OMIA 002182-9823 : Abortion due to haplotype LA2 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 (LA2) is the subject of this entry.

Molecular basis: Derks et al. (2019) reported the following variant as being likely causal for the embryonic lethality of haplotype LA2: "[a] frameshift mutation in exon 38 of the URB1 gene (13:g.195977038delC) caused by a 1-bp deletion . . . The frameshift (ENSSSCP00000036505:p.Val1961fs) introduces 26 novel amino acids and a premature stop codon, producing a truncated protein of 1,986 amino acids, lacking the final 261 amino acids compared to the wild-type protein (2,247 AA)."

Prevalence: Derks et al. (2019) reported the carrier frequency of haplotype LA2 as 8.4%, with 2 observed homozygotes (compared with 49.5 expected). The reduction in litter size (total number born) in carrier x carrier matings, compared with carrier x non-carrier matings, was 15.9%.

Breed: Landrace.

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
URB1 Sus scrofa - no genomic information (-..-) URB1 Ensembl

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 URB1 deletion, small (<=20) Sscrofa11.1 13 g.195977038delC p.Val1961fs Derks et al. (2019): "[a] frameshift mutation in exon 38 of the URB1 gene (13:g.195977038delC) caused by a 1-bp deletion . . . The frameshift (ENSSSCP00000036505:p.Val1961fs) introduces 26 novel amino acids and a premature stop codon, producing a truncated protein of 1,986 amino acids, lacking the final 261 amino acids compared to the wild-type protein (2,247 AA)." 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 26 Mar 2019