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NM_000539.3(RHO):c.165C>A (p.Asn55Lys) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 6, 2021
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001880087.6

Allele description [Variation Report for NM_000539.3(RHO):c.165C>A (p.Asn55Lys)]

NM_000539.3(RHO):c.165C>A (p.Asn55Lys)

Gene:
RHO:rhodopsin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q22.1
Genomic location:
Preferred name:
NM_000539.3(RHO):c.165C>A (p.Asn55Lys)
HGVS:
  • NC_000003.12:g.129528898C>A
  • NG_009115.1:g.5260C>A
  • NM_000539.3:c.165C>AMANE SELECT
  • NP_000530.1:p.Asn55Lys
  • NC_000003.11:g.129247741C>A
Protein change:
N55K
Links:
dbSNP: rs1312862210
NCBI 1000 Genomes Browser:
rs1312862210
Molecular consequence:
  • NM_000539.3:c.165C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV002237788Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jun 6, 2021)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Differential light-induced responses in sectorial inherited retinal degeneration.

Ramon E, CordomĂ­ A, AguilĂ  M, Srinivasan S, Dong X, Moore AT, Webster AR, Cheetham ME, Garriga P.

J Biol Chem. 2014 Dec 26;289(52):35918-28. doi: 10.1074/jbc.M114.609958. Epub 2014 Oct 30.

PubMed [citation]
PMID:
25359768
PMCID:
PMC4276860

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002237788.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Experimental studies have shown that this variant affects RHO protein function (PMID: 25359768). For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt RHO protein function. This variant has been observed in individual(s) with autosomal dominant retinitis pigmentosa (PMID: 25359768). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 984775). This variant is not present in population databases (ExAC no frequency). This sequence change replaces asparagine with lysine at codon 55 of the RHO protein (p.Asn55Lys). The asparagine residue is highly conserved and there is a moderate physicochemical difference between asparagine and lysine.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024