OMIA 002183-9823 : Abortion due to haplotype LA3 in Sus scrofa

Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 616267 , 613402

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 (LA3) is the subject of this entry.

Molecular basis: Derks et al. (2019) reported the following variant as being likely causal of the embryonic lethality due to homozygosity of haplotype LA3: "deleterious missense mutation in the PNKP gene (6:g.54880241G>T), predicted to be strongly deleterious by SIFT (0.02) and PROVEAN (-2.9). The missense mutation causes a glutamine to arginine amino acid substitution (ENSSSCP00000003467:p.Gln96Arg)"

Prevalence: Derks et al. (2019) reported the carrier frequency of haplotype LA2 as 4.7%, 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 15.1%.

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
PNKP polynucleotide kinase 3'-phosphatase Sus scrofa 6 NC_010448.4 (54880814..54870359) PNKP 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 PNKP missense Sscrofa11.1 6 g.54880241G>T p.Gln96Arg Derks et al. (2019): "deleterious missense mutation in the PNKP gene (6:g.54880241G>T), predicted to be strongly deleterious by SIFT (0.02) and PROVEAN (-2.9). The missense mutation causes a glutamine to arginine amino acid substitution (ENSSSCP00000003467:p.Gln96Arg)" 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., 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 26 Mar 2019
  • Changed by Frank Nicholas on 26 Mar 2019