RAB3GAP2 p.Ala1130=
c.3390G>A · rs140377995 · VCV295642
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0676%, nfe)
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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.4 | GERP -3 |
| Overall | ||
| CADD | 2.362 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0676%
European (non-Finnish) · 798/1,180,018 alleles
Filtering AF
0.0637%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0621%
Overall
0.0541%
873/1,613,994 alleles · ultra-rare
exomes 801/1,461,812 · genomes 72/152,182 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0676% | 1,479 |
| Middle Eastern | 0.0665% | 1,504 |
| Remaining individualsnot grpmax-eligible | 0.0528% | 1,894 |
| Admixed American | 0.0333% | 3,000 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0203% | 4,934 |
| African / African-American | 0.00667% | 14,998 |
| South Asian | 0.00549% | 18,215 |
| East Asian | 0.00223% | 44,872 |
| Finnishnot grpmax-eligible | 0.00156% | 64,004 |
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.Ala1130=
- Coding
- c.3390G>A
- MANE Select
- NM_012414
- dbSNP
- rs140377995
- Type
- single nucleotide variant
- Location
- chr1:220157435 (GRCh38)
- Gene constraint
- LOEUF 0.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.77 · 1 PDB
Similar variants
- 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
- RAB3GAP2 p.Ala684Glu 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-ala1130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown