Is RAB3GAP2 p.Pro1332fs (c.3995del) pathogenic?

RAB3GAP2 p.Pro1332fs (c.3995del) is classified Uncertain significance in RAB3GAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-15). No gnomAD frequency available for this variant; Associated with Warburg micro syndrome 2.

What condition is associated with RAB3GAP2 p.Pro1332fs (c.3995del)?

RAB3GAP2 p.Pro1332fs (c.3995del) is associated with Warburg micro syndrome 2, Martsolf syndrome (ClinVar).

How common is RAB3GAP2 p.Pro1332fs (c.3995del) in the general population?

RAB3GAP2 p.Pro1332fs (c.3995del) is no gnomAD frequency available for this variant (gnomAD).

RAB3GAP2 p.Pro1332fs

c.3995del · rs2528604812 · VCV1928960

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Warburg micro 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	escapes	premature termination codon within the last 50 nt of the penultimate exon (34 of 35, 31 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -11	GERP -3.6

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: RAB3GAP2
Protein: p.Pro1332fs
Coding: c.3995del
MANE Select: NM_012414
dbSNP: rs2528604812
Type: Deletion
Location: chr1:220151637 (GRCh38)
Gene constraint: LOEUF 0.535 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.77 · 1 PDB

Full RAB3GAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Also linked: Martsolf syndrome

Similar variants

RAB3GAP2 p.Pro1332= Likely benign ★ same residue
RAB3GAP2 c.1715-8del Likely benign ★★ same condition
RAB3GAP2 c.613-14del Benign ★★ same condition
RAB3GAP2 c.812-6del Benign ★★ same condition
RAB3GAP2 c.812-7_812-6del Benign/Likely benign ★★ same condition
RAB3GAP2 p.Ala400_Val401insTer Likely pathogenic ★ same condition
RAB3GAP2 p.Gly242fs Likely pathogenic ★ same condition
RAB3GAP2 p.Met114fs 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/rab3gap2-p-pro1332fs (accessed [today's date]).

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