RAB3GAP1 p.Val328=
c.984C>T · VCV3354745
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Conditions
1
RAB3GAP1-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.24 | GERP -0.82, phastCons 0.26 |
| Overall | ||
| CADD | 5.696 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,173,372 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000125%
2/1,603,028 alleles · very rare
exomes 2/1,452,794 · genomes 0/150,234 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- RAB3GAP1
- Protein
- p.Val328=
- Coding
- c.984C>T
- MANE Select
- NM_012233
- Type
- single nucleotide variant
- Location
- chr2:135130005 (GRCh38)
- Gene constraint
- LOEUF 0.798 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.46 · 1 PDB
Disease context
RAB3GAP1-related disorder
Similar variants
- RAB3GAP1 c.18+1G>C Likely pathogenic ★★ same condition
- RAB3GAP1 c.899+1G>A Pathogenic ★★ same condition
- RAB3GAP1 p.Arg174Ter Pathogenic/Likely pathogenic ★★ same condition
- RAB3GAP1 p.Arg337Ter Pathogenic/Likely pathogenic ★★ same condition
- RAB3GAP1 p.Arg491Ter Pathogenic ★★ same condition
- RAB3GAP1 p.Arg315Ter Pathogenic ★ same condition
- RAB3GAP1 p.Val328fs Pathogenic ★ same residue
- RAB3GAP1 p.Arg942Pro Uncertain significance ★ ⚠ 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-val328 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown