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OMIA 002289-9615 : Progressive retinal atrophy, IMPG2-related in Canis lupus familiaris

Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 613581 (trait) , 616152 (trait) , 607056 (gene)

Mendelian trait/disorder: yes

Considered a defect: yes

Key variant known: yes

Year key variant first reported: 2020

Species-specific name: Progressive retinal atrophy 4

Species-specific symbol: PRA4

Mapping: Hitti-Malin et al. (2020) "undertook a genome-wide association study (GWAS), which identified a 1.3 Mb disease-associated region on canine chromosome 33".

Molecular basis: Hitti-Malin et al. (2020): "whole-genome sequencing analysis that revealed a long interspersed element-1 (LINE-1) insertion upstream of the IMPG2 gene."

Prevalence: Hitti-Malin et al. (2020): "validation of this variant [the LINE-1 variant] in 447 dogs of 123 breeds determined it was private to LA dogs. . . . The recently estimated mutant allele frequency of 0.1, generated from the 911 DNA tested LA during 2 years of use of a DNA test based on this work, indicates that 1 in 100 dogs are likely to be affected with this form of PRA, and an 18% carrier frequency within the LA population."

Breed: Lhasa Apso.

Associated gene:

Symbol Description Species Chr Location OMIA gene details page Other Links
IMPG2 interphotoreceptor matrix proteoglycan 2 Canis lupus familiaris 33 NC_051837.1 (7924899..7842019) IMPG2 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.

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 Inferred EVA rsID Year Published PubMed ID(s) Acknowledgements
1253 Lhasa Apso Progressive retinal atrophy 4 (PRA4) IMPG2 insertion, gross (>20) Naturally occurring variant CanFam3.1 33 " LINE-1 insertion was identified within the critical region in this PRA-affected LA, situated within 200 bp upstream of the interphotoreceptor matrix proteoglycan 2 (IMPG2) gene within the following coordinates: CANFA33: 7,785,475-7,785,491" (Hitti-Malin et al., 2020) 2020 32894063
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References


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.
2020 Hitti-Malin, R.J., Burmeister, L.M., Ricketts, S.L., Lewis, T.W., Pettitt, L., Boursnell, M., Schofield, E.C., Sargan, D., Mellersh, C.S. :
A LINE-1 insertion situated in the promoter of IMPG2 is associated with autosomal recessive progressive retinal atrophy in Lhasa Apso dogs. BMC Genet 21:100, 2020. Pubmed reference: 32894063. DOI: 10.1186/s12863-020-00911-w.
2012 Miyadera, K., Acland, G.M., Aguirre, G.D. :
Genetic and phenotypic variations of inherited retinal diseases in dogs: the power of within- and across-breed studies. Mamm Genome 23:40-61, 2012. Pubmed reference: 22065099. DOI: 10.1007/s00335-011-9361-3.

Edit History


  • Created by Frank Nicholas on 26 Oct 2020
  • Changed by Frank Nicholas on 26 Oct 2020