NM_020366.4(RPGRIP1):c.1116del (p.Lys372fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 6, 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:: RCV001238890.8

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.1116del (p.Lys372fs)]

NM_020366.4(RPGRIP1):c.1116del (p.Lys372fs)

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.1116del (p.Lys372fs)

HGVS:

NC_000014.9:g.21312471del
NG_008933.1:g.29495del
NM_020366.4:c.1116delMANE SELECT
NP_065099.3:p.Lys372fs
NP_065099.3:p.Lys372fs
NC_000014.8:g.21780627del
NC_000014.8:g.21780630del
NM_020366.3:c.1116del
NM_020366.3:c.1116delA

Protein change:

K372fs

Links:

dbSNP: rs776880045

NCBI 1000 Genomes Browser:

rs776880045

Molecular consequence:

NM_020366.4:c.1116del - 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
SCV001411723	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 6, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 11528500, 23105016, 28041643, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001411723

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 6, 2023)

germline

clinical testing

PubMed (4)
[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 (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001411723.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Lys372Asnfs*3) 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 present in population databases (rs776880045, gnomAD 0.003%). This premature translational stop signal has been observed in individual(s) with Leber congenital amaurosis (PMID: 28041643). ClinVar contains an entry for this variant (Variation ID: 438160). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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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