WT1 p.Ala242=
c.726G>T · rs1473494675 · VCV476717
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Conditions
4
WAGR syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.9 | GERP -4.5 |
| Overall | ||
| CADD | 7.619 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,024 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,074 alleles · very rare
exomes 2/1,461,780 · genomes 0/152,294 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- WT1
- Protein
- p.Ala242=
- Coding
- c.726G>T
- MANE Select
- NM_024426
- dbSNP
- rs1473494675
- Type
- single nucleotide variant
- Location
- chr11:32428555 (GRCh38)
- Gene constraint
- LOEUF 0.253 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 52.09 · 31 PDB
Similar variants
- WT1 p.Ala242Thr Uncertain significance ★★ same residue
- WT1 p.Ala242Val Uncertain significance ★★ same residue
- WT1 p.Ala242Glu Uncertain significance ★ same residue
- WT1 c.1354+2T>C Pathogenic/Likely pathogenic ★★ same condition
- WT1 c.1447+2T>C Pathogenic ★★ same condition
- WT1 c.1447+4C>T Pathogenic/Likely pathogenic ★★ same condition
- WT1 c.1447+5G>A Pathogenic/Likely pathogenic ★★ same condition
- WT1 c.1448-1G>A Pathogenic/Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/wt1-p-ala242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown