RAB3GAP2 p.Ser905=
c.2715C>T · rs775564285 · VCV391686
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00339%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 10.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00339%
European (non-Finnish) · 40/1,180,036 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00225%
Overall
0.00273%
44/1,614,084 alleles · very rare
exomes 42/1,461,868 · genomes 2/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00339% | 29,501 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| Admixed American | 0.00167% | 60,008 |
| African / African-American | 0.00133% | 74,934 |
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.Ser905=
- Coding
- c.2715C>T
- MANE Select
- NM_012414
- dbSNP
- rs775564285
- Type
- single nucleotide variant
- Location
- chr1:220170983 (GRCh38)
- Gene constraint
- LOEUF 0.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.77 · 1 PDB
Similar variants
- RAB3GAP2 p.Ser905Gly Uncertain significance ★ ⚠ same residue
- 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
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-ser905 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown