WNT1 p.Pro237=
c.711C>T · rs1592257842 · VCV740378
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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.7 | GERP -4.8, phastCons 1 |
| Overall | ||
| CADD | 14.11 | 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
- WNT1
- Protein
- p.Pro237=
- Coding
- c.711C>T
- MANE Select
- NM_005430
- dbSNP
- rs1592257842
- Type
- single nucleotide variant
- Location
- chr12:48981238 (GRCh38)
- Gene constraint
- LOEUF 0.957 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.53
Similar variants
- WNT1 p.Pro237_Leu239del Uncertain significance ★ same residue
- WNT1 p.Ala133Thr Likely pathogenic ★★ same type
- WNT1 p.Cys227Ter Pathogenic/Likely pathogenic ★★ same type
- WNT1 p.Gly222Arg Likely pathogenic ★★ same type
- WNT1 p.Phe298Cys Likely pathogenic ★★ same type
- WNT1 p.Ser295Ter Pathogenic/Likely pathogenic ★★ same type
- WNT1 p.Trp167Cys Pathogenic/Likely pathogenic ★★ same type
- WNT1 p.Ala18Thr 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/wnt1-p-pro237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown