Is WNT3 p.Ser264= (c.792G>A) pathogenic?

WNT3 p.Ser264= (c.792G>A) is classified Likely benign in WNT3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-07). Very rare (popmax 0.004%, afr).

How common is WNT3 p.Ser264= (c.792G>A) in the general population?

WNT3 p.Ser264= (c.792G>A) is very rare (popmax 0.004%, afr) (gnomAD).

WNT3 p.Ser264=

c.792G>A · rs374511226 · VCV1528068

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.004%, afr)

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -11	GERP -1.9
Overall
CADD	2.527	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.004% African / African-American · 3/74,928 alleles

Filtering AF 0.00164% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00142%

Overall 0.00198% 32/1,614,050 alleles · very rare exomes 28/1,461,852 · genomes 4/152,198 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.004%	24,976
European (non-Finnish)	0.00237%	42,145
Admixed American	0.00167%	60,008

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: WNT3
Protein: p.Ser264=
Coding: c.792G>A
MANE Select: NM_030753
dbSNP: rs374511226
Type: single nucleotide variant
Location: chr17:46768596 (GRCh38)

Full WNT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

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/wnt3-p-ser264 (accessed [today's date]).

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