WT1 p.Pro381=
c.1143G>A · rs1554939849 · VCV543155
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
5
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.053 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -4.8 | GERP -5.4 |
| Overall | ||
| CADD | 8.474 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,032 alleles
Overall
6.2e-05%
1/1,614,066 alleles · very rare
exomes 1/1,461,824 · genomes 0/152,242 · 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.Pro381=
- Coding
- c.1143G>A
- MANE Select
- NM_024426
- dbSNP
- rs1554939849
- Type
- single nucleotide variant
- Location
- chr11:32396378 (GRCh38)
- Gene constraint
- LOEUF 0.253 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 52.09 · 31 PDB
- Residue 381
- the 'important for interaction with target dna' region
Similar variants
- WT1 p.Pro381Leu Uncertain significance ★★ same residue
- WT1 p.Pro381Ala Uncertain significance ★ same residue
- WT1 p.Pro381Gln Uncertain significance ★ same residue
- WT1 p.Pro381Ser Conflicting classifications of pathogenicity ★ same residue
- WT1 p.Pro381fs Likely pathogenic ★ 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
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-pro381 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown