rs121907903
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PM5PP3
The ENST00000452863.10(WT1):c.1400G>T(p.Arg467Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 10/17 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as other (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R467Q) has been classified as Likely pathogenic.
Frequency
Consequence
ENST00000452863.10 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
WT1 | NM_024426.6 | c.1400G>T | p.Arg467Leu | missense_variant | 9/10 | ENST00000452863.10 | NP_077744.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
WT1 | ENST00000452863.10 | c.1400G>T | p.Arg467Leu | missense_variant | 9/10 | 1 | NM_024426.6 | ENSP00000415516 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Acute myeloid leukemia Other:1
-, no assertion criteria provided | clinical testing | Molecular Diagnostics Laboratory, Fox Chase Cancer Center - Temple Health | Jan 24, 2024 | This variant was detected in a relapsed acute myeloid leukemia patient as a somatic mutation accompanied by a AKAP9::PDGFRA translocation. This variant is similar to WT1 p.Arg467Pro, which also substitutes a non-polar amino acid for the charged polar Arg and was classified Pathogenic in ClinVar (VCV000003491.3). ClinVar accession VCV000419332.13 classifies WT1 p.Arg467Gln as Likely Pathogenic/Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.