OMIA 002181-9823 : Abortion due to haplotype LA1 in Sus scrofa

Mendelian trait/disorder: yes

Mode of inheritance: Recessive Embryonic Lethal

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2019

Species-specific description: Derks et al. (2019) identified five relatively frequent haplotypes for which there was either a deficit or a complete lack of homozygotes in large populations of Landrace (28,085) and Duroc (11,255). One of the four Landrace haplotypes (LA1) is the subject of this entry.

Molecular basis: Derks et al. (2019): "splice mutation affects a conserved adenine in the GTRAG splice site motif (positive strand: 3:g.43952776T>G. . . . the splice region mutation causes exon skipping of exon 14 . . . Skipping of exon 14 introduces a glutamic acid and a premature stop codon in the second codon of the terminal exon, lacking the final 370 amino acids located in the conserved subunit 2, hybrid-binding domain (binding to the DNA strand) . . . Hence, this splice-region mutation likely causes a complete LoF of the POLR1B protein."

Prevalence: Derks et al. (2019) reported the carrier frequency of haplotype LA1 as 13.4%, with zero observed homozygotes. The reduction in litter size (total number born) in carrier x carrier matings, compared with carrier x non-carrier matings, was 18.8%.

Breed: Landrace.

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
POLR1B polymerase (RNA) I polypeptide B, 128kDa Sus scrofa 3 NC_010445.4 (43974283..43949032) POLR1B 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.

Breed(s) Variant Phenotype Gene Allele Type of Variant Reference Sequence Chr. g. or m. c. or n. p. Verbal Description EVA ID Year Published PubMed ID(s) Acknowledgements
Landrace Embryonic lethality POLR1B splicing Sscrofa11.1 3 g.43952776T>G Derks et al. (2019): "Skipping of exon 14 introduces a glutamic acid and a premature stop codon in the second codon of the terminal exon, lacking the final 370 amino acids located in the conserved subunit 2, hybrid-binding domain (binding to the DNA strand)" 2019 30875370

Reference


2019 Derks, M.F.L., Gjuvsland, A.B., Bosse, M., Lopes, M.S., van Son, M., Harlizius, B., Tan, B.F., Hamland, H., Grindflek, E., Groenen, M.A.M., Megens, H.J. :
Loss of function mutations in essential genes cause embryonic lethality in pigs. PLoS Genet 15:e1008055, 2019. Pubmed reference: 30875370. DOI: 10.1371/journal.pgen.1008055.

Edit History


  • Created by Frank Nicholas on 25 Mar 2019
  • Changed by Frank Nicholas on 25 Mar 2019
  • Changed by Frank Nicholas on 26 Mar 2019