RAB3GAP1 p.Phe755=
c.2265T>C · rs17261772 · VCV130067
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 12 submitters
gnomAD v4.1
Common
common (popmax 99.8%, eas) — too common for a highly-penetrant pathogenic allele
Conditions
2
Martsolf syndrome 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -3.5 |
| Overall | ||
| CADD | 4.993 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
99.8%
East Asian · 44,800/44,876 alleles
Filtering AF
99.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 98.7%
Overall
35.9%
579,309/1,613,426 alleles · common
exomes 496,730/1,461,330 · genomes 82,579/152,096 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 99.8% | 1 |
| African / African-American | 88.1% | 1 |
| Ashkenazi Jewishnot grpmax-eligible | 71.7% | 1 |
| Admixed American | 70.5% | 1 |
| Middle Eastern | 68.6% | 1 |
| South Asian | 68.1% | 1 |
| Remaining individualsnot grpmax-eligible | 44% | 2 |
| Finnishnot grpmax-eligible | 31.2% | 3 |
| European (non-Finnish) | 24.7% | 4 |
| Amishnot grpmax-eligible | 22.2% | 4 |
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.Phe755=
- Coding
- c.2265T>C
- MANE Select
- NM_012233
- dbSNP
- rs17261772
- Type
- single nucleotide variant
- Location
- chr2:135153852 (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 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-phe755 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown