RAB3GAP2 p.Pro60=
c.180T>A · rs138809681 · VCV463028
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0669%, eas)
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 -0.046 | GERP 0.58, phastCons 0.014 |
| Overall | ||
| CADD | 6.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0669%
East Asian · 30/44,838 alleles
Filtering AF
0.0481%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0417%
Overall
0.00192%
31/1,611,430 alleles · ultra-rare
exomes 27/1,459,084 · genomes 4/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0669% | 1,495 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,438 |
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.Pro60=
- Coding
- c.180T>A
- MANE Select
- NM_012414
- dbSNP
- rs138809681
- Type
- single nucleotide variant
- Location
- chr1:220232799 (GRCh38)
- Gene constraint
- LOEUF 0.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.77 · 1 PDB
- Residue 60
- the 'disordered' region
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-pro60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown