WNT3A p.Phe169=
c.507C>T · rs141170201 · VCV1586441
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.121%, afr)
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 -3.2 | GERP -5.6 |
| Overall | ||
| CADD | 4.449 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.121%
African / African-American · 90/74,168 alleles
Filtering AF
0.101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0935%
Overall
0.00795%
127/1,597,082 alleles · rare
exomes 67/1,445,256 · genomes 60/151,826 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.121% | 824 |
| Admixed American | 0.0191% | 5,239 |
| Remaining individualsnot grpmax-eligible | 0.00974% | 10,264 |
| South Asian | 0.00777% | 12,867 |
| East Asian | 0.00225% | 44,532 |
| European (non-Finnish) | 0.00103% | 97,491 |
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
- WNT3A
- Protein
- p.Phe169=
- Coding
- c.507C>T
- MANE Select
- NM_033131
- dbSNP
- rs141170201
- Type
- single nucleotide variant
- Location
- chr1:228050849 (GRCh38)
- Gene constraint
- LOEUF 0.76 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 88.62 · 4 PDB
- Residue 169
- an α-helix
Similar variants
- WNT3A p.Ala318Pro Uncertain significance ★★ ⚠ same type
- WNT3A p.Arg141His Uncertain significance ★★ ⚠ same type
- WNT3A p.Arg141Pro Uncertain significance ★★ ⚠ same type
- WNT3A p.Arg322Gln Uncertain significance ★★ ⚠ same type
- WNT3A p.Arg324Trp Uncertain significance ★★ ⚠ same type
- WNT3A p.Arg82His Uncertain significance ★★ ⚠ same type
- WNT3A p.Glu160Lys Uncertain significance ★★ ⚠ same type
- WNT3A p.Glu68Lys 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/wnt3a-p-phe169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown