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NM_024426.6(WT1):c.69_70del (p.Arg24fs) AND Wilms tumor 1

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 3, 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:
RCV004017079.2

Allele description [Variation Report for NM_024426.6(WT1):c.69_70del (p.Arg24fs)]

NM_024426.6(WT1):c.69_70del (p.Arg24fs)

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.69_70del (p.Arg24fs)
HGVS:
  • NC_000011.10:g.32435291_32435292del
  • NG_009272.1:g.5250_5251del
  • NG_050766.1:g.4544_4545del
  • NG_050766.2:g.5223_5224del
  • NM_000378.6:c.69_70del
  • NM_001407044.1:c.69_70del
  • NM_001407045.1:c.69_70del
  • NM_001407046.1:c.69_70del
  • NM_001407047.1:c.69_70del
  • NM_001407048.1:c.69_70del
  • NM_001407049.1:c.69_70del
  • NM_001407050.1:c.69_70del
  • NM_001429031.1:c.-151_-150delCC
  • NM_001429032.1:c.-151_-150delCC
  • NM_001429033.1:c.-151_-150delCC
  • NM_001429034.1:c.-151_-150delCC
  • NM_024424.5:c.69_70del
  • NM_024425.2:c.54_55delCC
  • NM_024426.6:c.69_70delMANE SELECT
  • NP_000369.4:p.Arg24fs
  • NP_001393973.1:p.Arg24fs
  • NP_001393974.1:p.Arg24fs
  • NP_001393975.1:p.Arg24fs
  • NP_001393976.1:p.Arg24fs
  • NP_001393977.1:p.Arg24fs
  • NP_001393978.1:p.Arg24fs
  • NP_001393979.1:p.Arg24fs
  • NP_077742.3:p.Arg24fs
  • NP_077743.2:p.Arg19Leufs
  • NP_077744.3:p.Arg19Leufs
  • NP_077744.4:p.Arg24fs
  • LRG_525t1:c.54_55del
  • LRG_525:g.5250_5251del
  • LRG_525p1:p.Arg19Leufs
  • NC_000011.9:g.32456837_32456838del
  • NM_024426.3:c.54_55delCC
  • NR_160306.1:n.248_249del
  • NR_176266.1:n.248_249del
Protein change:
R24fs
Molecular consequence:
  • NM_000378.6:c.69_70del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407044.1:c.69_70del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407045.1:c.69_70del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407046.1:c.69_70del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407047.1:c.69_70del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407048.1:c.69_70del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407049.1:c.69_70del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001407050.1:c.69_70del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_024424.5:c.69_70del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_024425.2:c.54_55delCC - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_024426.6:c.69_70del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_160306.1:n.248_249del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_176266.1:n.248_249del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004845806All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain Significance
(Apr 3, 2023) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided108544not providedclinical testing

Citations

PubMed

Isolation and characterization of a zinc finger polypeptide gene at the human chromosome 11 Wilms' tumor locus.

Call KM, Glaser T, Ito CY, Buckler AJ, Pelletier J, Haber DA, Rose EA, Kral A, Yeger H, Lewis WH, et al.

Cell. 1990 Feb 9;60(3):509-20.

PubMed [citation]
PMID:
2154335

Homozygous deletion in Wilms tumours of a zinc-finger gene identified by chromosome jumping.

Gessler M, Poustka A, Cavenee W, Neve RL, Orkin SH, Bruns GA.

Nature. 1990 Feb 22;343(6260):774-8.

PubMed [citation]
PMID:
2154702
See all PubMed Citations (3)

Details of each submission

From All of Us Research Program, National Institutes of Health, SCV004845806.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (3)

Description

This variant deletes 2 basepairs in exon 1 of the WT1 gene, and it is predicted to cause a frameshift at codon 19 and create a premature termination codon in exon 1 which may trigger nonsense-mediated decay. However, the WT1 gene has a protein isoform with translation initiation at p.Met69 that retains the functional domains for the WT protein (PMID: 2154335, 2154702). Therefore, the severity of the impact from this frameshift variant is unknown. This variant is also known as c.69_70 del (p.Arg24Leufs*32) based the reference transcripts, ENST00000452863 and NM_024426.6. To our knowledge, this variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided1not providednot providednot provided

Last Updated: Jun 9, 2024