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NM_201253.3(CRB1):c.1172-1G>T AND multiple conditions

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 18, 2020
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:
RCV001379001.5

Allele description [Variation Report for NM_201253.3(CRB1):c.1172-1G>T]

NM_201253.3(CRB1):c.1172-1G>T

Gene:
CRB1:crumbs cell polarity complex component 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1q31.3
Genomic location:
Preferred name:
NM_201253.3(CRB1):c.1172-1G>T
HGVS:
  • NC_000001.11:g.197420999G>T
  • NG_008483.2:g.224538G>T
  • NG_008483.3:g.224497G>T
  • NM_001193640.2:c.836-1G>T
  • NM_001257965.2:c.965-1G>T
  • NM_001257966.2:c.1172-1G>T
  • NM_201253.3:c.1172-1G>TMANE SELECT
  • NC_000001.10:g.197390129G>T
Links:
dbSNP: rs2125468776
NCBI 1000 Genomes Browser:
rs2125468776
Molecular consequence:
  • NM_001193640.2:c.836-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001257965.2:c.965-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001257966.2:c.1172-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_201253.3:c.1172-1G>T - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:
Retinitis pigmentosa 12 (RP12)
Synonyms:
RP 12; RP WITH OR WITHOUT PPRPE; RP WITH OR WITHOUT PRESERVED PARAARTERIOLE RETINAL PIGMENT EPITHELIUM; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010818; MedGen: C1838647; Orphanet: 791; OMIM: 600105
Name:
Leber congenital amaurosis 8 (LCA8)
Identifiers:
MONDO: MONDO:0013453; MedGen: C3151202; Orphanet: 65; OMIM: 613835

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001576715Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Aug 18, 2020) 		germlineclinical testing

PubMed (9)
[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

Mutations in a human homologue of Drosophila crumbs cause retinitis pigmentosa (RP12).

den Hollander AI, ten Brink JB, de Kok YJ, van Soest S, van den Born LI, van Driel MA, van de Pol DJ, Payne AM, Bhattacharya SS, Kellner U, Hoyng CB, Westerveld A, Brunner HG, Bleeker-Wagemakers EM, Deutman AF, Heckenlively JR, Cremers FP, Bergen AA.

Nat Genet. 1999 Oct;23(2):217-21.

PubMed [citation]
PMID:
10508521
See all PubMed Citations (9)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001576715.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (9)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CRB1 are known to be pathogenic (PMID: 10508521, 22065545, 23379534, 25412400, 26957898, 28041643, 29391521). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with CRB1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change affects an acceptor splice site in intron 5 of the CRB1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product.

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

Last Updated: Sep 29, 2024