chr11-32391968-G-A

Variant names:

• chr11-32391968-G-A
• rs587776577
• NM_024426.6:c.1447+4C>T

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2 PP5_Very_Strong

The NM_024426.6(WT1):​c.1447+4C>T variant causes a splice region, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,742 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: WT1 NM_024426.6 splice_region, intron
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:16 O:1
• Conservation: PhyloP100: 8.05

Genes affected

WT1 (HGNC:12796): (WT1 transcription factor) This gene encodes a transcription factor that contains four zinc-finger motifs at the C-terminus and a proline/glutamine-rich DNA-binding domain at the N-terminus. It has an essential role in the normal development of the urogenital system, and it is mutated in a small subset of patients with Wilms tumor. This gene exhibits complex tissue-specific and polymorphic imprinting pattern, with biallelic, and monoallelic expression from the maternal and paternal alleles in different tissues. Multiple transcript variants have been described. In several variants, there is evidence for the use of a non-AUG (CUG) translation initiation codon upstream of, and in-frame with the first AUG. Authors of PMID:7926762 also provide evidence that WT1 mRNA undergoes RNA editing in human and rat, and that this process is tissue-restricted and developmentally regulated. [provided by RefSeq, Mar 2015]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 11-32391968-G-A is Pathogenic according to our data. Variant chr11-32391968-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 3500.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-32391968-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
WT1	NM_024426.6	c.1447+4C>T		splice_region_variant, intron_variant	Intron 9 of 9	ENST00000452863.10	NP_077744.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
WT1	ENST00000452863.10	c.1447+4C>T		splice_region_variant, intron_variant	Intron 9 of 9	1	NM_024426.6	ENSP00000415516.5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1460742 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 726790

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 9.00e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:16 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Frasier syndrome Pathogenic:5

Jan 17, 2019

Yale Center for Mendelian Genomics, Yale University

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Aug 09, 2018

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1432+4C>T variant in WT1 has been previously reported in >10 individuals with clinical features of Frasier syndrome, including in at 3 individuals with de novo occurrence (Barbaux 1997, Bastian 20115, Guaragna 2013, Hersmus 2012, Li 2010, Lispka 2013, Wang 2017) and segregated with disease in one affected family member. It was absent from large population studies and has been reported in ClinVar (Variation ID 3500). This variant is variant is located in the 5' splice region. Computational analyses and In vitro functional studies provide some evidence that the c.1432+4C>T variant may impact protein function (Barbaux 1997); however, these types of assays may not accurately represent biological function. In summary, this variant meets criteria to be classified as pathogenic for Frasier syndrome in an autosomal dominant manner based upon de novo occurences, presence in affected individuals, absence from controls and functional evidence. ACMG/AMP Criteria applied: PM6_Strong, PP1_strong, PM2, PS3_supporting (Richards 2015). -

Mar 31, 2020

Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 09, 2024

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative is a known mechanism of disease in this gene and is associated with Denys-Drash syndrome (MIM#194080); Frasier syndrome (MIM#136680); Meacham syndrome (MIM#608978) and Nephrotic syndrome, type 4 (MIM#256370) (PMID: 32352694). Loss of function is a known mechanism of disease in this gene and is associated with Wilms tumour, type 1 (MIM#194070). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0209 - Splice site variant proven to affect splicing of the transcript with uncertain effect on protein sequence. RT-PCR of total RNA obtained from patients' samples indicated an increase in KTS- transcripts. This is suggestive of an increased use of an alternative splice site, which results in the loss of three amino acids (PMID: 9398852, 12050205). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0505 - Abnormal splicing is predicted by in silico tools and affected nucleotide is highly conserved. (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as likely pathogenic and pathogenic by multiple clinical laboratories in ClinVar. This variant has also been observed as a de novo or inherited variant in multiple individuals with Frasier syndrome (PMID: 9398852, 12050205, 30655312). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Jun 01, 2002

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Nephrotic syndrome, type 4 Pathogenic:4

Jun 01, 2002

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Dec 01, 2023

Precision Medicine Center, Zhengzhou University

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PS2,PM2_p,PP3 -

Feb 23, 2021

Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

ACMG classification criteria: PS3 supporting, PS4, PM2, PM6, PP1 -

-

Neuberg Centre For Genomic Medicine, NCGM

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The splice site donor variant c.1447+4C>T in the WT1 gene has been observed in individuals with WT1-related disorders Gomes et al., 2018. Studies have shown that this variant results in the activation of a cryptic splice site in exon 9 Buratti et al., 2007. The variant is novel not in any individuals in gnomAD Exomes and 1000 Genomes. This splice variant in intron 9 affects the position of four nucleotides downstream of exon 9. It is submitted to ClinVar as Pathogenic multiple submissions. For these reasons, this variant has been classified as Pathogenic -

Wilms tumor 1 Pathogenic:1 Other:1

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

Common pathogenic variant; typical for 46,XY 46,XY complete gonadal dysgenesis -

Dec 18, 2023

All of Us Research Program, National Institutes of Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant substitutes a C nucleotide with a T nucleotide in the +4 position of the intron 9 splice donor site in the WT1 gene. This variant is also known as c.1447+4C>T and IVS9+4C>T in the literature. RNA studies have found that this variant results in the increased splicing at an alternative donor site in exon 9, resulting in the deletion of the last nine nucleotides of exon 9 and the in-frame deletion of lysine (K), threonine (T) and serine (S) located in between zinc fingers 3 and 4 in the WT1 protein (PMID: 10792605, 34622098). Altered ratio between the two WT1 isoforms with and without the KTS motif are associated with Frasier syndrome (PMID: 9499425, 10561752). This variant has been reported in over 60 individuals affected with Frasier syndromes (PMID: 9398852, 9499425, 10094551, 10505699, 10670748, 10792605, 11007843, 12050205, 22908070, 25623218, 29668062, 34622098, 35211794, 36980135) and related clinical features (PMID: 9529364, 20442690, 23515051, 24161391, 30655312) and three individuals affected with Denys-Drash syndrome (PMID: 9475094). Among individuals diagnosed with Frasier syndrome at least one was affected with Wilms tumor and 19 individuals were affected with gonadal tumors (PMID: 10094551, 22908070, 25623218, 34622098). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Nephrotic range proteinuria Pathogenic:1

-

NIHR Bioresource Rare Diseases, University of Cambridge

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: research

- -

11p partial monosomy syndrome;C0950121:Drash syndrome;C0950122:Frasier syndrome;CN033288:Wilms tumor 1 Pathogenic:1

Sep 03, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change falls in intron 9 of the WT1 gene. It does not directly change the encoded amino acid sequence of the WT1 protein. RNA analysis indicates that this variant induces altered splicing and likely results in the loss of 3 amino acid residue(s), but is expected to preserve the integrity of the reading-frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with WT1-related disorders (PMID: 9398852, 9499425, 29668062). In at least one individual the variant was observed to be de novo. This variant is also known as IVS9+4C>T. ClinVar contains an entry for this variant (Variation ID: 3500). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in the activation of a cryptic splice site in exon 9 (PMID: 9398852, 12050205). For these reasons, this variant has been classified as Pathogenic. -

Mesothelioma, malignant;C0950121:Drash syndrome;C0950122:Frasier syndrome;C1837026:Meacham syndrome;C3151568:Nephrotic syndrome, type 4;CN033288:Wilms tumor 1 Pathogenic:1

Feb 21, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Familial idiopathic steroid-resistant nephrotic syndrome Pathogenic:1

Nov 27, 2014

Blueprint Genetics

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not provided Pathogenic:1

Dec 30, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published functional studies demonstrate a damaging effect: abnormal gene splicing (Barbaux et al., 1997); Not observed in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 1658787, 9398852, 22908070, 24856380, 17934764, 27300205, 34392242, 32838737, 31937884, 30348286, 24161391, 19484379, 21508141, 23515051, 20442690, 22815844, 9529364, 25905393, 10792605, 10670748, 9475094, 12050205, 25818337, 26668027, 16439601, 16780544, 10094551, 9499425, 25813279, 28204945, 28921387, 28476686, 29869118, 29668062, 30655312, 32581362, 32887937, 32381729, 32604935) -

WT1-related disorder Pathogenic:1

Jan 13, 2023

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The WT1 c.1432+4C>T variant is predicted to interfere with splicing. This variant has been well documented to be pathogenic for Frasier syndrome and steroid-resistant nephrotic syndrome with FSGS (Barbaux et al. 1997. PubMed ID: 9398852; Melo et al. 2002. PubMed ID: 12050205; Li et al. 2010. PubMed ID: 20442690; Lipska et al. 2013. PubMed ID: 23515051). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Benign	22
DANN	Uncertain	0.98

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.50		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.50		Position offset: 4

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs587776577; hg19: chr11-32413514; COSMIC: COSV105901703; COSMIC: COSV105901703;