NM_024426.6(WT1):c.1149del (p.Val384fs) AND multiple conditions

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 9, 2017
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:: RCV000653783.7

Allele description [Variation Report for NM_024426.6(WT1):c.1149del (p.Val384fs)]

NM_024426.6(WT1):c.1149del (p.Val384fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

11p13

Genomic location:

Preferred name:

NM_024426.6(WT1):c.1149del (p.Val384fs)

HGVS:

NC_000011.10:g.32396373del
NG_009272.1:g.44170del
NM_000378.6:c.1098del
NM_001198551.2:c.497delT
NM_001198552.2:c.447del
NM_001367854.1:c.-40del
NM_001407044.1:c.1142delT
NM_001407045.1:c.1097delT
NM_001407046.1:c.1148delT
NM_001407047.1:c.1025delT
NM_001407048.1:c.1097delT
NM_001407049.1:c.1097delT
NM_001407050.1:c.974delT
NM_001407051.1:c.386delT
NM_024424.5:c.1149del
NM_024425.2:c.1082delT
NM_024426.6:c.1149delMANE SELECT
NP_000369.4:p.Val367fs
NP_001185480.1:p.Val167Tyrfs
NP_001185480.1:p.Val167fs
NP_001185481.1:p.Val150fs
NP_001393973.1:p.Val382Tyrfs
NP_001393974.1:p.Val367Tyrfs
NP_001393975.1:p.Val384Tyrfs
NP_001393976.1:p.Val343Tyrfs
NP_001393977.1:p.Val367Tyrfs
NP_001393978.1:p.Val367Tyrfs
NP_001393979.1:p.Val326Tyrfs
NP_001393980.1:p.Val130Tyrfs
NP_077742.3:p.Val384fs
NP_077743.2:p.Val362Tyrfs
NP_077744.3:p.Val379Tyrfs
NP_077744.4:p.Val384fs
LRG_525t1:c.1133del
LRG_525t2:c.498del
LRG_525:g.44170del
LRG_525p1:p.Val379Tyrfs
LRG_525p2:p.Val167fs
NC_000011.9:g.32417918del
NC_000011.9:g.32417919del
NM_001198551.1:c.498del
NM_024426.3:c.1133delT
NM_024426.4:c.1134del
NR_160306.1:n.1481del
NR_176266.1:n.1429delT

Protein change:

V150fs

Links:

dbSNP: rs1554939839

NCBI 1000 Genomes Browser:

rs1554939839

Molecular consequence:

NM_001367854.1:c.-40del - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000378.6:c.1098del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001198551.2:c.497delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001198552.2:c.447del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407044.1:c.1142delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407045.1:c.1097delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407046.1:c.1148delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407047.1:c.1025delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407048.1:c.1097delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407049.1:c.1097delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407050.1:c.974delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001407051.1:c.386delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024424.5:c.1149del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024425.2:c.1082delT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_024426.6:c.1149del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_160306.1:n.1481del - 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
SCV000775673	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 9, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 15150775, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000775673

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 9, 2017)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Twenty-four new cases of WT1 germline mutations and review of the literature: genotype/phenotype correlations for Wilms tumor development.

Royer-Pokora B, Beier M, Henzler M, Alam R, Schumacher V, Weirich A, Huff V.

Am J Med Genet A. 2004 Jun 15;127A(3):249-57.

PubMed [citation]

PMID:: 15150775

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000775673.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in WT1 are known to be pathogenic (PMID: 15150775). This variant has been reported in an individual affected with Wilms tumor (PMID: 15150775). This variant is also known as 929del1 (L310fs380X) in the literature. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Val379Tyrfs*70) in the WT1 gene. It is expected to result in an absent or disrupted protein product.

#	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: Mar 5, 2024

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