OMIA:001941-9913 : Haplotype with homozygous deficiency HH5, TFB1M-related in Bos taurus (taurine cattle) |
Categories: Mortality / aging (incl. embryonic lethal) , Embryo phene
Links to possible relevant human trait(s) and/or gene(s) in OMIM: 607033 (gene)
Single-gene trait/disorder: yes
Mode of inheritance: Autosomal recessive lethal
Disease-related: yes
Key variant known: yes
Year key variant first reported: 2016
Species-specific name: Haplotype HH5
Species-specific symbol: HH5
Species-specific description: [FN thanks Ekkehard Schütz for feedback on an earlier version of the text on this page]
Mapping: Using a strategy similar to that of VanRaden et al. (2011), Cooper et al. (2013) discovered reduced-fertility haplotype HH5, located on chromosome BTA9. In their table of reduced-fertility haplotypes, Cole et al. (2014) list this haplotype as being located at 92,350,052 – 93,910,957bp on chromosome BTA9. Schütz et al. (2016) fine-mapped the likely causal region of HH5 to be "an approximately 138kb region spanning 93.233Mb to 93.371Mb".
Molecular basis: Schütz et al. (2016) identified the likely causal mutation as "a deletion of 138kbp, spanning position 93,233kb to 93,371kb on chromosome 9 (BTA9), harboring only dimethyl-adenosine transferase 1 (TFB1M). The deletion breakpoints are flanked by bovine long interspersed nuclear elements Bov-B (upstream) and L1ME3 (downstream), suggesting a homologous recombination/deletion event. TFB1M di-methylates adenine residues in the hairpin loop at the 3’-end of mitochondrial 12S rRNA, being essential for synthesis and function of the small ribosomal subunit of mitochondria." The causality of this deletion is reinforced by the fact that homozygous TFB1M knockout mice are not viable and suffer fetal death (Schütz et al., 2016).
Clinical features: Pérez-Gómez et al. (2024) identified that embryos homozugous for the TFB1M variant "are able to develop to early embryonic disc stage but fail to undergo early conceptus elongation, required for pregnancy recognition."
Prevalence: Using direct PCR for the deletion, Schütz et al (2016) estimated the prevalence of carriers to be 5.5% in the interrogated German Holstein population.
Breed:
Holstein (black and white) (Cattle) (VBO_0000237).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).
Associated gene:
Symbol | Description | Species | Chr | Location | OMIA gene details page | Other Links |
---|---|---|---|---|---|---|
TFB1M | transcription factor B1, mitochondrial | Bos taurus | 9 | NC_037336.1 (91932590..91865226) | TFB1M | Homologene, Ensembl , NCBI gene |
Variants
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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 | Year Published | PubMed ID(s) | Acknowledgements |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
963 | Holstein (black and white) (Cattle) | Abortion due to haplotype HH5 | TFB1M | complex rearrangement | Naturally occurring variant | 9 | "a deletion of 138kbp, spanning position 93,233kb to 93,371kb on chromosome 9 (BTA9), harboring only dimethyl-adenosine transferase 1 (TFB1M). The deletion breakpoints are flanked by bovine long interspersed nuclear elements Bov-B (upstream) and L1ME3 (downstream), suggesting a homologous recombination/deletion event." | 2016 | 27128314 |
Cite this entry
Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2024). OMIA:001941-9913: Online Mendelian Inheritance in Animals (OMIA) [dataset]. https://omia.org/. https://doi.org/10.25910/2AMR-PV70
References
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.
2024 | Gozdek, M., Mucha, S., Prostek, A., Kamola, D., Sadkowski, T. : |
Distribution of recessive genetic defect carriers in Holstein Friesian cattle: A polish perspective. Animals (Basel) 14:3170, 2024. Pubmed reference: 39595223. DOI: 10.3390/ani14223170. | |
Khan, M.Y.A., Dai, D., Su, X., Tian, J., Zhou, J., Ma, L., Wang, Y., Wen, W., Zhang, Y. : | |
Multiplex fluorescent amplification-refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay. Anim Genet 55:457-464, 2024. Pubmed reference: 38622758. DOI: 10.1111/age.13432. | |
Pérez-Gómez, A., Hamze, J.G., Flores-Borobia, I., Galiano-Cogolludo, B., Lamas-Toranzo, I., González-Brusi, L., Ramos-Ibeas, P., Bermejo-Álvarez, P. : | |
HH5 double-carrier embryos fail to progress through early conceptus elongation. J Dairy Sci 107:6371-6382, 2024. Pubmed reference: 38642647. DOI: 10.3168/jds.2023-24482. | |
Shormanova, M., Makhmutov, A., Shormanova, A., Muslimova, Z., Ussenbekov, Y. : | |
Development of alternative diagnosis of HH1, HH3, HH5 and HCD fertility haplotypes and subfertility syndrome in cattle. Reprod Domest Anim 59:e14533, 2024. Pubmed reference: 38268216. DOI: 10.1111/rda.14533. | |
van den Berg, I., Nguyen, T.V., Nguyen, T.T.T., Pryce, J.E., Nieuwhof, G.J., MacLeod, I.M. : | |
Imputation accuracy and carrier frequency of deleterious recessive defects in Australian dairy cattle. J Dairy Sci 107:9591-9601, 2024. Pubmed reference: 38945256. DOI: 10.3168/jds.2024-24780. | |
2023 | Ask-Gullstrand, P., Strandberg, E., Båge, R., Rius-Vilarrasa, E., Berglund, B. : |
The effect of genetic defects on pregnancy loss in Swedish dairy cattle. J Dairy Sci 107:2999-3005, 2023. Pubmed reference: 37977438. DOI: 10.3168/jds.2023-24159. | |
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. | |
Schütz, E., Wehrhahn, C., Wanjek, M., Bortfeld, R., Wemheuer, W.E., Beck, J., Brenig, B. : | |
The Holstein Friesian Lethal Haplotype 5 (HH5) Results from a Complete Deletion of TFB1M and Cholesterol Deficiency (CDH) from an ERV-(LTR) Insertion into the Coding Region of APOB. PLoS One 11:e0154602, 2016. Pubmed reference: 27128314. DOI: 10.1371/journal.pone.0154602. | |
Schütz, E., Wehrhahn, C., Wanjek, M., Bortfeld, R., Wemheuer, W.E., Beck, J., Brenig, B. : | |
Correction: The Holstein Friesian Lethal Haplotype 5 (HH5) Results from a Complete Deletion of TBF1M and Cholesterol Deficiency (CDH) from an ERV-(LTR) Insertion into the Coding Region of APOB. PLoS One 11:e0157618, 2016. Pubmed reference: 27280705. DOI: 10.1371/journal.pone.0157618. | |
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 | 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 | Cooper, T.A., Wiggans, G.R., VanRaden, P.M., Hutchison, J.L., Cole, J.B., Null, D.J. : |
Genomic evaluation of Ayrshire dairy cattle and new haplotypes affecting fertility and stillbirth in Holstein, Brown Swiss and Ayrshire breeds. ADSA-ASAS Joint Annual Meeting :poster T206, 2013. | |
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. |
Edit History
- 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 02 May 2016
- Changed by Frank Nicholas on 03 May 2016
- Changed by Imke Tammen2 on 22 Apr 2024