RAB3GAP2 p.Ser869=
c.2607A>G · rs1658167378 · VCV3029288
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000847%, nfe)
Conditions
1
RAB3GAP2-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 -7.2 | GERP -3.6 |
| Overall | ||
| CADD | 5.356 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000847%
European (non-Finnish) · 10/1,179,998 alleles
Filtering AF
0.000429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000312%
Overall
0.00062%
10/1,614,164 alleles · very rare
exomes 10/1,461,830 · genomes 0/152,334 · 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.Ser869=
- Coding
- c.2607A>G
- MANE Select
- NM_012414
- dbSNP
- rs1658167378
- Type
- single nucleotide variant
- Location
- chr1:220171091 (GRCh38)
- Gene constraint
- LOEUF 0.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.77 · 1 PDB
Disease context
RAB3GAP2-related disorder
Similar variants
- RAB3GAP2 c.3225+1G>A Likely pathogenic ★ same condition
- RAB3GAP2 p.Arg699Ter Likely pathogenic ★ same condition
- RAB3GAP2 p.Leu411= Likely benign same condition
- RAB3GAP2 p.Arg1272del Likely pathogenic ★ same condition
- RAB3GAP2 p.Ile265fs Likely pathogenic ★ same condition
- RAB3GAP2 p.Val698fs Likely pathogenic ★ same condition
- RAB3GAP2 c.713-2A>C Likely pathogenic ★★ same type
- RAB3GAP2 p.Arg1213Ter 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-ser869 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown