Submissions for variant NM_024426.6(WT1):c.151del (p.Ala51fs)

gnomAD frequency: 0.00003  dbSNP: rs776155094

Total submissions: 5

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000255852	SCV000322013	uncertain significance	not provided	2023-06-23	criteria provided, single submitter	clinical testing	Nonsense variant predicted to result in protein truncation; however a downstream in-frame ATG could serve as an alternate initiator codon which may result in a smaller, yet still functional, protein (Bruenig et al., 1996; Scharnhorst et al., 1999; Yang et al., 2007).; Not observed at significant frequency in large population cohorts (gnomAD); Observed in individuals with pancreatic cancer and pediatric glioma (Skaro et al., 2019; Muskens et al., 2020); Also known as c.151del/p.(A51Pfs*31); This variant is associated with the following publications: (PMID: 26633542, 30665703, 31970404, 30716324, 8621495, 10438524, 17361230)
Invitae	RCV000705265	SCV000834254	uncertain significance	Drash syndrome; Frasier syndrome; Wilms tumor 1; 11p partial monosomy syndrome	2023-11-02	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Ala46Profs*31) in the WT1 gene. It is unclear whether it will result in an absent or disrupted protein product because a major initiation site located at codon 69 has the potential to rescue this variant. This variant is present in population databases (rs776155094, gnomAD 0.002%). This premature translational stop signal has been observed in individual(s) with anaplastic astrocytoma (PMID: 31970404). ClinVar contains an entry for this variant (Variation ID: 265295). Downstream of the non-canonical translation start site (CTG) at codon 1, the nearest methionine codon that can be used to initiate translation of the WT1 protein lies at codon 69. This downstream in-frame ATG is known as a major initiation site (PMID: 28811308, 16987884, 8621495). The functional significance of the different WT1 protein isoforms is unknown (PMID: 8621495), however mice lacking the N-terminal 68 amino acids develop normally and are fertile (PMID: 12640141). Based on these results, the impact of this variant on WT1 protein function is uncertain. 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.
St. Jude Molecular Pathology, St. Jude Children's Research Hospital	RCV000722020	SCV000853195	likely pathogenic	Precursor B-cell acute lymphoblastic leukemia	2016-03-16	criteria provided, single submitter	clinical testing	This is a frameshift variant, in which a G is deleted at coding position 136 and is predicted to change an Alanine to a Proline and shift the reading frame.
Baylor Genetics	RCV003463715	SCV004208935	uncertain significance	Drash syndrome	2023-09-03	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV003967694	SCV004783346	uncertain significance	WT1-related condition	2024-02-29	criteria provided, single submitter	clinical testing	The WT1 c.136delG variant is predicted to result in a frameshift and premature protein termination (p.Ala46Profs*31). This variant has been reported in an individual with anaplastic astrocytoma (Muskens et al. 2020. PubMed ID: 31970404) and another individual with intraductal papillary mucinous neoplasms (IPMNs) at risk for developing pancreatic cancer (Skaro et al. 2019. PubMed ID: 30716324), but it has not been reported in patients with established WT-related disorders. This variant would typically be expected to cause a frameshift leading to premature termination; however there is a downstream, in-frame methionine residue (p.Met69) that has been shown to act as an alternate initiation site and potentially rescue WT1 translation (Bruening and Pelletier. 1996. PubMed ID: 8621495; Scharnhorst et al. 1999. PubMed ID: 10438524). Furthermore, significant N-terminal variation has been observed in functional WT1 isoforms (same studies), and a mouse model lacking the 68 N-terminal amino acids developed normally and remained capable of reproduction (Miles et al. 2003. PubMed ID: 12640141). This variant is reported in 0.0020% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as a variant of uncertain significance by most submitters in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/265295/). Taken together, the clinical significance of this variant is uncertain at this time due to the absence of conclusive functional and genetic evidence.