RAB3GAP2 p.Ala841=
c.2523G>A · rs201668103 · VCV1970665
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
Conditions
2
Warburg micro syndrome 2
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 -7.3 | GERP -3.6 |
| Overall | ||
| CADD | 4.291 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,928 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00161%
26/1,614,076 alleles · very rare
exomes 21/1,461,878 · genomes 5/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,732 |
| Admixed American | 0.00167% | 60,006 |
| European (non-Finnish) | 0.00161% | 62,107 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| South Asian | 0.0011% | 91,080 |
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.Ala841=
- Coding
- c.2523G>A
- MANE Select
- NM_012414
- dbSNP
- rs201668103
- Type
- single nucleotide variant
- Location
- chr1:220171943 (GRCh38)
- Gene constraint
- LOEUF 0.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.77 · 1 PDB
Similar variants
- RAB3GAP2 p.Ala841Val Uncertain significance ★★ ⚠ same residue
- RAB3GAP2 c.713-2A>C Likely pathogenic ★★ same condition
- RAB3GAP2 p.Arg1213Ter Pathogenic ★★ same condition
- RAB3GAP2 p.Arg426Cys Pathogenic/Likely pathogenic ★★ same condition
- RAB3GAP2 c.*2171A>G Uncertain significance ★★ same condition
- RAB3GAP2 p.Ala16Thr Uncertain significance ★★ ⚠ same condition
- RAB3GAP2 p.Ala240Pro Uncertain significance ★★ ⚠ same condition
- RAB3GAP2 p.Ala300Thr 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/rab3gap2-p-ala841 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown