NM_024426.6(WT1):c.1069G>C (p.Ala357Pro) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 8, 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:: RCV001936338.7

Allele description [Variation Report for NM_024426.6(WT1):c.1069G>C (p.Ala357Pro)]

NM_024426.6(WT1):c.1069G>C (p.Ala357Pro)

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.1069G>C (p.Ala357Pro)

HGVS:

NC_000011.10:g.32399992C>G
NG_009272.1:g.40550G>C
NM_000378.6:c.1018G>C
NM_001198551.2:c.418G>C
NM_001198552.2:c.367G>C
NM_001367854.1:c.-120G>C
NM_001407044.1:c.1063G>C
NM_001407045.1:c.1018G>C
NM_001407046.1:c.1069G>C
NM_001407047.1:c.946G>C
NM_001407048.1:c.1018G>C
NM_001407049.1:c.1018G>C
NM_001407050.1:c.895G>C
NM_001407051.1:c.307G>C
NM_024424.5:c.1069G>C
NM_024425.2:c.1003G>C
NM_024426.6:c.1069G>CMANE SELECT
NP_000369.4:p.Ala340Pro
NP_001185480.1:p.Ala140Pro
NP_001185480.1:p.Ala140Pro
NP_001185481.1:p.Ala123Pro
NP_001393973.1:p.Ala355Pro
NP_001393974.1:p.Ala340Pro
NP_001393975.1:p.Ala357Pro
NP_001393976.1:p.Ala316Pro
NP_001393977.1:p.Ala340Pro
NP_001393978.1:p.Ala340Pro
NP_001393979.1:p.Ala299Pro
NP_001393980.1:p.Ala103Pro
NP_077742.3:p.Ala357Pro
NP_077743.2:p.Ala335Pro
NP_077744.3:p.Ala352Pro
NP_077744.4:p.Ala357Pro
LRG_525t1:c.1054G>C
LRG_525t2:c.418G>C
LRG_525:g.40550G>C
LRG_525p1:p.Ala352Pro
LRG_525p2:p.Ala140Pro
NC_000011.9:g.32421538C>G
NM_001198551.1:c.418G>C
NM_024426.3:c.1054G>C
NR_160306.1:n.1401G>C
NR_176266.1:n.1350G>C

Protein change:

A103P

Links:

dbSNP: rs1362066206

NCBI 1000 Genomes Browser:

rs1362066206

Molecular consequence:

NM_001367854.1:c.-120G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000378.6:c.1018G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001198551.2:c.418G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001198552.2:c.367G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407044.1:c.1063G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407045.1:c.1018G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407046.1:c.1069G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407047.1:c.946G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407048.1:c.1018G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407049.1:c.1018G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407050.1:c.895G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001407051.1:c.307G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_024424.5:c.1069G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_024425.2:c.1003G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_024426.6:c.1069G>C - missense variant - [Sequence Ontology: SO:0001583]
NR_160306.1:n.1401G>C - 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
SCV002204148	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 8, 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

SCV002204148

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 8, 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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002204148.3

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

Description

This variant is present in population databases (no rsID available, gnomAD 0.01%). This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 352 of the WT1 protein (p.Ala352Pro). This variant has not been reported in the literature in individuals affected with WT1-related conditions. 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. ClinVar contains an entry for this variant (Variation ID: 1428489). This missense change has been observed to be homozygous or hemizygous in an individual who did not have the expected clinical features for that genetic result (Invitae).

#	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: Sep 29, 2024

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Relating variation to medicine