OMIA:001455-9615 : Retinal atrophy - Cone-rod dystrophy, NPHP4-related in Canis lupus familiaris (dog) |
Categories: Vision / eye phene
Links to possible relevant human trait(s) and/or gene(s) in OMIM: 606996 (trait) , 607215 (gene)
Links to relevant human diseases in MONDO:
Mendelian trait/disorder: yes
Mode of inheritance: Autosomal recessive
Disease-related: yes
Key variant known: yes
Year key variant first reported: 2008
Cross-species summary: In 2012, this disorder had been renamed in OMIA as 'Cone-rod dystrophy, Standard Wire-haired Dachshund' on the basis of the review by Miyadera et al. (2012). While this name is used in dogs a cross-species phene name 'Cone-rod dystrophy, NPHP4-related' was introduced in 2023 [08/06/2023].
Species-specific name: Cone-rod dystrophy, standard Wire-haired dachshund; progressive retinal atrophy crd SWD
Species-specific symbol: CRD^SWHD
Mapping: Wiik et al. (2008) conducted a GWAS on 13 affected and 13 control Standard Wire-Haired Dachshunds, each genotyped with the Affymetrix version 2 Dog SNP (yielding 49,663 informative SNPs for analysis). They reporte that "For the first time, we use genome-wide association-based Sibling Transmission Disequilibrium Test (sibTDT) analysis of only 13 discordant sib-pairs to identify a single significantly associated 6.5-Mb region (PrawTDT = 4.8 × 10−5, PgenomeTDT = 6 × 10−4) on canine chromosome 5, containing more than 70 genes".
Molecular basis: Sequencing of positional candidate genes in the CFA5 region (see Mapping section) by Wiik et al. (2008) "identified a 180-bp deletion in exon/intron 5 of NPHP4 (nephronophthisis 4, also known as nephroretinin)". Palánová et al. (2014) "analyzed all varieties of Dachshunds from the Czech Republic and five other dog breeds and found that the deletion in the NPHP4 (in heterozygous state) is present not only in standard-, but also in miniature wire-haired Dachshunds, but not in other varieties of Dachshunds or in other breeds."
Breeds:
Dachshund, Miniature Wire-Haired (Dog) (VBO_0200411),
Dachshund, Standard Wire-Haired (Dog) (VBO_0200421).
Breeds in which the phene has been documented. (If a likely causal variant has been documented for the phene, see the variant table breeds in which the variant has been reported).
Associated gene:
| Symbol | Description | Species | Chr | Location | OMIA gene details page | Other Links |
|---|---|---|---|---|---|---|
| NPHP4 | nephronophthisis 4 | Canis lupus familiaris | 5 | NC_051809.1 (60152631..60022493) | NPHP4 | 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 | Year Published | PubMed ID(s) | Acknowledgements |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 634 | Dachshund, Miniature Wire-Haired (Dog) Dachshund, Standard Wire-Haired (Dog) | Cone-rod dystrophy, Standard Wire-haired Dachshund | NPHP4 | deletion, gross (>20) | Naturally occurring variant | CanFam3.1 | 5 | g.59912991_59913168del | c.479_526+130del | NM_001135788.1; 178-bp deletion in exon/intron 5 of NPHP4 (nephronophthisis 4, also known as nephroretinin) | 2008 | 18687878 |
Cite this entry
Nicholas, F. W., Tammen, I., & Sydney Informatics Hub. (2023). OMIA:001455-9615: Online Mendelian Inheritance in Animals (OMIA) [dataset]. https://omia.org/. https://doi.org/10.25910/2AMR-PV70
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.
| 2023 | Ghilardi, S., Bagardi, M., Frattini, S., Barbariga, G.E., Brambilla, P.G., Minozzi, G., Polli, M. : |
| Genotypic and allelic frequencies of progressive rod-cone degeneration and other main variants associated with progressive retinal atrophy in Italian dogs. Vet Rec Open 10:e77, 2023. Pubmed reference: 38028226. DOI: 10.1002/vro2.77. | |
| 2021 | Genetics Committee of the American College of Veterinary Opthalmologists : |
| The Blue Book: Ocular disorders presumed to be inherited in purebred dogs. 13th Edition https://ofa.org/wp-content/uploads/2022/10/ACVO-Blue-Book-2021.pdf , 2021. | |
| 2014 | Palánová, A., Schröffelová, D., Přibáňová, M., Dvořáková, V., Stratil, A. : |
| Analysis of a deletion in the nephronophthisis 4 gene in different dog breeds. Vet Ophthalmol 17:76-8, 2014. Pubmed reference: 23998563. DOI: 10.1111/vop.12092. | |
| 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. | |
| 2009 | Wiik, AC., Thoresen, SI., Wade, C., Lindblad-Toh, K., Lingaas, F. : |
| A population study of a mutation allele associated with cone-rod dystrophy in the standard wire-haired dachshund. Anim Genet 40:572-4, 2009. Pubmed reference: 19392817. DOI: 10.1111/j.1365-2052.2009.01877.x. | |
| 2008 | Ropstad, E.O., Narfström, K., Lingaas, F., Wiik, C., Bruun, A., Bjerkås, E. : |
| Functional and structural changes in the retina of wire-haired dachshunds with early-onset cone-rod dystrophy. Invest Ophthalmol Vis Sci 49:1106-15, 2008. Pubmed reference: 18326738. DOI: 10.1167/iovs.07-0848. | |
| Wiik, A.C., Wade, C., Biagi, T., Ropstad, E.O., Bjerkås, E., Lindblad-Toh, K., Lingaas, F. : | |
| A deletion in nephronophthisis 4 (NPHP4) is associated with recessive cone-rod dystrophy in standard wire-haired dachshund. Genome Res 18:1415-21, 2008. Pubmed reference: 18687878. DOI: 10.1101/gr.074302.107. | |
| 2007 | Ropstad, E.O., Bjerkås, E., Narfström, K. : |
| Clinical findings in early onset cone-rod dystrophy in the Standard Wire-haired Dachshund. Vet Ophthalmol 10:69-75, 2007. Pubmed reference: 17324160. DOI: 10.1111/j.1463-5224.2007.00503.x. |
Edit History
- Created by Frank Nicholas on 28 Aug 2008
- Changed by Frank Nicholas on 26 Sep 2011
- Changed by Frank Nicholas on 07 Dec 2011
- Changed by Frank Nicholas on 12 Dec 2011
- Changed by Frank Nicholas on 05 Dec 2012
- Changed by Frank Nicholas on 21 May 2013
- Changed by Frank Nicholas on 10 Sep 2014
- Changed by Imke Tammen2 on 08 Jun 2023