NM_201253.3(CRB1):c.3320T>C (p.Leu1107Pro) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 29, 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:: RCV001378740.6

Allele description [Variation Report for NM_201253.3(CRB1):c.3320T>C (p.Leu1107Pro)]

NM_201253.3(CRB1):c.3320T>C (p.Leu1107Pro)

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.3320T>C (p.Leu1107Pro)

HGVS:

NC_000001.11:g.197435183T>C
NG_008483.2:g.238722T>C
NM_001193640.2:c.2984T>C
NM_001257965.2:c.3248T>C
NM_001257966.2:c.2129-417T>C
NM_201253.3:c.3320T>CMANE SELECT
NP_001180569.1:p.Leu995Pro
NP_001244894.1:p.Leu1083Pro
NP_957705.1:p.Leu1107Pro
NC_000001.10:g.197404313T>C
NM_201253.2:c.3320T>C
NR_047563.2:n.3273T>C
NR_047564.2:n.3481T>C
P82279:p.Leu1107Pro

Protein change:

L1083P

Links:

UniProtKB: P82279#VAR_022975; dbSNP: rs62636276

NCBI 1000 Genomes Browser:

rs62636276

Molecular consequence:

NM_001257966.2:c.2129-417T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001193640.2:c.2984T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001257965.2:c.3248T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_201253.3:c.3320T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_047563.2:n.3273T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_047564.2:n.3481T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001576379	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 29, 2023)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 28819299, 15024725, 20956273, 34884448, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001576379

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 29, 2023)

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

The correlation between CRB1 variants and the clinical severity of Brazilian patients with different inherited retinal dystrophy phenotypes.

Motta FL, Salles MV, Costa KA, Filippelli-Silva R, Martin RP, Sallum JMF.

Sci Rep. 2017 Aug 17;7(1):8654. doi: 10.1038/s41598-017-09035-1.

PubMed [citation]

PMID:: 28819299
PMCID:: PMC5561187

Leber congenital amaurosis: comprehensive survey of the genetic heterogeneity, refinement of the clinical definition, and genotype-phenotype correlations as a strategy for molecular diagnosis.

Hanein S, Perrault I, Gerber S, Tanguy G, Barbet F, Ducroq D, Calvas P, Dollfus H, Hamel C, Lopponen T, Munier F, Santos L, Shalev S, Zafeiriou D, Dufier JL, Munnich A, Rozet JM, Kaplan J.

Hum Mutat. 2004 Apr;23(4):306-17.

PubMed [citation]

PMID:: 15024725

See all PubMed Citations (5)

Details of each submission

From Invitae, SCV001576379.4

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Leu1107 amino acid residue in CRB1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15024725, 28819299). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CRB1 protein function. ClinVar contains an entry for this variant (Variation ID: 99897). This missense change has been observed in individual(s) with CRB1-related conditions (PMID: 15024725, 20956273, 34884448). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs62636276, gnomAD 0.0009%). This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 1107 of the CRB1 protein (p.Leu1107Pro).

#	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: Jun 23, 2024

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