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NM_020366.4(RPGRIP1):c.128G>A (p.Arg43Gln) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 26, 2023
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:
RCV001058602.5

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.128G>A (p.Arg43Gln)]

NM_020366.4(RPGRIP1):c.128G>A (p.Arg43Gln)

Gene:
RPGRIP1:RPGR interacting protein 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
14q11.2
Genomic location:
Preferred name:
NM_020366.4(RPGRIP1):c.128G>A (p.Arg43Gln)
HGVS:
  • NC_000014.9:g.21294719G>A
  • NG_008933.1:g.11743G>A
  • NM_020366.4:c.128G>AMANE SELECT
  • NP_065099.3:p.Arg43Gln
  • NP_065099.3:p.Arg43Gln
  • NC_000014.8:g.21762878G>A
  • NM_020366.3:c.128G>A
Protein change:
R43Q
Links:
dbSNP: rs762187880
NCBI 1000 Genomes Browser:
rs762187880
Molecular consequence:
  • NM_020366.4:c.128G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Cone-rod dystrophy 13 (CORD13)
Identifiers:
MONDO: MONDO:0011987; MedGen: C2750720; Orphanet: 1872; OMIM: 608194
Name:
Leber congenital amaurosis 6 (LCA6)
Identifiers:
MONDO: MONDO:0013446; MedGen: C1854260; Orphanet: 65; OMIM: 613826

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001223186Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Dec 26, 2023)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

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

Citations

PubMed

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001223186.5

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

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 43 of the RPGRIP1 protein (p.Arg43Gln). This variant is present in population databases (rs762187880, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with RPGRIP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 853730). 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 not expected to disrupt RPGRIP1 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Mar 5, 2024