RAB3GAP1 p.Val119=
c.357A>G · rs73959261 · VCV130070
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.53%, afr)
Conditions
1
Warburg micro syndrome 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.53 | donor loss, 3 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP -0.32, phastCons 1 |
| Overall | ||
| CADD | 8.415 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.53%
African / African-American · 2,646/74,870 alleles
Filtering AF
3.42%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.38%
Overall
0.184%
2,960/1,608,324 alleles · low-frequency
exomes 1,497/1,456,026 · genomes 1,463/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.53% | 28 |
| Remaining individualsnot grpmax-eligible | 0.245% | 407 |
| Admixed American | 0.202% | 496 |
| Middle Eastern | 0.116% | 865 |
| South Asian | 0.0165% | 6,064 |
| European (non-Finnish) | 0.00153% | 65,266 |
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.Val119=
- Coding
- c.357A>G
- MANE Select
- NM_012233
- dbSNP
- rs73959261
- Type
- single nucleotide variant
- Location
- chr2:135093688 (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 119
- an α-helix
Similar variants
- RAB3GAP1 c.2607-1G>C Pathogenic ★★ same condition
- RAB3GAP1 c.748+1G>A Pathogenic ★★ same condition
- RAB3GAP1 c.899+1G>A Pathogenic ★★ same condition
- RAB3GAP1 p.Arg187Ter Pathogenic ★★ same condition
- RAB3GAP1 p.Arg337Ter Pathogenic/Likely pathogenic ★★ same condition
- RAB3GAP1 p.Arg347Ter Pathogenic ★★ same condition
- RAB3GAP1 p.Arg392Ter Pathogenic ★★ same condition
- RAB3GAP1 p.Gln246Ter Pathogenic ★★ 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/rab3gap1-p-val119 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown