NM_024426.6(WT1):c.1440T>C (p.Gly480=) AND WT1-related disorder

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 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:: RCV004548579.1

Allele description [Variation Report for NM_024426.6(WT1):c.1440T>C (p.Gly480=)]

NM_024426.6(WT1):c.1440T>C (p.Gly480=)

Gene:

WT1:WT1 transcription factor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p13

Genomic location:

Preferred name:

NM_024426.6(WT1):c.1440T>C (p.Gly480=)

HGVS:

NC_000011.10:g.32391979A>G
NG_009272.1:g.48563T>C
NM_000378.6:c.1387+2T>C
NM_001198551.2:c.787+2T>C
NM_001198552.2:c.738T>C
NM_001367854.1:c.252T>C
NM_001407044.1:c.1432+2T>C
NM_001407045.1:c.1389T>C
NM_001407046.1:c.1354+687T>C
NM_001407047.1:c.1315+2T>C
NM_001407048.1:c.1299T>C
NM_001407049.1:c.1303+687T>C
NM_001407050.1:c.1266T>C
NM_001407051.1:c.678T>C
NM_024424.3:c.1423+2T>C
NM_024424.5:c.1438+2T>C
NM_024425.2:c.1374T>C
NM_024426.6:c.1440T>CMANE SELECT
NP_001185481.1:p.Gly246=
NP_001354783.1:p.Gly84=
NP_001393974.1:p.Gly463=
NP_001393977.1:p.Gly433=
NP_001393979.1:p.Gly422=
NP_001393980.1:p.Gly226=
NP_077743.2:p.Gly458=
NP_077744.3:p.Gly475=
NP_077744.4:p.Gly480=
LRG_525t1:c.1425T>C
LRG_525:g.48563T>C
LRG_525p1:p.Gly475=
NC_000011.9:g.32413525A>G
NM_024426.3:c.1425T>C
NM_024426.4:c.1425T>C
NR_160306.1:n.1772T>C

Molecular consequence:

NM_001407046.1:c.1354+687T>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001407049.1:c.1303+687T>C - intron variant - [Sequence Ontology: SO:0001627]
NR_160306.1:n.1772T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000378.6:c.1387+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001198551.2:c.787+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407044.1:c.1432+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407047.1:c.1315+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_024424.5:c.1438+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001198552.2:c.738T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001367854.1:c.252T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407045.1:c.1389T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407048.1:c.1299T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407050.1:c.1266T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001407051.1:c.678T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_024425.2:c.1374T>C - synonymous variant - [Sequence Ontology: SO:0001819]
NM_024426.6:c.1440T>C - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004111058	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Aug 11, 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

SCV004111058

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Aug 11, 2023)

germline

clinical testing

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

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

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, SCV004111058.1

#	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.1423+2T>C variant is predicted to disrupt the GT donor site and interfere with normal splicing. However, in the more commonly reported transcript (NM_024426.6) this variant is designated as c.1440T>C, which is not predicted to result in an amino acid change (p.=). 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. Although we suspect that this variant may be pathogenic, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

#	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 13, 2024

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