WT1 p.Thr482Lys
c.1445C>A · VCV4634876
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.46 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>A here scores Δ0.26 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.7, phastCons 1 |
| Regional constraint | o/e 0.16 | constrained · MANE · 7,138 bp · p 4.9e-17 · regional, not allelic |
| Overall | ||
| CADD | 29.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- WT1
- Protein
- p.Thr482Lys
- Coding
- c.1445C>A
- MANE Select
- NM_024426
- Type
- single nucleotide variant
- Location
- chr11:32391974 (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.Thr482Ile Uncertain significance ★ same residue
- WT1 c.1016+4A>C Uncertain significance ★★ same condition
- WT1 c.1113+5G>A Uncertain significance ★★ same condition
- WT1 c.1113+5G>C Uncertain significance ★★ same condition
- WT1 c.1448-3C>T Uncertain significance ★★ same condition
- WT1 c.888-1G>A Uncertain significance ★★ same condition
- WT1 c.965+5G>A Uncertain significance ★★ same condition
- WT1 p.Ala18Glu Uncertain significance ★★ 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-thr482lys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown