NM_020366.4(RPGRIP1):c.1363del (p.Glu455fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 26, 2022
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:: RCV001387658.7

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.1363del (p.Glu455fs)]

NM_020366.4(RPGRIP1):c.1363del (p.Glu455fs)

Gene:

RPGRIP1:RPGR interacting protein 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

14q11.2

Genomic location:

Preferred name:

NM_020366.4(RPGRIP1):c.1363del (p.Glu455fs)

HGVS:

NC_000014.9:g.21320073del
NG_008933.1:g.37097del
NM_001377523.1:c.289del
NM_001377948.1:c.289del
NM_001377949.1:c.289del
NM_001377950.1:c.289del
NM_020366.4:c.1363delMANE SELECT
NP_001364452.1:p.Glu97fs
NP_001364877.1:p.Glu97fs
NP_001364878.1:p.Glu97fs
NP_001364879.1:p.Glu97fs
NP_065099.3:p.Glu455fs
NC_000014.8:g.21788231del
NC_000014.8:g.21788232del

Protein change:

E455fs

Links:

dbSNP: rs763671264

NCBI 1000 Genomes Browser:

rs763671264

Molecular consequence:

NM_001377523.1:c.289del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001377948.1:c.289del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001377949.1:c.289del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001377950.1:c.289del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_020366.4:c.1363del - frameshift variant - [Sequence Ontology: SO:0001589]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001588330	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 26, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 11528500, 23105016, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001588330

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 26, 2022)

germline

clinical testing

PubMed (3)
[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 (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001588330.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Glu455Lysfs*2) 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). For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1074385). This premature translational stop signal has been observed in individual(s) with bone spicules, nyctalopia, and vision loss (Invitae). This variant is present in population databases (rs763671264, gnomAD 0.01%).

#	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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