Is DVL3 p.Arg113= (c.339A>T) pathogenic?

DVL3 p.Arg113= (c.339A>T) is classified Likely benign in DVL3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-07-06). Absent from gnomAD v4.1; Associated with DVL3-related disorder.

What condition is associated with DVL3 p.Arg113= (c.339A>T)?

DVL3 p.Arg113= (c.339A>T) is associated with DVL3-related disorder (ClinVar).

How common is DVL3 p.Arg113= (c.339A>T) in the general population?

DVL3 p.Arg113= (c.339A>T) is absent from gnomAD v4.1 (gnomAD).

DVL3 p.Arg113=

c.339A>T · rs2473697509 · VCV3048202

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

DVL3-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.8	GERP -3.1, phastCons 1
Overall
CADD	9.058	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: DVL3
Protein: p.Arg113=
Coding: c.339A>T
MANE Select: NM_004423
dbSNP: rs2473697509
Type: single nucleotide variant
Location: chr3:184164374 (GRCh38)
Gene constraint: LOEUF 0.536 · pLI 0.70 (gnomAD)
Structure: AlphaFold pLDDT 59.50 · 9 PDB
Residue 113: the 'disordered' region

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

Disease context

DVL3-related disorder

Similar variants

DVL3 p.Arg113Ter Likely benign ★ same residue
DVL3 p.Ser646Arg Uncertain significance ★★ ⚠ same condition
DVL3 p.Arg73Gln Uncertain significance ★ ⚠ same condition
DVL3 p.Asp510Tyr Uncertain significance ★ ⚠ same condition
DVL3 p.Pro683Leu Uncertain significance ★ ⚠ same condition
DVL3 c.354-6C>T Likely benign same condition
DVL3 c.763+9G>A Likely benign same condition
DVL3 p.Arg619= Likely benign 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/dvl3-p-arg113 (accessed [today's date]).

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