RAB3GAP1 p.Pro7=
c.21C>G · rs776821620 · VCV1594330
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0166%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.27 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.22 | GERP -1.8, phastCons 0.97 |
| Overall | ||
| CADD | 15.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0166%
Middle Eastern · 1/6,014 alleles
Filtering AF
0.000878%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000717%
Overall
0.00124%
20/1,614,094 alleles · ultra-rare
exomes 17/1,461,830 · genomes 3/152,264 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0166% | 6,014 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,498 |
| European (non-Finnish) | 0.00144% | 69,414 |
| South Asian | 0.0011% | 91,084 |
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
- RAB3GAP1
- Protein
- p.Pro7=
- Coding
- c.21C>G
- MANE Select
- NM_012233
- dbSNP
- rs776821620
- Type
- single nucleotide variant
- Location
- chr2:135052432 (GRCh38)
- Gene constraint
- LOEUF 0.798 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.46 · 1 PDB
Similar variants
- RAB3GAP1 c.18+1G>C Likely pathogenic ★★ same type
- RAB3GAP1 c.2607-1G>C Pathogenic ★★ same type
- RAB3GAP1 c.748+1G>A Pathogenic ★★ same type
- RAB3GAP1 c.899+1G>A Pathogenic ★★ same type
- RAB3GAP1 p.Arg174Ter Pathogenic/Likely pathogenic ★★ same type
- RAB3GAP1 p.Arg187Ter Pathogenic ★★ same type
- RAB3GAP1 p.Arg231Ter Pathogenic ★★ same type
- RAB3GAP1 p.Arg337Ter Pathogenic/Likely 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/rab3gap1-p-pro7 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown