RAB3GAP1 p.Thr883=
c.2649C>T · rs755368009 · VCV2886636
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00668%, afr)
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 -5.2 | GERP -3.4 |
| Overall | ||
| CADD | 5.094 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
African / African-American · 5/74,888 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00162%
Overall
0.00105%
17/1,613,272 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00668% | 14,978 |
| South Asian | 0.0033% | 30,348 |
| European (non-Finnish) | 0.000763% | 131,069 |
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.Thr883=
- Coding
- c.2649C>T
- MANE Select
- NM_012233
- dbSNP
- rs755368009
- Type
- single nucleotide variant
- Location
- chr2:135164636 (GRCh38)
- Gene constraint
- LOEUF 0.798 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.46 · 1 PDB
- Residue 883
- a turn
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-thr883 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown