NM_024426.6(WT1):c.381del (p.Ala128fs) AND WT1-related disorder

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 21, 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:: RCV004550668.1

Allele description [Variation Report for NM_024426.6(WT1):c.381del (p.Ala128fs)]

NM_024426.6(WT1):c.381del (p.Ala128fs)

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.381del (p.Ala128fs)

HGVS:

NC_000011.10:g.32434983del
NG_009272.1:g.5562del
NG_050766.1:g.4236del
NG_050766.2:g.4915del
NM_000378.6:c.381del
NM_001407044.1:c.381del
NM_001407045.1:c.381del
NM_001407046.1:c.381del
NM_001407047.1:c.381del
NM_001407048.1:c.381del
NM_001407049.1:c.381del
NM_001407050.1:c.381del
NM_024424.5:c.381del
NM_024425.2:c.363delC
NM_024426.6:c.381delMANE SELECT
NP_000369.4:p.Ala128fs
NP_001393973.1:p.Ala128fs
NP_001393974.1:p.Ala128fs
NP_001393975.1:p.Ala128fs
NP_001393976.1:p.Ala128fs
NP_001393977.1:p.Ala128fs
NP_001393978.1:p.Ala128fs
NP_001393979.1:p.Ala128fs
NP_077742.3:p.Ala128fs
NP_077743.2:p.Ala123Argfs
NP_077744.3:p.Ala123Argfs
NP_077744.4:p.Ala128fs
LRG_525t1:c.363del
LRG_525:g.5562del
LRG_525p1:p.Ala123Argfs
NC_000011.9:g.32456529del
NM_024426.3:c.363delC
NM_024426.4:c.366delC
NR_160306.1:n.560del
NR_176266.1:n.560del

Protein change:

A128fs

Molecular consequence:

NM_000378.6:c.381del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407044.1:c.381del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407045.1:c.381del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407046.1:c.381del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407047.1:c.381del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407048.1:c.381del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407049.1:c.381del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407050.1:c.381del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024424.5:c.381del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024425.2:c.363delC - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024426.6:c.381del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_160306.1:n.560del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176266.1:n.560del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: WT1-related disorder
Identifiers:: MedGen: CN377814

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Acheilognathus koreensis mitochondrion, complete genome
Acheilognathus koreensis mitochondrion, complete genome
gi|146142371|gb|EF483932.1|

Nucleotide
As3mt arsenite methyltransferase [Mus musculus]
As3mt arsenite methyltransferase [Mus musculus]
Gene ID:57344

Gene
Xab2 XPA binding protein 2 [Mus musculus]
Xab2 XPA binding protein 2 [Mus musculus]
Gene ID:67439

Gene
LMOD1 leiomodin 1 [Homo sapiens]
LMOD1 leiomodin 1 [Homo sapiens]
Gene ID:25802

Gene
Gene Links for Nucleotide (Select 1519313318) (1)
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004103614	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Sep 21, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004103614

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Sep 21, 2023)

germline

clinical testing

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

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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

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 PreventionGenetics, part of Exact Sciences, SCV004103614.1

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

Description

The WT1 c.366delC variant is predicted to result in a frameshift and premature protein termination (p.Ala123Argfs*35). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Frameshift variants in WT1 are expected to be pathogenic. This variant is interpreted 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: Oct 26, 2024

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