Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Common
common (popmax 9.58%, afr) — too common for a highly-penetrant pathogenic allele
Conditions
1
Warburg micro syndrome 1
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 -2.4 | GERP -3.8 |
| Overall | ||
| CADD | 4.215 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.58%
African / African-American · 7,184/74,994 alleles
Filtering AF
9.39%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.32%
Overall
0.546%
8,813/1,614,136 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 9.58% | 10 |
| Middle Eastern | 0.875% | 114 |
| Remaining individualsnot grpmax-eligible | 0.789% | 127 |
| Admixed American | 0.783% | 128 |
| Ashkenazi Jewishnot grpmax-eligible | 0.409% | 245 |
| European (non-Finnish) | 0.0396% | 2,527 |
| South Asian | 0.0263% | 3,795 |
| East Asian | 0.00223% | 44,886 |
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.Ser664=
- Coding
- c.1992G>A
- MANE Select
- NM_012233
- dbSNP
- rs7595725
- Type
- single nucleotide variant
- Location
- chr2:135150437 (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 664
- a modified residue (phosphoserine)
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-ser664 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown