NM_174878.3(CLRN1):c.190G>A (p.Gly64Arg) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 2, 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:: RCV002541387.3

Allele description [Variation Report for NM_174878.3(CLRN1):c.190G>A (p.Gly64Arg)]

NM_174878.3(CLRN1):c.190G>A (p.Gly64Arg)

Gene:

CLRN1:clarin 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q25.1

Genomic location:

Preferred name:

NM_174878.3(CLRN1):c.190G>A (p.Gly64Arg)

HGVS:

NC_000003.12:g.150972519C>T
NG_009168.1:g.5481G>A
NM_001195794.1:c.190G>A
NM_001256819.2:c.190G>A
NM_174878.3:c.190G>AMANE SELECT
NP_001182723.1:p.Gly64Arg
NP_001243748.1:p.Gly64Arg
NP_777367.1:p.Gly64Arg
LRG_700t1:c.190G>A
LRG_700:g.5481G>A
LRG_700p1:p.Gly64Arg
NC_000003.11:g.150690306C>T
NM_174878.2:c.190G>A
NR_046380.3:n.209G>A

Protein change:

G64R

Links:

dbSNP: rs1380661508

NCBI 1000 Genomes Browser:

rs1380661508

Molecular consequence:

NM_001195794.1:c.190G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001256819.2:c.190G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_174878.3:c.190G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_046380.3:n.209G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003525465	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 2, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 25472526, 26338283, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003525465

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 2, 2023)

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

Next-generation sequencing-based molecular diagnosis of 82 retinitis pigmentosa probands from Northern Ireland.

Zhao L, Wang F, Wang H, Li Y, Alexander S, Wang K, Willoughby CE, Zaneveld JE, Jiang L, Soens ZT, Earle P, Simpson D, Silvestri G, Chen R.

Hum Genet. 2015 Feb;134(2):217-30. doi: 10.1007/s00439-014-1512-7. Epub 2014 Dec 4.

PubMed [citation]

PMID:: 25472526
PMCID:: PMC4347882

Comprehensive molecular diagnosis of 67 Chinese Usher syndrome probands: high rate of ethnicity specific mutations in Chinese USH patients.

Jiang L, Liang X, Li Y, Wang J, Zaneveld JE, Wang H, Xu S, Wang K, Wang B, Chen R, Sui R.

Orphanet J Rare Dis. 2015 Sep 4;10:110. doi: 10.1186/s13023-015-0329-3.

PubMed [citation]

PMID:: 26338283
PMCID:: PMC4559966

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003525465.2

#	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 replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 64 of the CLRN1 protein (p.Gly64Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Usher syndrome (PMID: 25472526, 26338283). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 1331448). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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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