Is WNT3 p.Phe293Val (c.877T>G) pathogenic?

WNT3 p.Phe293Val (c.877T>G) is classified Uncertain significance in WNT3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-31). AlphaMissense: ambiguous (0.4254); Absent from gnomAD v4.1.

How common is WNT3 p.Phe293Val (c.877T>G) in the general population?

WNT3 p.Phe293Val (c.877T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about WNT3 p.Phe293Val (c.877T>G)?

AlphaMissense predicts ambiguous (score 0.4254) — an in-silico prediction, not a clinical call.

WNT3 p.Phe293Val

c.877T>G · rs2545981494 · VCV2766983

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4254 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

⚠ 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
AlphaMissense	0.4254	ambiguous
REVEL	0.455	indeterminate
SaProt	LLR -4.28	tolerated
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 11	GERP 3.9, phastCons 1
Regional constraint	o/e 0.46	unconstrained · MANE · 50 kb · p 2.1e-26 · regional, not allelic
Overall
CADD	28.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: WNT3
Protein: p.Phe293Val
Coding: c.877T>G
MANE Select: NM_030753
dbSNP: rs2545981494
Type: single nucleotide variant
Location: chr17:46768511 (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-phe293val (accessed [today's date]).

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