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NM_024426.6(WT1):c.507_511delinsCACTGT (p.Ser170fs) AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Mar 29, 2022
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:
RCV003022908.3

Allele description [Variation Report for NM_024426.6(WT1):c.507_511delinsCACTGT (p.Ser170fs)]

NM_024426.6(WT1):c.507_511delinsCACTGT (p.Ser170fs)

Genes:
WT1:WT1 transcription factor [Gene - OMIM - HGNC]
LOC107982234:WT1/WT1-AS bi-directional promoter region [Gene]
Variant type:
Indel
Cytogenetic location:
11p13
Genomic location:
Preferred name:
NM_024426.6(WT1):c.507_511delinsCACTGT (p.Ser170fs)
HGVS:
  • NC_000011.10:g.32434850_32434854delinsACAGTG
  • NG_009272.1:g.5688_5692delinsCACTGT
  • NG_050766.1:g.4103_4107delinsACAGTG
  • NG_050766.2:g.4782_4786delinsACAGTG
  • NM_000378.6:c.507_511delinsCACTGT
  • NM_001407044.1:c.507_511delTTCCGinsCACTGT
  • NM_001407045.1:c.507_511delTTCCGinsCACTGT
  • NM_001407046.1:c.507_511delTTCCGinsCACTGT
  • NM_001407047.1:c.507_511delTTCCGinsCACTGT
  • NM_001407048.1:c.507_511delTTCCGinsCACTGT
  • NM_001407049.1:c.507_511delTTCCGinsCACTGT
  • NM_001407050.1:c.507_511delTTCCGinsCACTGT
  • NM_024424.5:c.507_511delinsCACTGT
  • NM_024425.2:c.492_496delTTCCGinsCACTGT
  • NM_024426.6:c.507_511delinsCACTGTMANE SELECT
  • NP_000369.4:p.Ser170fs
  • NP_001393973.1:p.Ser170Thrfs
  • NP_001393974.1:p.Ser170Thrfs
  • NP_001393975.1:p.Ser170Thrfs
  • NP_001393976.1:p.Ser170Thrfs
  • NP_001393977.1:p.Ser170Thrfs
  • NP_001393978.1:p.Ser170Thrfs
  • NP_001393979.1:p.Ser170Thrfs
  • NP_077742.3:p.Ser170fs
  • NP_077743.2:p.Ser165Thrfs
  • NP_077744.3:p.Ser165Thrfs
  • NP_077744.4:p.Ser170fs
  • LRG_525t1:c.492_496delTTCCGinsCACTGT
  • LRG_525:g.5688_5692delinsCACTGT
  • LRG_525p1:p.Ser165Thrfs
  • NC_000011.9:g.32456396_32456400delinsACAGTG
  • NM_024426.3:c.492_496delTTCCGinsCACTGT
  • NR_160306.1:n.686_690delinsCACTGT
  • NR_176266.1:n.686_690delTTCCGinsCACTGT
Protein change:
S170fs
Molecular consequence:
  • NM_000378.6:c.507_511delinsCACTGT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407044.1:c.507_511delTTCCGinsCACTGT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407045.1:c.507_511delTTCCGinsCACTGT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407046.1:c.507_511delTTCCGinsCACTGT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407047.1:c.507_511delTTCCGinsCACTGT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407048.1:c.507_511delTTCCGinsCACTGT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407049.1:c.507_511delTTCCGinsCACTGT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407050.1:c.507_511delTTCCGinsCACTGT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_024424.5:c.507_511delinsCACTGT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_024425.2:c.492_496delTTCCGinsCACTGT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_024426.6:c.507_511delinsCACTGT - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_160306.1:n.686_690delinsCACTGT - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Drash syndrome (DDS)
Synonyms:
WILMS TUMOR AND PSEUDO- OR TRUE HERMAPHRODITISM; Wilms tumor and pseudohermaphroditism; Nephropathy, wilms tumor, and genital anomalies; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008682; MedGen: C0950121; Orphanet: 220; OMIM: 194080
Name:
Frasier syndrome
Identifiers:
MONDO: MONDO:0007635; MeSH: D052159; MedGen: C0950122; Orphanet: 347; OMIM: 136680
Name:
Wilms tumor 1 (WT1)
Synonyms:
Wilms tumor, somatic
Identifiers:
MONDO: MONDO:0008679; MedGen: CN033288; Orphanet: 654; OMIM: 194070
Name:
11p partial monosomy syndrome (WAGR)
Synonyms:
CHROMOSOME 11p13 DELETION SYNDROME; WAGR syndrome; WAGR Complex; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008681; MedGen: C0206115; Orphanet: 893; OMIM: 194072

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003315324Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Mar 29, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Twenty-four new cases of WT1 germline mutations and review of the literature: genotype/phenotype correlations for Wilms tumor development.

Royer-Pokora B, Beier M, Henzler M, Alam R, Schumacher V, Weirich A, Huff V.

Am J Med Genet A. 2004 Jun 15;127A(3):249-57.

PubMed [citation]
PMID:
15150775

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003315324.2

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with WT1-related conditions. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This sequence change creates a premature translational stop signal (p.Ser165Thrfs*34) in the WT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in WT1 are known to be pathogenic (PMID: 15150775).

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

Last Updated: Sep 29, 2024