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NM_006005.3(WFS1):c.1243_1245del (p.Val415del) AND Rare genetic deafness

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Apr 14, 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:
RCV000611263.6

Allele description [Variation Report for NM_006005.3(WFS1):c.1243_1245del (p.Val415del)]

NM_006005.3(WFS1):c.1243_1245del (p.Val415del)

Gene:
WFS1:wolframin ER transmembrane glycoprotein [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
4p16.1
Genomic location:
Preferred name:
NM_006005.3(WFS1):c.1243_1245del (p.Val415del)
Other names:
WFS1, 3-BP DEL, VAL415DEL
HGVS:
  • NC_000004.11:g.6302763_6302765del
  • NC_000004.12:g.6301038_6301040del
  • NG_011700.1:g.36189_36191del
  • NM_001145853.1:c.1243_1245del
  • NM_006005.3:c.1243_1245delMANE SELECT
  • NP_001139325.1:p.Val415del
  • NP_005996.2:p.Val415del
  • LRG_1417t1:c.1243_1245del
  • LRG_1417:g.36189_36191del
  • LRG_1417p1:p.Val415del
  • NC_000004.11:g.6302763_6302765del
  • NC_000004.11:g.6302765_6302767del
  • NC_000004.11:g.6302765_6302767delGTC
  • NM_006005.3:c.1243_1245del
  • NM_006005.3:c.1243_1245delGTCMANE SELECT
  • p.V415del
Protein change:
V415del; VAL415DEL
Links:
OMIM: 606201.0029; dbSNP: rs863224265
NCBI 1000 Genomes Browser:
rs863224265
Molecular consequence:
  • NM_001145853.1:c.1243_1245del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_006005.3:c.1243_1245del - inframe_deletion - [Sequence Ontology: SO:0001822]
Observations:
1

Condition(s)

Name:
Rare genetic deafness
Identifiers:
MedGen: C5680250; Orphanet: 96210

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000731608Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)
Pathogenic
(Apr 14, 2017)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

Mutation analysis of the WFS1 gene in seven Danish Wolfram syndrome families; four new mutations identified.

Hansen L, Eiberg H, Barrett T, Bek T, Kjaersgaard P, Tranebjaerg L, Rosenberg T.

Eur J Hum Genet. 2005 Dec;13(12):1275-84.

PubMed [citation]
PMID:
16151413

Neurologic features and genotype-phenotype correlation in Wolfram syndrome.

Chaussenot A, Bannwarth S, Rouzier C, Vialettes B, Mkadem SA, Chabrol B, Cano A, Labauge P, Paquis-Flucklinger V.

Ann Neurol. 2011 Mar;69(3):501-8. doi: 10.1002/ana.22160. Epub 2010 Dec 28.

PubMed [citation]
PMID:
21446023
See all PubMed Citations (10)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000731608.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (10)

Description

The p.Val415del variant in WFS1 has been reported in >10 individuals with Wolfra m syndrome (Hardy 1999, Smith 2004, Hansen 2005, Gasparin 2009, Chaussenot 2011, Rohayem 2011, Rendtorff 2011, de Heredia ML 2013, Bodoor 2016) and segregated i n 7 affected relatives (Hardy 1999, Hansen 2005, Gasparin 2009, Rendtorff 2011, Bodoor 2016). All of these individuals were homozygous or compound heterozygous. This variant has also been reported in ClinVar (Variation ID: 215406). This var iant was identified in 9/33582 Latino chromosomes by the Genome Aggregation Data base (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs750767821); however, its frequency is low enough to be consistent with a recessive carrier frequency. In addition, in vitro studies suggest that the p.Val415del variant may impact expr ession of WFS1 (Rendtorff 2011). In summary, this variant meets criteria to be c lassified as pathogenic for autosomal recessive Wolfram syndrome based upon repo rted familial cases, low frequency in controls, and functional evidence.

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

Last Updated: Nov 3, 2024