NM_024426.6(WT1):c.1052C>T (p.Thr351Met) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 26, 2019
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:: RCV001229571.7

Allele description [Variation Report for NM_024426.6(WT1):c.1052C>T (p.Thr351Met)]

NM_024426.6(WT1):c.1052C>T (p.Thr351Met)

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.1052C>T (p.Thr351Met)

HGVS:

NC_000011.10:g.32400009G>A
NG_009272.1:g.40533C>T
NM_000378.6:c.1001C>T
NM_001198551.2:c.401C>T
NM_001198552.2:c.350C>T
NM_001367854.1:c.-137C>T
NM_001407044.1:c.1046C>T
NM_001407045.1:c.1001C>T
NM_001407046.1:c.1052C>T
NM_001407047.1:c.929C>T
NM_001407048.1:c.1001C>T
NM_001407049.1:c.1001C>T
NM_001407050.1:c.878C>T
NM_001407051.1:c.290C>T
NM_024424.5:c.1052C>T
NM_024425.2:c.986C>T
NM_024426.6:c.1052C>TMANE SELECT
NP_000369.4:p.Thr334Met
NP_001185480.1:p.Thr134Met
NP_001185480.1:p.Thr134Met
NP_001185481.1:p.Thr117Met
NP_001393973.1:p.Thr349Met
NP_001393974.1:p.Thr334Met
NP_001393975.1:p.Thr351Met
NP_001393976.1:p.Thr310Met
NP_001393977.1:p.Thr334Met
NP_001393978.1:p.Thr334Met
NP_001393979.1:p.Thr293Met
NP_001393980.1:p.Thr97Met
NP_077742.3:p.Thr351Met
NP_077743.2:p.Thr329Met
NP_077744.3:p.Thr346Met
NP_077744.4:p.Thr351Met
LRG_525t1:c.1037C>T
LRG_525t2:c.401C>T
LRG_525:g.40533C>T
LRG_525p1:p.Thr346Met
LRG_525p2:p.Thr134Met
NC_000011.9:g.32421555G>A
NM_001198551.1:c.401C>T
NM_024426.3:c.1037C>T
NM_024426.4:c.1037C>T
NR_160306.1:n.1384C>T
NR_176266.1:n.1333C>T

Protein change:

T117M

Links:

dbSNP: rs761627098

NCBI 1000 Genomes Browser:

rs761627098

Molecular consequence:

NM_001367854.1:c.-137C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000378.6:c.1001C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001198551.2:c.401C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001198552.2:c.350C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407044.1:c.1046C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407045.1:c.1001C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407046.1:c.1052C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407047.1:c.929C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407048.1:c.1001C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407049.1:c.1001C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407050.1:c.878C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407051.1:c.290C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_024424.5:c.1052C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_024425.2:c.986C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_024426.6:c.1052C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_160306.1:n.1384C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Drash syndrome (DDS)
Synonyms:: WILMS TUMOR AND PSEUDO- OR TRUE HERMAPHRODITISM; Wilms tumor and pseudohermaphroditism; Nephropathy, wilms tumor, and genital anomalies; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008682; MedGen: C0950121; Orphanet: 220; OMIM: 194080

Name:: Frasier syndrome
Identifiers:: MONDO: MONDO:0007635; MeSH: D052159; MedGen: C0950122; Orphanet: 347; OMIM: 136680

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

Name:: 11p partial monosomy syndrome (WAGR)
Synonyms:: CHROMOSOME 11p13 DELETION SYNDROME; WAGR syndrome; WAGR Complex; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008681; MedGen: C0206115; Orphanet: 893; OMIM: 194072

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001402020	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 26, 2019)	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

SCV001402020

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 26, 2019)

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001402020.5

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C15"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals with WT1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces threonine with methionine at codon 346 of the WT1 protein (p.Thr346Met). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and methionine.

#	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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