NM_024426.6(WT1):c.49C>A (p.Pro17Thr) AND Wilms tumor 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 16, 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:: RCV004014730.2

Allele description [Variation Report for NM_024426.6(WT1):c.49C>A (p.Pro17Thr)]

NM_024426.6(WT1):c.49C>A (p.Pro17Thr)

Genes:

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

Variant type:

single nucleotide variant

Cytogenetic location:

11p13

Genomic location:

Preferred name:

NM_024426.6(WT1):c.49C>A (p.Pro17Thr)

HGVS:

NC_000011.10:g.32435312G>T
NG_009272.1:g.5230C>A
NG_050766.1:g.4565G>T
NG_050766.2:g.5244G>T
NM_000378.6:c.49C>A
NM_001407044.1:c.49C>A
NM_001407045.1:c.49C>A
NM_001407046.1:c.49C>A
NM_001407047.1:c.49C>A
NM_001407048.1:c.49C>A
NM_001407049.1:c.49C>A
NM_001407050.1:c.49C>A
NM_001429031.1:c.-171C>A
NM_001429032.1:c.-171C>A
NM_001429033.1:c.-171C>A
NM_001429034.1:c.-171C>A
NM_024424.5:c.49C>A
NM_024425.2:c.34C>A
NM_024426.6:c.49C>AMANE SELECT
NP_000369.4:p.Pro17Thr
NP_001393973.1:p.Pro17Thr
NP_001393974.1:p.Pro17Thr
NP_001393975.1:p.Pro17Thr
NP_001393976.1:p.Pro17Thr
NP_001393977.1:p.Pro17Thr
NP_001393978.1:p.Pro17Thr
NP_001393979.1:p.Pro17Thr
NP_077742.3:p.Pro17Thr
NP_077743.2:p.Pro12Thr
NP_077744.3:p.Pro12Thr
NP_077744.4:p.Pro17Thr
LRG_525t1:c.34C>A
LRG_525:g.5230C>A
LRG_525p1:p.Pro12Thr
NC_000011.9:g.32456858G>T
NM_024426.3:c.34C>A
NR_160306.1:n.228C>A
NR_176266.1:n.228C>A

Protein change:

P12T

Molecular consequence:

NM_000378.6:c.49C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407044.1:c.49C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407045.1:c.49C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407046.1:c.49C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407047.1:c.49C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407048.1:c.49C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407049.1:c.49C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407050.1:c.49C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024424.5:c.49C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024425.2:c.34C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024426.6:c.49C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_160306.1:n.228C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176266.1:n.228C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004827694	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (May 16, 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

SCV004827694

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(May 16, 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	1	not provided	not provided	108544	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 All of Us Research Program, National Institutes of Health, SCV004827694.1

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

Description

This missense variant replaces proline with threonine at codon 12 of the WT1 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with WT1-related disorders in the literature. This variant has been identified in 1/129436 chromosomes 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Jun 9, 2024

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