NM_020366.4(RPGRIP1):c.2935C>T (p.Gln979Ter) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 17, 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:: RCV001862727.4

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.2935C>T (p.Gln979Ter)]

NM_020366.4(RPGRIP1):c.2935C>T (p.Gln979Ter)

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.2935C>T (p.Gln979Ter)

HGVS:

NC_000014.9:g.21328463C>T
NG_008933.1:g.45487C>T
NM_001377523.1:c.913C>T
NM_001377948.1:c.1861C>T
NM_001377949.1:c.1021C>T
NM_001377950.1:c.913C>T
NM_001377951.1:c.415C>T
NM_020366.4:c.2935C>TMANE SELECT
NP_001364452.1:p.Gln305Ter
NP_001364877.1:p.Gln621Ter
NP_001364878.1:p.Gln341Ter
NP_001364879.1:p.Gln305Ter
NP_001364880.1:p.Gln139Ter
NP_065099.3:p.Gln979Ter
NP_065099.3:p.Gln979Ter
NC_000014.8:g.21796622C>T
NC_000014.8:g.21796622C>T
NM_020366.3:c.2935C>T

Protein change:

Q139*

Links:

dbSNP: rs1371805993

NCBI 1000 Genomes Browser:

rs1371805993

Molecular consequence:

NM_001377523.1:c.913C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001377948.1:c.1861C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001377949.1:c.1021C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001377950.1:c.913C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001377951.1:c.415C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_020366.4:c.2935C>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

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Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002236128	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 17, 2021)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 11528500, 23105016, 29178642, 31456290, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002236128

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 17, 2021)

germline

clinical testing

PubMed (5)
[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

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 (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002236128.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change creates a premature translational stop signal (p.Gln979*) 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 (ExAC no frequency). This premature translational stop signal has been observed in individual(s) with Leber congenital amaurosis and retinitis pigmentosa (PMID: 29178642, 31456290). ClinVar contains an entry for this variant (Variation ID: 812426). For these reasons, this variant has been classified as Pathogenic.

#	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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