VCV002182681.3 - ClinVar

NM_024426.6(WT1):c.392C>T (p.Pro131Leu)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Conflicting classifications of pathogenicity
Likely pathogenic(1); Uncertain significance(1)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_024426.6(WT1):c.392C>T (p.Pro131Leu)

Variation ID: 2182681 Accession: VCV002182681.3

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 11p13 11: 32434969 (GRCh38) [ NCBI UCSC ] 11: 32456515 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 8, 2023	Jun 23, 2024	Dec 1, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_024426.6:c.392C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_077744.4:p.Pro131Leu	missense
NM_000378.6:c.392C>T	NP_000369.4:p.Pro131Leu	missense
NM_001407044.1:c.392C>T	NP_001393973.1:p.Pro131Leu	missense
NM_001407045.1:c.392C>T	NP_001393974.1:p.Pro131Leu	missense
NM_001407046.1:c.392C>T	NP_001393975.1:p.Pro131Leu	missense
NM_001407047.1:c.392C>T	NP_001393976.1:p.Pro131Leu	missense
NM_001407048.1:c.392C>T	NP_001393977.1:p.Pro131Leu	missense
NM_001407049.1:c.392C>T	NP_001393978.1:p.Pro131Leu	missense
NM_001407050.1:c.392C>T	NP_001393979.1:p.Pro131Leu	missense
NM_024424.5:c.392C>T	NP_077742.3:p.Pro131Leu	missense
NM_024425.2:c.377C>T	NP_077743.2:p.Pro126Leu	missense
NR_160306.1:n.571C>T		non-coding transcript variant
NR_176266.1:n.571C>T
NC_000011.10:g.32434969G>A
NC_000011.9:g.32456515G>A
NG_009272.1:g.5573C>T
NG_050766.2:g.4901G>A
LRG_525:g.5573C>T
LRG_525t1:c.377C>T	LRG_525p1:p.Pro126Leu

... more HGVS ... less HGVS

Protein change

P126L, P131L

Other names

Canonical SPDI

NC_000011.10:32434968:G:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
WT1		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	916	1675
LOC107982234	-	-	-	GRCh38	-	734

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
11p partial monosomy syndrome Drash syndrome Frasier syndrome Wilms tumor 1	Uncertain significance (1)	criteria provided, single submitter	Jun 23, 2023	RCV002592136.3
Nephrotic syndrome, type 4	Likely pathogenic (1)	criteria provided, single submitter	Dec 1, 2023	RCV004577571.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely pathogenic (Dec 01, 2023)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Nephrotic syndrome, type 4 Affected status: yes Allele origin: de novo	Precision Medicine Center, Zhengzhou University Accession: SCV004218504.1 First in ClinVar: Jun 23, 2024 Last updated: Jun 23, 2024	Publications: PubMed (1) PubMed: 25741868 Comment: PS2,PM2_p,PP3 Sex: female
Uncertain significance (Jun 23, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Wilms tumor 1 Drash syndrome 11p partial monosomy syndrome Frasier syndrome Explanation for multiple conditions: Uncertain. The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV003500535.2 First in ClinVar: Feb 07, 2023 Last updated: Feb 28, 2024	Comment: 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 … (more) 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: 2182681). This variant has not been reported in the literature in individuals affected with WT1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 126 of the WT1 protein (p.Pro126Leu). (less)

Comment:

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: 2182681). This variant has not been reported in the literature in individuals affected with WT1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 126 of the WT1 protein (p.Pro126Leu).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
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	Genetics in medicine : official journal of the American College of Medical Genetics	2015	PMID: 25741868

Text-mined citations for this variant ...

Record last updated Sep 29, 2024

ClinVar Genomic variation as it relates to human health

NM_024426.6(WT1):c.392C>T (p.Pro131Leu)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...