Is DVL1 p.Pro533fs (c.1598del) pathogenic?

DVL1 p.Pro533fs (c.1598del) is classified Pathogenic in DVL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2015-12-01). Absent from gnomAD; Associated with autosomal dominant Robinow syndrome 2.

What condition is associated with DVL1 p.Pro533fs (c.1598del)?

DVL1 p.Pro533fs (c.1598del) is associated with autosomal dominant Robinow syndrome 2 (ClinVar).

How common is DVL1 p.Pro533fs (c.1598del) in the general population?

DVL1 p.Pro533fs (c.1598del) is absent from gnomAD (gnomAD).

DVL1 p.Pro533fs

c.1598del · rs869025220 · VCV219223

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 2

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 -0.87	GERP -4.7

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: DVL1
Protein: p.Pro533fs
Coding: c.1598del
MANE Select: NM_001330311
dbSNP: rs869025220
Type: Deletion
Location: chr1:1338093 (GRCh38)
Gene constraint: LOEUF 1.046 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 60.70 · 3 PDB

Full DVL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autosomal dominant Robinow syndrome 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DVL1 p.Pro524fs Pathogenic/Likely pathogenic ★★ same condition
DVL1 p.Ser567fs Pathogenic ★★ same condition
DVL1 p.Thr516fs Pathogenic/Likely pathogenic ★★ same condition
DVL1 p.Trp532fs Pathogenic ★★ same condition
DVL1 p.Gly535fs Pathogenic ★ same condition
DVL1 p.Gly544fs Pathogenic ★ same condition
DVL1 p.His527fs Pathogenic ★ same condition
DVL1 p.Pro528fs 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/dvl1-p-pro533fs (accessed [today's date]).

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