RAB3GAP2 p.Arg229=
c.687T>C · VCV4823599
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.034 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 10.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,006 alleles
Overall
6.21e-05%
1/1,609,284 alleles · very rare
exomes 1/1,456,946 · genomes 0/152,338 · 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
- RAB3GAP2
- Protein
- p.Arg229=
- Coding
- c.687T>C
- MANE Select
- NM_012414
- Type
- single nucleotide variant
- Location
- chr1:220205932 (GRCh38)
- Gene constraint
- LOEUF 0.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.77 · 1 PDB
- Residue 229
- an α-helix
Similar variants
- RAB3GAP2 c.713-2A>C Likely pathogenic ★★ same type
- RAB3GAP2 p.Arg1213Ter Pathogenic ★★ same type
- RAB3GAP2 p.Arg426Cys Pathogenic/Likely pathogenic ★★ same type
- RAB3GAP2 c.1631+8G>T Uncertain significance ★★ same type
- RAB3GAP2 c.*2171A>G Uncertain significance ★★ same type
- RAB3GAP2 p.Ala16Thr Uncertain significance ★★ ⚠ same type
- RAB3GAP2 p.Ala240Pro Uncertain significance ★★ ⚠ same type
- RAB3GAP2 p.Ala300Thr Uncertain significance ★★ ⚠ 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-arg229 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown