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

Considered a defect: 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


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 Year Published PubMed ID(s) Acknowledgements
287 Jersey (Cattle) Abortion due to haplotype JH1 CWC15 nonsense (stop-gain) Naturally occurring variant ARS-UCD1.2 15 g.15449431C>T c.163C>T 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)" ( 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].


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.

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