OMIA:001824-9913 : Haplotype with homozygous deficiency HH3, SMC2-related in Bos taurus (taurine cattle) |
Categories: Mortality / aging (incl. embryonic lethal)
Links to possible relevant human trait(s) and/or gene(s) in OMIM: 605576 (gene)
Single-gene trait/disorder: yes
Mode of inheritance: Autosomal recessive lethal
Disease-related: yes
Key variant known: yes
Year key variant first reported: 2013
Species-specific name: Haplotype HH3
Species-specific symbol: HH3
Inheritance: Häfliger et al. (2022) reported that "no single homozygous carrier of the SMC2 . . . [variant] was observed neither in the current population of more than 14 thousand Swiss dairy cattle nor in any other breed of cattle included in the 1000 Bull Genomes project".
Mapping: Using genotype data from tens of thousands of North American Holsteins, Jerseys and Brown Swiss cattle each genotyped with approximately 50K SNPs on the BovineSNP50 BeadChip, VanRaden et al. (2011) identified five new recessive lethal haplotypes by searching for common haplotypes that are never homozygous in live animals. Three of these haplotypes occur in Holsteins only, and (following a convention proposed by breed-association staff) VanRaden et al. (2011) named them HH1, HH2 and HH3, where the first H stands for Holstein and the second H for haplotype. The disorder described in this OMIA entry is HH3, which maps to chromosome BTA8, at 90-95Mb (UMD 3.0 genome assembly). Fritz et al. (2013) confirmed the existence and location of this deleterious haplotype. By genotyping each of 7,937 Nordic Holstein bulls with the BovineSNP50 BeadChip, yielding 36,387 informative autosomal SNPs, and then searching for 25-marker haplotypes that never occur as a homozygote where the minimum expectation is 6 occurrences, Sahana et al. (2013) "identified 17 homozygote deficient haplotypes which could be loosely clustered into eight genomic regions harboring possible recessive lethal alleles". One of the eight regions (marked by haplotypes 08-1276, 08-1301, 08-1326 and 08-1351) seems to coincide with HH3. McClure et al. (2014) refined the map location of haplotype HH3 on chromosome BTA8 to 95,057,877 to 95,468,310 (UMD3.1).
Molecular basis: Using inferred haplotypes from the 1000-bull-genomes project, Hayes et al. (2013) announced the discovery of the likely HH3 causal mutation. Using exome capture and next-gen sequencing, McClure et al. (2014) confirmed and validated Hayes et al. (2013)'s causal mutation mutation as "a non-synonymous SNP (T/C) within exon 24 of the Structural Maintenance of Chromosomes 2 (SMC2) on Chromosome 8 at position 95,410,507 (UMD3.1). This polymorphism changes amino acid 1135 from phenylalanine to serine and causes a non-neutral, non-tolerated, and evolutionarily unlikely substitution within the NTPase domain of the encoded protein. . . . Given the essential role of SMC2 in DNA repair, chromosome condensation and segregation during cell division, our findings strongly support the non-synonymous SNP (T/C) in SMC2 as the likely causative mutation." Full details of the Hayes et al. (2013) discovery were provided by Daetwyler et al. (2014). In summary: "There was a single bull identified as a carrier of the derived HH3 region in the 1000 bull genomes project data set on the basis of the inferred haplotype. After filtering for mutations that were (i) carried in the heterozygous state by the HH3 carrier bull, (ii) absent in the 63 predicted non-carrier Holstein bulls, (iii) absent in the homozygous state in the Holstein bulls with unknown status and (iv) absent in the other breeds (assuming that the deleterious mutation is recent), only 1 candidate mutation was retained in the HH3 region: a thymine-to-cytosine transition at position 95,410,507 (g.95410507T>C) [UMD3.1]." For validation, the mutation "was genotyped by PCR and Sanger sequencing in a panel of 10 known HH3 carriers; all were heterozygous for the mutation, supporting the association between the HH3 region and the g.95410507C allele. As an additional test, 5,606 Holstein individuals were each genotyped in duplicate for the g.95410507T>C mutation using a custom Illumina BeadChip (all duplicate pairs were concordant). In agreement with the hypothesis that this mutation causes embryonic lethality, no individual with a CC genotype was detected (P < 0.06), whereas 2,476 individuals with the TT genotype and 171 individuals with the TC genotype were identified. In addition, 2,344 Montbeliarde individuals and 615 Normandy individuals were homozygous for the wild-type allele." Häfliger et al. (2022) confirmed the effect of the SMC2 variant (OMIA variant 211) in Swiss Holsteins.
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 |
---|---|---|---|---|---|---|
SMC2 | structural maintenance of chromosomes 2 | Bos taurus | 8 | NC_037335.1 (93705318..93756197) | SMC2 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
211 | Holstein (black and white) (Cattle) | Abortion due to haplotype HH3 | SMC2 | missense | Naturally occurring variant | ARS-UCD1.3 | 8 | NC_037335.1:g.93753358T>C | XM_015472668.2:c.3404T>C | XP_015328154.1:p.(F1135S) | XM_015472668.2; XP_015328154.1 | rs456206907 | 2014 | 24667746 | Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool; Breed information kindly provided or confirmed by Matt McClure and Jennifer McClure from "Understanding Genetics and Complete Genetic Disease and Trait Definition (Expanded 2016 Edition)" (https://www.icbf.com/wp/?page_id=2170) |
Cite this entry
Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2022). OMIA:001824-9913: 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., Flores-Borobia, I., Hamze, J.G., Galiano-Cogolludo, B., Lamas-Toranzo, I., González-Brusi, L., Ramos-Ibeas, P., Bermejo-Álvarez, P. : | |
SMC2 ablation impairs bovine embryo development shortly after blastocyst hatching. Reproduction 168, 2024. Pubmed reference: 39231091. DOI: 10.1530/REP-24-0211. | |
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. | |
Bengtsson, C., Stålhammar, H., Thomasen, J.R., Fikse, W.F., Strandberg, E., Eriksson, S. : | |
Mating allocations in Holstein combining genomic information and linear programming optimization at the herd level. J Dairy Sci 106:3359-3375, 2023. Pubmed reference: 37028963. DOI: 10.3168/jds.2022-22926. | |
Sudhakar, A., Nayee, N., Saha, S., Donthula, S.K., Poojara, H.V., Gohil, T., Patel, A.C., Maurya, B.K. : | |
Role of genetic introgression in introducing mutant alleles in Bos indicus cattle and prevalence of lethal genetic disorders in Bos taurus × Bos indicus and Bos indicus cattle in India. Trop Anim Health Prod 55:399, 2023. Pubmed reference: 37940810. DOI: 10.1007/s11250-023-03798-8. | |
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. | |
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 | Daetwyler, H.D., Capitan, A., Pausch, H., Stothard, P., van Binsbergen, R., Brøndum, R.F., Liao, X., Djari, A., Rodriguez, S.C., Grohs, C., Esquerré, D., Bouchez, O., Rossignol, M.N., Klopp, C., Rocha, D., Fritz, S., Eggen, A., Bowman, P.J., Coote, D., Chamberlain, A.J., Anderson, C., VanTassell, C.P., Hulsegge, I., Goddard, M.E., Guldbrandtsen, B., Lund, M.S., Veerkamp, R.F., Boichard, D.A., Fries, R., Hayes, B.J. : |
Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet 46:858-65, 2014. Pubmed reference: 25017103. DOI: 10.1038/ng.3034. | |
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. | |
2013 | Fritz, S., Capitan, A., Djari, A., Rodriguez, S.C., Barbat, A., Baur, A., Grohs, C., Weiss, B., Boussaha, M., Esquerré, D., Klopp, C., Rocha, D., Boichard, D. : |
Detection of haplotypes associated with prenatal death in dairy cattle and identification of deleterious mutations in GART, SHBG and SLC37A2. PLoS One 8:e65550, 2013. Pubmed reference: 23762392. DOI: 10.1371/journal.pone.0065550. | |
Hayes, B. , Daetwyler, H.D., Fries, R., Guldbrandtsen, B., Lund, M.S., Boichard, D.A., Stothard, P., Veerkamp, R.F., Hulsegge, I., Rocha, D., Van Tassell, C., Mullaart, E., Gredler, B., Druet, T., Bagnato, A., Goddard, M., Chamberlain, A., 1000 Bull Genomes Consortium : | |
The 1000 Bull Genomes Project - Toward Genomic Selection From Whole Genome Sequence Data In Dairy and Beef Cattle Plant Anim Genome XXI Conf. San Diego, CA :Abstr W150, 2013. | |
Sahana, G., Nielsen, U.S., Aamand, G.P., Lund, M.S., Guldbrandtsen, B. : | |
Novel harmful recessive haplotypes identified for fertility traits in nordic holstein cattle. PLoS One 8:e82909, 2013. Pubmed reference: 24376603. DOI: 10.1371/journal.pone.0082909. | |
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 12 Jun 2013
- Changed by Frank Nicholas on 12 Jun 2013
- Changed by Frank Nicholas on 14 Jun 2013
- Changed by Frank Nicholas on 12 Feb 2014
- Changed by Frank Nicholas on 01 Apr 2014
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- Changed by Frank Nicholas on 04 Apr 2022