WNT4 p.Pro147=
c.441A>G · VCV4806812
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.9 | GERP -4 |
| Overall | ||
| CADD | 0.762 | 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
- WNT4
- Protein
- p.Pro147=
- Coding
- c.441A>G
- MANE Select
- NM_030761
- Type
- single nucleotide variant
- Location
- chr1:22121449 (GRCh38)
- Gene constraint
- LOEUF 0.694 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 91.41
Similar variants
- WNT4 p.Ala114Ser Uncertain significance ★★ ⚠ same type
- WNT4 p.Ala223Thr Uncertain significance ★★ ⚠ same type
- WNT4 p.Arg126Gln Uncertain significance ★★ ⚠ same type
- WNT4 p.Arg126Trp Uncertain significance ★★ ⚠ same type
- WNT4 p.Arg247Cys Uncertain significance ★★ same type
- WNT4 p.Arg285His Uncertain significance ★★ ⚠ same type
- WNT4 p.Arg294His Uncertain significance ★★ ⚠ same type
- WNT4 p.Arg85Gln Uncertain significance ★★ ⚠ same type
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/wnt4-p-pro147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown