WNT4 p.Pro96=
c.288C>T · rs566208847 · VCV2731317
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.038 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -4.1 |
| Overall | ||
| CADD | 0.147 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
East Asian · 7/44,864 alleles
Filtering AF
0.00726%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00515%
Overall
0.00062%
10/1,613,588 alleles · ultra-rare
exomes 7/1,461,280 · genomes 3/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0156% | 6,409 |
| African / African-American | 0.00133% | 75,054 |
| European (non-Finnish) | 0.000169% | 589,995 |
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
- WNT4
- Protein
- p.Pro96=
- Coding
- c.288C>T
- MANE Select
- NM_030761
- dbSNP
- rs566208847
- Type
- single nucleotide variant
- Location
- chr1:22129641 (GRCh38)
- Gene constraint
- LOEUF 0.694 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 91.41
Similar variants
- WNT4 p.Pro96Arg Uncertain significance ★ same residue
- 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
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-pro96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown