WNT10A p.Val337=
c.1011C>A · rs748769072 · VCV1617550
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
odonto-onycho-dermal dysplasia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.029 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.2 | GERP 1.1, phastCons 0.97 |
| Overall | ||
| CADD | 12.39 | 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
- WNT10A
- Protein
- p.Val337=
- Coding
- c.1011C>A
- MANE Select
- NM_025216
- dbSNP
- rs748769072
- Type
- single nucleotide variant
- Location
- chr2:218893028 (GRCh38)
- Gene constraint
- LOEUF 1.484 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.36
- Residue 337
- a UniProt-annotated variant site (in sthag4)
Disease context
odonto-onycho-dermal dysplasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: tooth agenesis, selective, 4
For Odonto-onycho-dermal dysplasia (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Childhood
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-val337 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown