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NM_006005.3(WFS1):c.1769C>T (p.Thr590Met) AND not specified

Germline classification:
Likely benign (1 submission)
Last evaluated:
Nov 13, 2016
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:
RCV000608372.4

Allele description [Variation Report for NM_006005.3(WFS1):c.1769C>T (p.Thr590Met)]

NM_006005.3(WFS1):c.1769C>T (p.Thr590Met)

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.1769C>T (p.Thr590Met)
HGVS:
  • NC_000004.12:g.6301564C>T
  • NG_011700.1:g.36715C>T
  • NM_001145853.1:c.1769C>T
  • NM_006005.3:c.1769C>TMANE SELECT
  • NP_001139325.1:p.Thr590Met
  • NP_005996.2:p.Thr590Met
  • LRG_1417t1:c.1769C>T
  • LRG_1417:g.36715C>T
  • LRG_1417p1:p.Thr590Met
  • NC_000004.11:g.6303291C>T
Protein change:
T590M
Links:
dbSNP: rs760280308
NCBI 1000 Genomes Browser:
rs760280308
Molecular consequence:
  • NM_001145853.1:c.1769C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_006005.3:c.1769C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000712589Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Likely benign
(Nov 13, 2016) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000712589.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

p.Thr590Met in exon 8 of WFS1: This variant is not expected to have clinical sig nificance due to a lack of conservation across species, including mammals. Of no te, 6 mammals have a methionine (Met) at this position despite high nearby amino acid conservation. In addition, computational prediction tools do not suggest a high likelihood of impact to the protein. It has been identified in 1/16512 Sou th Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broa dinstitute.org; dbSNP rs760280308).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

Last Updated: Mar 5, 2024