OMIA:001876-9615 : Progressive retinal atrophy, Basenji in Canis lupus familiaris
Categories: Vision / eye phene
Possibly relevant human trait(s) and/or gene(s)s (MIM numbers): 258100 (trait) , 613758 (trait) , 181031 (gene)
Links to MONDO diseases: No links.
Mendelian trait/disorder: yes
Mode of inheritance: Autosomal recessive
Considered a defect: yes
Key variant known: yes
Year key variant first reported: 2013
History: This particular form of PRA was first mentioned by Goldstein et al. (2006), who, by judicious matings, showed that even though its clinical sings are very similar to Progressive rod-cone degeneration (prcd) (OMIA 001298-9615) in a wide range of breeds, the Basenji disorder is not allelic to prcd.
Inheritance: The mating results of Goldstein et al. (2006) suggested autosomal recessive inheritance.
Mapping: A GWAS conducted by Goldstein et al. (2013) on 6 affected and 3 control Basenjis, each genotyped with the Illumina HD Canine SNP Chip comprising 173,662 SNPs, implicated regions on chromosomes CFA4, CFA13 and CFA25. Haplotype analysis suggested the CFA25 region as the most likely candidate region. Homozygosity mapping analysis confirmed the CFA25 region as most likely.
Molecular basis: Sequencing of the two candidate genes in this region led Goldstein et al. (2013) to the discovery of the causal mutation as a stop-loss or extensionl base substitution in the SAG gene (encoding S-antigen): a "tyrosine to cysteine transition mutation at position CFA25:47,845,680 (c.1216T>C . . .) that changed the normal stop codon to code for the amino acid arginine, which would result in a deduced addition of 25 amino acids (p.*405Rext*25) to the normal 405 amino acid protein".
|Symbol||Description||Species||Chr||Location||OMIA gene details page||Other Links|
|SAG||S-antigen; retina and pineal gland (arrestin)||Canis lupus familiaris||25||NC_051829.1 (45060350..45103430)||SAG||Homologene, Ensembl , NCBI gene|
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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|
|359||Basenji||Progressive retinal atrophy, Basenji||SAG||extension (stop-lost)||Naturally occurring variant||CanFam3.1||25||g.44843440T>C||c.1216T>C||p.(*405Rext*25)||2013||24019744||Variant coordinates obtained from or confirmed by EBI's Some Effect Predictor (VEP) tool|
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.
|2013||Goldstein, O., Jordan, J.A., Aguirre, G.D., Acland, G.M. :|
|A non-stop S-antigen gene mutation is associated with late onset hereditary retinal degeneration in dogs. Mol Vis 19:1871-84, 2013. Pubmed reference: 24019744 .|
|2006||Goldstein, O., Zangerl, B., Pearce-Kelling, S., Sidjanin, D.J., Kijas, J.W., Felix, J., Acland, G.M., Aguirre, G.D. :|
|Linkage disequilibrium mapping in domestic dog breeds narrows the progressive rod-cone degeneration interval and identifies ancestral disease-transmitting chromosome. Genomics 88:541-50, 2006. Pubmed reference: 16859891 . DOI: 10.1016/j.ygeno.2006.05.013.|
- Changed by Frank Nicholas on 03 Sep 2013
- Created by Frank Nicholas on 03 Sep 2013
- Changed by Frank Nicholas on 28 Aug 2016