Is DVL3 p.Pro531fs (c.1592del) pathogenic?

DVL3 p.Pro531fs (c.1592del) is classified Pathogenic in DVL3 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-12-31). Absent from gnomAD; Associated with autosomal dominant Robinow syndrome 3.

What condition is associated with DVL3 p.Pro531fs (c.1592del)?

DVL3 p.Pro531fs (c.1592del) is associated with autosomal dominant Robinow syndrome 3 (ClinVar).

How common is DVL3 p.Pro531fs (c.1592del) in the general population?

DVL3 p.Pro531fs (c.1592del) is absent from gnomAD (gnomAD).

DVL3 p.Pro531fs

c.1592del · rs1577052471 · VCV689755

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

autosomal dominant Robinow syndrome 3

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 14 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.7	GERP 0.45, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DVL3
Protein: p.Pro531fs
Coding: c.1592del
MANE Select: NM_004423
dbSNP: rs1577052471
Type: Deletion
Location: chr3:184170096 (GRCh38)
Gene constraint: LOEUF 0.536 · pLI 0.70 (gnomAD)
Structure: AlphaFold pLDDT 59.50 · 9 PDB

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

Disease context

autosomal dominant Robinow syndrome 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DVL3 p.Ala529fs Pathogenic ★ same condition
DVL3 p.Asp584fs Pathogenic ★ same condition
DVL3 p.Ser573fs Pathogenic ★ same condition
DVL3 p.Ser583fs Pathogenic ★ same condition
DVL3 p.Tyr558fs Pathogenic ★ same condition
DVL3 p.Pro531Ser Uncertain significance ★ ⚠ same residue
DVL3 c.1715-2del Likely pathogenic same condition
DVL3 p.Glu98fs 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/dvl3-p-pro531fs (accessed [today's date]).

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