Is WNT10A p.Ser366= (c.1098C>T) pathogenic?

WNT10A p.Ser366= (c.1098C>T) is classified Likely benign in WNT10A (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-21). Ultra-rare (popmax 0.0344%, mid); Associated with odonto-onycho-dermal dysplasia.

What condition is associated with WNT10A p.Ser366= (c.1098C>T)?

WNT10A p.Ser366= (c.1098C>T) is associated with odonto-onycho-dermal dysplasia, tooth agenesis, selective, 4 (ClinVar).

How common is WNT10A p.Ser366= (c.1098C>T) in the general population?

WNT10A p.Ser366= (c.1098C>T) is ultra-rare (popmax 0.0344%, mid) (gnomAD).

How is Odonto-onycho-dermal dysplasia inherited?

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

WNT10A p.Ser366=

c.1098C>T · rs748882359 · VCV1128786

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0344%, mid)

Conditions

odonto-onycho-dermal dysplasia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.079	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.098	GERP -3.9, phastCons 0.002
Overall
CADD	12.6	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0344% Middle Eastern · 2/5,818 alleles

Filtering AF 0.00604% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0025%

Overall 0.000815% 13/1,595,364 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0344%	2,909
Remaining individualsnot grpmax-eligible	0.00161%	62,106
African / African-American	0.00134%	74,870
European (non-Finnish)	0.000764%	130,948

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.Ser366=
Coding: c.1098C>T
MANE Select: NM_025216
dbSNP: rs748882359
Type: single nucleotide variant
Location: chr2:218893115 (GRCh38)
Gene constraint: LOEUF 1.484 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.36
Residue 366: a disulfide bond; a UniProt-annotated variant site (in sthag4); a UniProt-annotated variant site (found in patients with dental anomalies; uncertain significance)

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.Ser366Arg 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-ser366 (accessed [today's date]).

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