NM_024426.6(WT1):c.1447+5G>A AND not provided

Germline classification:: Pathogenic (5 submissions)
Last evaluated:: May 24, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001288155.13

Allele description [Variation Report for NM_024426.6(WT1):c.1447+5G>A]

NM_024426.6(WT1):c.1447+5G>A

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.1447+5G>A

Other names:

splice site; 1432+5G>A; IVS9+5G>A

HGVS:

NC_000011.10:g.32391967C>T
NG_009272.1:g.48575G>A
NM_000378.6:c.1387+14G>A
NM_001198551.2:c.787+14G>A
NM_001198552.2:c.745+5G>A
NM_001367854.1:c.259+5G>A
NM_001407044.1:c.1432+14G>A
NM_001407045.1:c.1396+5G>A
NM_001407046.1:c.1354+699G>A
NM_001407047.1:c.1315+14G>A
NM_001407048.1:c.1306+5G>A
NM_001407049.1:c.1303+699G>A
NM_001407050.1:c.1273+5G>A
NM_001407051.1:c.685+5G>A
NM_024424.5:c.1438+14G>A
NM_024426.6:c.1447+5G>AMANE SELECT
LRG_525:g.48575G>A
NC_000011.9:g.32413513C>T
NM_024426.2:c.1228+5G>A
NM_024426.4:c.1432+5G>A

Nucleotide change:

IVS9DS, G-A, +5

Links:

OMIM: 607102.0009; OMIM: 607102.0020; dbSNP: rs587776576

NCBI 1000 Genomes Browser:

rs587776576

Molecular consequence:

NM_000378.6:c.1387+14G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001198551.2:c.787+14G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001198552.2:c.745+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001367854.1:c.259+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407044.1:c.1432+14G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407045.1:c.1396+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407046.1:c.1354+699G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407047.1:c.1315+14G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407048.1:c.1306+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407049.1:c.1303+699G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407050.1:c.1273+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407051.1:c.685+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_024424.5:c.1438+14G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_024426.6:c.1447+5G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001475083	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Pathogenic (Oct 14, 2019)	unknown	clinical testing	PubMed (14) [See all records that cite these PMIDs] 1302008, 20442690, 9499425, 10762296, 28204945, 30406062, 28780565, 25818337, 23515051, 21499692, 17694336, 22099579, 24856380, 26467025
SCV001767447	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Pathogenic (Nov 27, 2019)	germline	clinical testing	Citation Link,
SCV002020923	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Oct 21, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002051463	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 9, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005199006	Clinical Genetics Laboratory, Skane University Hospital Lund	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (May 24, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Germline intronic and exonic mutations in the Wilms' tumour gene (WT1) affecting urogenital development.

Bruening W, Bardeesy N, Silverman BL, Cohn RA, Machin GA, Aronson AJ, Housman D, Pelletier J.

Nat Genet. 1992 May;1(2):144-8.

PubMed [citation]

PMID:: 1302008

WT1 gene mutations in Chinese children with early onset nephrotic syndrome.

Li J, Ding J, Zhao D, Yu Z, Fan Q, Chen Y, Zhang H, Zhong X, Huang J, Yao Y, Xiao H.

Pediatr Res. 2010 Aug;68(2):155-8. doi: 10.1203/00006450-201011001-00302.

PubMed [citation]

PMID:: 20442690

See all PubMed Citations (15)

Details of each submission

From Athena Diagnostics, SCV001475083.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (14)

Description

Not found in the total gnomAD dataset, and the data is high quality. Predicted to negatively affect a known splice site. Assessment of experimental evidence suggests this variant results in abnormal protein function. 3 de novo cases with parental identity not confirmed.

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

From GeneDx, SCV001767447.1

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

Description

Published functional studies demonstrate a damaging effect: aberrant splicing resulting in disruption of the ratio of WT1 isoforms (Bruening 1992, Klamt 1998); Not observed in large population cohorts (Lek 2016); Also known as c.1228+5G>A; This variant is associated with the following publications: (PMID: 32203225, 31447099, 7959750, 8281163, 1302008, 9499425, 30406062, 28780565, 28204945, 25818337, 20442690, 23515051, 10505700, 11354777)

#	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

From Revvity Omics, Revvity, SCV002020923.3

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

#	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

From Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center, SCV002051463.2

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

Description

PS3, PS4, PP3, PM2

#	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

From Clinical Genetics Laboratory, Skane University Hospital Lund, SCV005199006.1

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

#	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: Nov 3, 2024

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