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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002237788	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 6, 2021)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25359768, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002237788

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 6, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Differential light-induced responses in sectorial inherited retinal degeneration.

Ramon E, Cordomí A, Aguilà 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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