RAB3GAP1 p.Lys89=
c.267G>A · rs757292994 · VCV448153
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0801%, amr)
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 1 | GERP -3.3, phastCons 1 |
| Overall | ||
| CADD | 7.127 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0801%
Admixed American · 48/59,940 alleles
Filtering AF
0.062%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0556%
Overall
0.00358%
57/1,594,158 alleles · ultra-rare
exomes 54/1,442,056 · genomes 3/152,102 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0801% | 1,249 |
| Remaining individualsnot grpmax-eligible | 0.0097% | 10,309 |
| African / African-American | 0.00134% | 74,406 |
| European (non-Finnish) | 0.000172% | 581,166 |
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.Lys89=
- Coding
- c.267G>A
- MANE Select
- NM_012233
- dbSNP
- rs757292994
- Type
- single nucleotide variant
- Location
- chr2:135091114 (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 p.Lys89fs Pathogenic same residue
- 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
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-lys89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown