Is DVL3 p.Ile477Val (c.1429A>G) pathogenic?

DVL3 p.Ile477Val (c.1429A>G) is classified Uncertain significance in DVL3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-27). AlphaMissense: ambiguous (0.4217); Very rare (popmax 0.00549%, sas).

How common is DVL3 p.Ile477Val (c.1429A>G) in the general population?

DVL3 p.Ile477Val (c.1429A>G) is very rare (popmax 0.00549%, sas) (gnomAD).

What do computational predictors say about DVL3 p.Ile477Val (c.1429A>G)?

AlphaMissense predicts ambiguous (score 0.4217) — an in-silico prediction, not a clinical call.

DVL3 p.Ile477Val

c.1429A>G · rs765018237 · VCV2969398

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4217 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00549%, sas)

Computational evidence

Protein change
AlphaMissense	0.4217	ambiguous
REVEL	0.365	indeterminate
SaProt	LLR -9.59	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.2	GERP 1.4, phastCons 1
Regional constraint	o/e 0.54	unconstrained · MANE · 1,228 bp · p 5.8e-11 · regional, not allelic
Overall
CADD	25.9	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

Grpmax group 0.00549% South Asian · 5/91,094 alleles

Filtering AF 0.0021% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00136%

Overall 0.000434% 7/1,614,158 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00549%	18,219
Remaining individualsnot grpmax-eligible	0.0032%	31,243

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: DVL3
Protein: p.Ile477Val
Coding: c.1429A>G
MANE Select: NM_004423
dbSNP: rs765018237
Type: single nucleotide variant
Location: chr3:184167996 (GRCh38)
Gene constraint: LOEUF 0.536 · pLI 0.70 (gnomAD)
Structure: AlphaFold pLDDT 59.50 · 9 PDB
Residue 477: the dep domain

Full DVL3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DVL3 c.1715-1G>A Pathogenic/Likely pathogenic ★★ same type
DVL3 p.Ala359Thr Uncertain significance ★★ ⚠ same type
DVL3 p.Ala565Val Uncertain significance ★★ ⚠ same type
DVL3 p.Ala593Val Uncertain significance ★★ ⚠ same type
DVL3 p.Ala629Thr Uncertain significance ★★ ⚠ same type
DVL3 p.Arg145Gln Uncertain significance ★★ ⚠ same type
DVL3 p.Arg157Gln Uncertain significance ★★ ⚠ same type
DVL3 p.Arg166Trp Uncertain significance ★★ ⚠ same type

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/dvl3-p-ile477val (accessed [today's date]).

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