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NM_020366.4(RPGRIP1):c.2017C>T (p.Gln673Ter) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 29, 2024
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:
RCV000701424.7

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.2017C>T (p.Gln673Ter)]

NM_020366.4(RPGRIP1):c.2017C>T (p.Gln673Ter)

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.2017C>T (p.Gln673Ter)
HGVS:
  • NC_000014.9:g.21324872C>T
  • NG_008933.1:g.41896C>T
  • NM_001377523.1:c.689-2751C>T
  • NM_001377948.1:c.943C>T
  • NM_001377949.1:c.796+147C>T
  • NM_001377950.1:c.689-2751C>T
  • NM_001377951.1:c.191-2751C>T
  • NM_020366.4:c.2017C>TMANE SELECT
  • NP_001364877.1:p.Gln315Ter
  • NP_065099.3:p.Gln673Ter
  • NP_065099.3:p.Gln673Ter
  • NC_000014.8:g.21793031C>T
  • NM_020366.3:c.2017C>T
Protein change:
Q315*
Links:
dbSNP: rs1566341956
NCBI 1000 Genomes Browser:
rs1566341956
Molecular consequence:
  • NM_001377523.1:c.689-2751C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377949.1:c.796+147C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377950.1:c.689-2751C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377951.1:c.191-2751C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001377948.1:c.943C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_020366.4:c.2017C>T - nonsense - [Sequence Ontology: SO:0001587]

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

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000830225Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 29, 2024) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Complete exon-intron structure of the RPGR-interacting protein (RPGRIP1) gene allows the identification of mutations underlying Leber congenital amaurosis.

Gerber S, Perrault I, Hanein S, Barbet F, Ducroq D, Ghazi I, Martin-Coignard D, Leowski C, Homfray T, Dufier JL, Munnich A, Kaplan J, Rozet JM.

Eur J Hum Genet. 2001 Aug;9(8):561-71.

PubMed [citation]
PMID:
11528500

Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes.

Abu-Safieh L, Alrashed M, Anazi S, Alkuraya H, Khan AO, Al-Owain M, Al-Zahrani J, Al-Abdi L, Hashem M, Al-Tarimi S, Sebai MA, Shamia A, Ray-Zack MD, Nassan M, Al-Hassnan ZN, Rahbeeni Z, Waheeb S, Alkharashi A, Abboud E, Al-Hazzaa SA, Alkuraya FS.

Genome Res. 2013 Feb;23(2):236-47. doi: 10.1101/gr.144105.112. Epub 2012 Oct 26.

PubMed [citation]
PMID:
23105016
PMCID:
PMC3561865
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000830225.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Gln673*) in the RPGRIP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in RPGRIP1 are known to be pathogenic (PMID: 11528500, 23105016). This variant is not present in population databases (gnomAD no frequency). 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: 578421). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024