Is RAB3GAP2 p.Asp656fs (c.1966del) pathogenic?

RAB3GAP2 p.Asp656fs (c.1966del) is classified Likely pathogenic in RAB3GAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-03). No gnomAD frequency available for this variant.

How common is RAB3GAP2 p.Asp656fs (c.1966del) in the general population?

RAB3GAP2 p.Asp656fs (c.1966del) is no gnomAD frequency available for this variant (gnomAD).

RAB3GAP2 p.Asp656fs

c.1966del · rs2102866080 · VCV1319795

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 19 of 35
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.17	GERP -1.8

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.Asp656fs
Coding: c.1966del
MANE Select: NM_012414
dbSNP: rs2102866080
Type: Deletion
Location: chr1:220184068 (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

Similar variants

RAB3GAP2 c.1715-8del Likely benign ★★ same type
RAB3GAP2 c.613-14del Benign ★★ same type
RAB3GAP2 c.812-6del Benign ★★ same type
RAB3GAP2 c.812-7_812-6del Benign/Likely benign ★★ same type
RAB3GAP2 c.3645+1del Likely pathogenic ★ same type
RAB3GAP2 p.Ala400_Val401insTer Likely pathogenic ★ same type
RAB3GAP2 p.Ala762_Gly763insTer Likely pathogenic ★ same type
RAB3GAP2 p.Arg1083fs Likely pathogenic ★ same type

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-asp656fs (accessed [today's date]).

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