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

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 17, 2021
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:
RCV001806792.1

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)

Name:
Usher syndrome
Synonyms:
Usher Syndromes; Usher's syndrome
Identifiers:
MONDO: MONDO:0019501; MeSH: D052245; MedGen: C0271097; Orphanet: 886; OMIM: PS276900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002051219Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely pathogenic
(Dec 17, 2021) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002051219.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: CLRN1 c.190G>A (p.Gly64Arg) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251472 control chromosomes (gnomAD). c.190G>A has been reported in the literature in a compound heterozygous individual and a homozygous individual affected with Usher Syndrome (Jiang_2015, Zhao_2015). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as likely pathogenic.

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

Last Updated: Sep 29, 2024