NM_024426.6(WT1):c.514del (p.Gln172fs) AND Wilms tumor 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 11, 2023
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:: RCV002266533.2

Allele description [Variation Report for NM_024426.6(WT1):c.514del (p.Gln172fs)]

NM_024426.6(WT1):c.514del (p.Gln172fs)

Genes:

WT1:WT1 transcription factor [Gene - OMIM - HGNC]
LOC107982234:WT1/WT1-AS bi-directional promoter region [Gene]

Variant type:

Deletion

Cytogenetic location:

11p13

Genomic location:

Preferred name:

NM_024426.6(WT1):c.514del (p.Gln172fs)

HGVS:

NC_000011.10:g.32434848del
NG_009272.1:g.5695del
NG_050766.1:g.4101del
NM_000378.6:c.514del
NM_024424.5:c.514del
NM_024426.6:c.514delMANE SELECT
NP_000369.4:p.Gln172fs
NP_077742.3:p.Gln172fs
NP_077744.4:p.Gln172fs
LRG_525:g.5695del
NC_000011.9:g.32456394del
NM_024426.4:c.499delC
NM_024426.6:c.514delCMANE SELECT
NR_160306.1:n.693del

Protein change:

Q172fs

Links:

dbSNP: rs2133102575

NCBI 1000 Genomes Browser:

rs2133102575

Molecular consequence:

NM_000378.6:c.514del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024424.5:c.514del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024426.6:c.514del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_160306.1:n.693del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Wilms tumor 1 (WT1)
Synonyms:: Wilms tumor, somatic
Identifiers:: MONDO: MONDO:0008679; MedGen: CN033288; Orphanet: 654; OMIM: 194070

Recent activity

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Tyrosine aminotransferase [Mus musculus]
Tyrosine aminotransferase [Mus musculus]
gi|21314992|gb|AAH30728.1|

Protein
SRP059727 (1)
SRA
Hoplophryne rogersi tyrosinase (TYR) gene, partial cds
Hoplophryne rogersi tyrosinase (TYR) gene, partial cds
gi|154795292|gb|EF395976.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002547568	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Apr 11, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002547568

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Apr 11, 2023)

germline

clinical testing

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

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Frequency of WT1 and 11p15 constitutional aberrations and phenotypic correlation in childhood Wilms tumour patients.

Segers H, Kersseboom R, Alders M, Pieters R, Wagner A, van den Heuvel-Eibrink MM.

Eur J Cancer. 2012 Nov;48(17):3249-56. doi: 10.1016/j.ejca.2012.06.008. Epub 2012 Jul 14.

PubMed [citation]

PMID:: 22796116

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002547568.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Variant summary: WT1 c.514delC (p.Gln172SerfsX119) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 244686 control chromosomes. c.514delC has been reported in the literature in individuals affected with Wilms Tumor, Type 1. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jun 9, 2024

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