Is WNT10A p.Phe294= (c.882C>T) pathogenic?

WNT10A p.Phe294= (c.882C>T) is classified Likely benign in WNT10A (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-14). Absent from gnomAD v4.1; Associated with odonto-onycho-dermal dysplasia.

What condition is associated with WNT10A p.Phe294= (c.882C>T)?

WNT10A p.Phe294= (c.882C>T) is associated with odonto-onycho-dermal dysplasia, tooth agenesis, selective, 4 (ClinVar).

How common is WNT10A p.Phe294= (c.882C>T) in the general population?

WNT10A p.Phe294= (c.882C>T) is absent from gnomAD v4.1 (gnomAD).

How is Odonto-onycho-dermal dysplasia inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

WNT10A p.Phe294=

c.882C>T · rs2469036476 · VCV2947301

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

odonto-onycho-dermal dysplasia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.29	benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.81	GERP -4.1, phastCons 1
Overall
CADD	13.59	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.Phe294=
Coding: c.882C>T
MANE Select: NM_025216
dbSNP: rs2469036476
Type: single nucleotide variant
Location: chr2:218892899 (GRCh38)
Gene constraint: LOEUF 1.484 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.36
Residue 294: a UniProt-annotated variant site (in sthag4)

Full WNT10A gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

odonto-onycho-dermal dysplasia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: tooth agenesis, selective, 4

For Odonto-onycho-dermal dysplasia (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood

Similar variants

WNT10A p.Phe294Val Uncertain significance ★ ⚠ same residue
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

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-phe294 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown