal, M. :|
|A genome-wide search for harmful recessive haplotypes in Brown Swiss and Fleckvieh cattle. EAAP annual meeting; http://old.eaap.org/Previous_Annual_Meetings/2012Bratislava/Papers/Published/22_Schwarzenbacher.pdf :Abstract p. 171, 2012.|
|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 31 Oct 2014
- Changed by Frank Nicholas on 31 Oct 2014
- Changed by Frank Nicholas on 24 Mar 2015
- Changed by Frank Nicholas on 03 Mar 2016
- Changed by Frank Nicholas on 04 Mar 2016
- Changed by Frank Nicholas on 02 Jun 2016
- Changed by Frank Nicholas on 23 Mar 2020
- Changed by Imke Tammen2 on 14 Jan 2022