NM_024426.6(WT1):c.1384C>T (p.Gln462Ter) AND multiple conditions

Germline classification:: Likely pathogenic (1 submission)
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:: RCV003985900.1

Allele description [Variation Report for NM_024426.6(WT1):c.1384C>T (p.Gln462Ter)]

NM_024426.6(WT1):c.1384C>T (p.Gln462Ter)

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.1384C>T (p.Gln462Ter)

HGVS:

NC_000011.10:g.32392035G>A
NG_009272.1:g.48507C>T
NM_000378.6:c.1333C>T
NM_001198551.2:c.733C>T
NM_001198552.2:c.682C>T
NM_001367854.1:c.196C>T
NM_001407044.1:c.1378C>T
NM_001407045.1:c.1333C>T
NM_001407046.1:c.1354+631C>T
NM_001407047.1:c.1261C>T
NM_001407048.1:c.1243C>T
NM_001407049.1:c.1303+631C>T
NM_001407050.1:c.1210C>T
NM_001407051.1:c.622C>T
NM_024424.5:c.1384C>T
NM_024425.2:c.1318C>T
NM_024426.6:c.1384C>TMANE SELECT
NP_000369.4:p.Gln445Ter
NP_001185480.1:p.Gln245Ter
NP_001185480.1:p.Gln245Ter
NP_001185481.1:p.Gln228Ter
NP_001354783.1:p.Gln66Ter
NP_001393973.1:p.Gln460Ter
NP_001393974.1:p.Gln445Ter
NP_001393976.1:p.Gln421Ter
NP_001393977.1:p.Gln415Ter
NP_001393979.1:p.Gln404Ter
NP_001393980.1:p.Gln208Ter
NP_077742.3:p.Gln462Ter
NP_077743.2:p.Gln440Ter
NP_077744.3:p.Gln457Ter
NP_077744.4:p.Gln462Ter
LRG_525t1:c.1369C>T
LRG_525t2:c.733C>T
LRG_525:g.48507C>T
LRG_525p1:p.Gln457Ter
LRG_525p2:p.Gln245Ter
NC_000011.9:g.32413581G>A
NM_001198551.1:c.733C>T
NM_024426.3:c.1369C>T
NR_160306.1:n.1716C>T
NR_176266.1:n.1665C>T

Protein change:

Q208*

Molecular consequence:

NM_001407046.1:c.1354+631C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001407049.1:c.1303+631C>T - intron variant - [Sequence Ontology: SO:0001627]
NR_160306.1:n.1716C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176266.1:n.1665C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000378.6:c.1333C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001198551.2:c.733C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001198552.2:c.682C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001367854.1:c.196C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001407044.1:c.1378C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001407045.1:c.1333C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001407047.1:c.1261C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001407048.1:c.1243C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001407050.1:c.1210C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001407051.1:c.622C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_024424.5:c.1384C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_024425.2:c.1318C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_024426.6:c.1384C>T - nonsense - [Sequence Ontology: SO:0001587]

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:: Meacham syndrome
Synonyms:: Meacham Winn Culler syndrome
Identifiers:: MONDO: MONDO:0012164; MedGen: C1837026; Orphanet: 3097; OMIM: 608978

Name:: Nephrotic syndrome, type 4 (NPHS4)
Synonyms:: Familial mesangial sclerosis; Nephrotic syndrome, early onset with diffuse mesangial sclerosis
Identifiers:: MONDO: MONDO:0009733; MedGen: C3151568; Orphanet: 656; OMIM: 256370

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004801785	Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	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

SCV004801785

Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

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	yes	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 Molecular Genetics Department, Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, SCV004801785.1

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

Description

A previously undescribed nucleotide variant creates a premature translation stop signal p.Gln462Ter in the WT1 gene. The variant was observed in heterozygous state in an individual affected with chronic kidney disease, terminal stage. Loss-of-function variants are reported in patients with Denys-Drash syndrome, 194080, Frasier syndrome, 136680, Meacham syndrome, 608978, Nephrotic syndrome, type 4, 256370, Wilms tumor, type 1, 194070. The variant is not present in population database (gnomAD no frequency). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as likely pathogenic.

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

Last Updated: Jun 29, 2024

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