OMIA:002134-9913 : Haplotype with homozygous deficiency AH2 in Bos taurus (taurine cattle)

Categories: Mortality / aging (incl. embryonic lethal)

Links to possible relevant human trait(s) and/or gene(s) in OMIM: 611476 (gene)

Mendelian trait/disorder: yes

Mode of inheritance: Autosomal recessive

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2017

History: Details of the first Ayrshire lethal haplotype (AH1) are presented in OMIA 001934-9913. Null et al. (2017) reported that "A second [Ayrshire] haplotype [AH2] reached the threshold for statistical significance (7 expected homozygotes and none observed) in October 2013. Sire conception rate was 6.1% lower for matings of carrier sires to cows with carrier maternal grandsires, but the effect was not significant. As of December 2016, 23.5 homozygotes were expected but none had been observed."

Molecular basis: Null et al. (2017): "A splice acceptor variant at 51,267,548 bp in the RNA Polymerase 2 Associated Protein (RPAP2) gene was the most likely causal variant in the [AH2] haplotype. RPAP2 is an essential component of the RNA polymerase 2 holoenzyme necessary for transcription of snRNA species. Experiments with mouse knockouts also found a deficiency of homozygotes, suggesting that RPAP2 is necessary for embryonic development."

Prevalence: Null et al. (2017) reported that the frequency of the AH2 haplotype in US Ayrshires "has increased from 6% in animals born in 1990 to 21.7% for animals born since 2008." Guarini et al. (2019) reported the frequency of the AH2 haplotype in Canadian Ayrshires was less than 1% from 1997 to 2010 after which it rose to be around 11.2% in 2014 (estimated from their Figure 2).

Breed: Ayrshire (Cattle) (VBO_0000120).
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
RPAP2 RNA polymerase II associated protein 2 Bos taurus 3 NC_037330.1 (51122203..50994696) RPAP2 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
858 Ayrshire (Cattle) Abortion due to haplotype AH2 RPAP2 splicing Naturally occurring variant 3 a splice acceptor variant at 51,267,548 bp [reference sequence not specified] in RPAP2 2017 Reference not in PubMed; see OMIA 002134-9913 for reference details

Cite this entry

Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2019). OMIA:002134-9913: 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 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 , 2023. Pubmed reference: 37977438. DOI: 10.3168/jds.2023-24159.
2019 Guarini, A.R., Sargolzaei, M., Brito, L.F., Kroezen, V., Lourenco, D.A.L., Baes, C.F., Miglior, F., Cole, J.B., Schenkel, F.S., Guarini, A.R., Sargolzaei, M., Brito, L.F., Kroezen, V., Lourenco, D.A.L., Baes, C.F., Miglior, F., Cole, J.B., Schenkel, F.S. :
Estimating the effect of the deleterious recessive haplotypes AH1 and AH2 on reproduction performance of Ayrshire cattle. J Dairy Sci 102:5315-5322, 2019. Pubmed reference: 30954262. DOI: 10.3168/jds.2018-15366.
2017 Null, D.J., Hutchison, J.L., Bickhart, D.M., VanRaden, P.M., Cole, J.B. :
Discovery of a haplotype affecting fertility in Ayrshire dairy cattle and identification of a putative causal variant. J. Dairy Sci. 100 (Suppl. 2):199 (Abstract 206), 2017.

Edit History

  • Created by Frank Nicholas on 22 Nov 2017
  • Changed by Frank Nicholas on 11 Apr 2019