WNT10A p.Phe396=
c.1188C>T · rs1326745283 · VCV1953433
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00228%, eas)
Conditions
2
tooth agenesis, selective, 4
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 2.7 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 14.92 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00228%
East Asian · 1/43,938 alleles
Overall
0.00019%
3/1,576,426 alleles · very rare
exomes 3/1,424,054 · genomes 0/152,372 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00228% | 43,938 |
| Finnishnot grpmax-eligible | 0.00212% | 47,154 |
| European (non-Finnish) | 8.56e-05% | 1,167,624 |
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
- WNT10A
- Protein
- p.Phe396=
- Coding
- c.1188C>T
- MANE Select
- NM_025216
- dbSNP
- rs1326745283
- Type
- single nucleotide variant
- Location
- chr2:218893205 (GRCh38)
- Gene constraint
- LOEUF 1.484 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.36
- Residue 396
- a UniProt-annotated variant site (in sthag4); a UniProt-annotated variant site (found in patients with dental anomalies; uncertain significance)
Similar variants
- WNT10A c.113+1G>A Likely pathogenic ★★ same condition
- WNT10A c.113+1G>T Likely pathogenic ★★ same condition
- WNT10A c.376+1G>A Pathogenic ★★ same condition
- WNT10A p.Ala131Thr Pathogenic/Likely pathogenic ★★ same condition
- WNT10A p.Ala297Thr Likely pathogenic ★★ same condition
- WNT10A p.Arg104Cys Pathogenic/Likely pathogenic ★★ same condition
- WNT10A p.Arg128Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- WNT10A p.Arg13Ter 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/wnt10a-p-phe396 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown