OMIA:001697-9913 : Haplotype with homozygous deficiency JH1 in Bos taurus (taurine cattle) |
In other species: indicine cattle (zebu)
Categories: Mortality / aging (incl. embryonic lethal)
Mendelian 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 JH1
Species-specific symbol: JH1
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. One of these haplotypes occurs in Jerseys only, and (following a convention proposed by breed-association staff) VanRaden et al. (2011) named it JH1, where J stands for Jersey and H for haplotype. It maps to chromosome BTA15, at 13-18Mb (UMD 3.0 genome assembly).
Molecular basis: Sonstegard et al (2013) investigated the lethal Jersey haplotype, namely haplotype JH1 on chromosome BTA15 (see Mapping section). They first refined the haplotype "to a 15-marker window (15,162,470 to 15,949,175)" and then obtained whole-genome sequence from 11 bulls carrying this haplotype. Analysis of the sequence of these carriers in the candidate region revealed a "high-impact stop-gain SNP located at position 15,707,169 on BTA15. This C-to-T transition SNP results in an Arginine to a stop codon in exon 3 of CWC15, the bovine protein CWC15 homolog of a spliceosome-associated protein . . . . This nonsense mutation would reduce the size of the CWC15 protein product from 231 amino acids in length to only 54 amino acids. A NCBI conserved domains search on the bovine CWC15 protein product reveals that this truncated protein would not have the conserved Cwf_Cwc_15 (pfam04889) domain present in the wildtype."
Breed:
Jersey (Cattle) (VBO_0000250).
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 |
|---|---|---|---|---|---|---|
| CWC15 | CWC15 spliceosome-associated protein | Bos taurus | 15 | NC_037342.1 (15447275..15456213) | CWC15 | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 287 | Jersey (Cattle) | Abortion due to haplotype JH1 | CWC15 | nonsense (stop-gain) | Naturally occurring variant | ARS-UCD1.3 | 15 | NC_037342.1:g.15449431C>T | NM_001046399.2:c.163C>T | NP_001039864.1:p.(R55*) | UMD3.1 position is g.15707169C>T, cDNA and protein positions based on XM_005215764.2 | rs1115118696 | 2013 | 23349982 | 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). The genomic location on ARS-UCD1.2 was determined by Katie Eager and Shernae Woolley, EMAI, NSW. Department of Primary Industries. |
Cite this entry
Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2020). OMIA:001697-9913: 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 | 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 | 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. | |
| 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. | |
| 2015 | Zhang, Y., Guo, G., Huang, H., Lu, L., Wang, L., Fang, L., Liu, L., Wang, Y., Zhang, S. : |
| Screening for JH1 genetic defect carriers in Jersey cattle by a polymerase chain reaction and restriction fragment length polymorphism assay. J Vet Diagn Invest 27:596-9, 2015. Pubmed reference: 26179100. DOI: 10.1177/1040638715589362. | |
| 2013 | Sonstegard, T.S., Cole, J.B., Vanraden, P.M., Van Tassell, C.P., Null, D.J., Schroeder, S.G., Bickhart, D., McClure, M.C. : |
| Identification of a Nonsense Mutation in CWC15 Associated with Decreased Reproductive Efficiency in Jersey Cattle. PLoS One 8:e54872, 2013. Pubmed reference: 23349982. DOI: 10.1371/journal.pone.0054872. | |
| 2012 | Sonstegard, T.S., VanRaden, P.M., Van Tassell, C.P., Adams, H.A., Lewin, H.A. : |
| Lethal haplotypes in dairy cattle: What lies beneath? Proceedings of the 33rd Conference of the International Society of Animal Genetics :abstract S0118, 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. |
Edit History
- Created by Frank Nicholas on 01 Jul 2012
- Changed by Frank Nicholas on 01 Jul 2012
- Changed by Frank Nicholas on 02 Feb 2013
- Changed by Frank Nicholas on 12 Jun 2013
- Changed by Frank Nicholas on 24 Mar 2015
- Changed by Frank Nicholas on 08 Aug 2017
- Changed by Frank Nicholas on 10 Aug 2020