Is RAB3GAP1 p.Ser797fs (c.2389del) pathogenic?

RAB3GAP1 p.Ser797fs (c.2389del) is classified Likely pathogenic in RAB3GAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-08). Associated with Martsolf syndrome 2.

What condition is associated with RAB3GAP1 p.Ser797fs (c.2389del)?

RAB3GAP1 p.Ser797fs (c.2389del) is associated with Martsolf syndrome 2, Warburg micro syndrome 1 (ClinVar).

RAB3GAP1 p.Ser797fs

c.2389del · VCV4845893

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Martsolf 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 21 of 24
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1

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

Variant & gene context

Gene: RAB3GAP1
Protein: p.Ser797fs
Coding: c.2389del
MANE Select: NM_012233
Type: Deletion
Location: chr2:135162748 (GRCh38)
Gene constraint: LOEUF 0.798 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 78.46 · 1 PDB
Residue 797: an α-helix

Full RAB3GAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Also linked: Warburg micro syndrome 1

Similar variants

RAB3GAP1 p.Pro219_Leu220insTer Pathogenic ★★ same condition
RAB3GAP1 c.2290-17_2290del Likely pathogenic ★ same condition
RAB3GAP1 p.Ala461fs Pathogenic ★ same condition
RAB3GAP1 p.Ile40fs Pathogenic ★ same condition
RAB3GAP1 p.Pro416fs Pathogenic ★ same condition
RAB3GAP1 p.Thr564_Asp565insTer Likely pathogenic ★ same condition
RAB3GAP1 p.Trp740fs Likely pathogenic ★ same condition
RAB3GAP1 p.Gly88fs Conflicting classifications of pathogenicity ★ 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/rab3gap1-p-ser797fs (accessed [today's date]).

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