RAB3GAP1 p.Ser581=
c.1743C>T · rs200166273 · VCV1974903
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.172%, amr)
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 -6.6 | GERP -3.5 |
| Overall | ||
| CADD | 5.086 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.172%
Admixed American · 103/59,984 alleles
Filtering AF
0.145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.135%
Overall
0.00799%
129/1,613,640 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.172% | 582 |
| East Asian | 0.0178% | 5,605 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,833 |
| African / African-American | 0.00267% | 37,445 |
| South Asian | 0.0011% | 91,062 |
| European (non-Finnish) | 0.00102% | 98,323 |
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.Ser581=
- Coding
- c.1743C>T
- MANE Select
- NM_012233
- dbSNP
- rs200166273
- Type
- single nucleotide variant
- Location
- chr2:135135752 (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 581
- a modified residue (phosphoserine)
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-ser581 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown