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NM_020366.4(RPGRIP1):c.800+1G>A AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 17, 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:
RCV001228179.8

Allele description [Variation Report for NM_020366.4(RPGRIP1):c.800+1G>A]

NM_020366.4(RPGRIP1):c.800+1G>A

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.800+1G>A
HGVS:
  • NC_000014.9:g.21303544G>A
  • NG_008933.1:g.20568G>A
  • NG_008933.2:g.28463G>A
  • NM_020366.4:c.800+1G>AMANE SELECT
  • NC_000014.8:g.21771703G>A
  • NM_020366.3:c.800+1G>A
Links:
dbSNP: rs376500610
NCBI 1000 Genomes Browser:
rs376500610
Molecular consequence:
  • NM_020366.4:c.800+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001400565Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 17, 2024) 		germlineclinical testing

PubMed (6)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

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
See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001400565.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change affects a donor splice site in intron 5 of the RPGRIP1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in RPGRIP1 are known to be pathogenic (PMID: 11528500, 23105016). This variant is present in population databases (rs376500610, gnomAD 0.003%). Disruption of this splice site has been observed in individuals with Leber congenital amaurosis (PMID: 30576320, 32865313). This variant is also known as IVS5+1G>A. ClinVar contains an entry for this variant (Variation ID: 803002). 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.

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

Last Updated: Apr 7, 2025