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NM_024426.6(WT1):c.1447+5G>A AND WT1-related disorder

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 9, 2024
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV004547457.2

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)

Name:
WT1-related disorder
Identifiers:
MedGen: CN377814

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004119771PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Pathogenic
(Feb 9, 2024) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004119771.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The WT1 c.1432+5G>A variant is predicted to interfere with splicing. This variant was reported in multiple individuals with Frasier syndrome and/or early-onset nephrotic syndrome (Lipska et al. 2013. PubMed ID: 23515051; Bruening et al. 1992. PubMed ID: 1302008, reported as 1228+5G>A; Li et al. 2010. PubMed ID: 20442690, reported as IVS9+5G>A). In vitro functional studies indicate that this variant results in defective splicing (Klamt et al. 1998. PubMed ID: 9499425). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024