NM_006005.3(WFS1):c.2322G>A (p.Lys774=) AND not specified

Clinical significance:Benign (Last evaluated: Nov 20, 2013)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
5 submissions [Details]
Record status:
current
Accession:
RCV000038656.14

Allele description [Variation Report for NM_006005.3(WFS1):c.2322G>A (p.Lys774=)]

NM_006005.3(WFS1):c.2322G>A (p.Lys774=)

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.2322G>A (p.Lys774=)
Other names:
p.K774K:AAG>AAA
HGVS:
  • NC_000004.12:g.6302117G>A
  • NG_011700.1:g.37268G>A
  • NM_001145853.1:c.2322G>A
  • NM_006005.3:c.2322G>AMANE SELECT
  • NP_001139325.1:p.Lys774=
  • NP_005996.2:p.Lys774=
  • LRG_1417t1:c.2322G>A
  • LRG_1417:g.37268G>A
  • LRG_1417p1:p.Lys774=
  • NC_000004.11:g.6303844G>A
  • NP_005996.2:p.(=)
  • c.2322G>A
  • p.K774K
  • p.Lys774Lys
Links:
dbSNP: rs2230721
NCBI 1000 Genomes Browser:
rs2230721
Molecular consequence:
  • NM_001145853.1:c.2322G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_006005.3:c.2322G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
179

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
SCV000062334Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Benign
(May 7, 2012)
germlineclinical testing

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

SCV000113267EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Benign
(Nov 20, 2013)
germlineclinical testing

Citation Link,

SCV000153531Genetic Services Laboratory, University of Chicagono assertion criteria providedLikely benigngermlineclinical testing

SCV000169834GeneDxcriteria provided, single submitter
Benign
(May 22, 2012)
germlineclinical testing

Citation Link,

SCV000311324PreventionGenetics,PreventionGeneticscriteria provided, single submitter
Benigngermlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided181179not providednot providednot providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown7not providednot 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

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000062334.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided181not providednot providedclinical testing PubMed (1)

Description

"Lys774Lys in Exon 08 of WFS1: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 7.3% (273/3734) of Af rican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs2230721)."

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided181not provided179not provided

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000113267.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided7not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided7not providednot providednot provided

From Genetic Services Laboratory, University of Chicago, SCV000153531.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

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

From GeneDx, SCV000169834.12

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From PreventionGenetics,PreventionGenetics, SCV000311324.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 7, 2021

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