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NM_006005.3(WFS1):c.1672C>T (p.Arg558Cys) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 5, 2017
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:
RCV000599628.8

Allele description [Variation Report for NM_006005.3(WFS1):c.1672C>T (p.Arg558Cys)]

NM_006005.3(WFS1):c.1672C>T (p.Arg558Cys)

Gene:
WFS1:wolframin ER transmembrane glycoprotein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
4p16.1
Genomic location:
Preferred name:
NM_006005.3(WFS1):c.1672C>T (p.Arg558Cys)
HGVS:
  • NC_000004.12:g.6301467C>T
  • NG_011700.1:g.36618C>T
  • NM_001145853.1:c.1672C>T
  • NM_006005.3:c.1672C>TMANE SELECT
  • NP_001139325.1:p.Arg558Cys
  • NP_005996.2:p.Arg558Cys
  • LRG_1417t1:c.1672C>T
  • LRG_1417:g.36618C>T
  • LRG_1417p1:p.Arg558Cys
  • NC_000004.11:g.6303194C>T
  • O76024:p.Arg558Cys
Protein change:
R558C
Links:
UniProtKB: O76024#VAR_068343; dbSNP: rs199946797
NCBI 1000 Genomes Browser:
rs199946797
Molecular consequence:
  • NM_001145853.1:c.1672C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006005.3:c.1672C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
3

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000271294Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Uncertain significance
(Sep 5, 2017)
germlineclinical testing

PubMed (10)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided53not providednot providednot providedclinical testing

Citations

PubMed

Identification of novel mutations in WFS1 and genotype-phenotype correlation in Wolfram syndrome.

Cano A, Rouzier C, Monnot S, Chabrol B, Conrath J, Lecomte P, Delobel B, Boileau P, Valero R, Procaccio V, Paquis-Flucklinger V; French Group of Wolfram Syndrome., Vialettes B.

Am J Med Genet A. 2007 Jul 15;143A(14):1605-12.

PubMed [citation]
PMID:
17568405

Atypical case of Wolfram syndrome revealed through targeted exome sequencing in a patient with suspected mitochondrial disease.

Lieber DS, Vafai SB, Horton LC, Slate NG, Liu S, Borowsky ML, Calvo SE, Schmahmann JD, Mootha VK.

BMC Med Genet. 2012 Jan 6;13:3. doi: 10.1186/1471-2350-13-3.

PubMed [citation]
PMID:
22226368
PMCID:
PMC3281774
See all PubMed Citations (10)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000271294.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedclinical testing PubMed (10)

Description

Variant classified as Uncertain Significance - Favor Pathogenic. The p.Arg558Cys variant in WFS1 has been previously reported in the homozygous or compound hete rozygous state in 5 individuals with Wolfram syndrome, at least 3 of whom were r eported to have late onset disease (Cano 2007, Chaussenot 2011, Lieber 2012, Cha ussenot 2015, Astuti 2017, Oakley 2017). It has also been identified in at least 2 individuals with nonsyndromic optic atrophy and 1 individual with progressive cerebellar ataxia (Fogel 2014, Grenier 2016, Sharma 2017). Additionally, our la boratory has identified the p.Arg558Cys variant in the heterozygous state in 2 i ndividuals with apparently nonsyndromic hearing loss, 1 of whom had an alternate explanation for their hearing loss. In vitro functional studies and in silico p rediction tools provide some evidence that the variant may impact protein functi on (Qian 2015, Sharma 2017); however, these types of assays may not accurately r epresent biological function. This variant has been identified in 1.4% (140/1015 0) of Ashkenazi Jewish chromosomes by the Genome Aggregation Database, including 1 homozygous individual (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs1999 46797). It should be noted that the gnomAD database may include individuals with late onset or adult disease such as diabetes mellitus and psychiatric disorders (http://gnomad.broadinstitute.org/about). In summary, while there is some suspi cion for a pathogenic role, because of its high frequency in the Ashkenazi Jewis h population and limited functional data, the clinical significance of this vari ant is uncertain.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided5not provided3not provided

Last Updated: Oct 26, 2024