RAB3GAP2 p.His356=
c.1068C>T · VCV4684195
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00407%, nfe)
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 -3.6 | GERP -3.2 |
| Overall | ||
| CADD | 1.456 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00407%
European (non-Finnish) · 48/1,179,996 alleles
Filtering AF
0.00315%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00279%
Overall
0.00335%
54/1,613,934 alleles · very rare
exomes 51/1,461,818 · genomes 3/152,116 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00407% | 24,583 |
| African / African-American | 0.00267% | 37,442 |
| East Asian | 0.00223% | 44,880 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| Finnishnot grpmax-eligible | 0.00156% | 64,018 |
| South Asian | 0.0011% | 91,082 |
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
- RAB3GAP2
- Protein
- p.His356=
- Coding
- c.1068C>T
- MANE Select
- NM_012414
- Type
- single nucleotide variant
- Location
- chr1:220195140 (GRCh38)
- Gene constraint
- LOEUF 0.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.77 · 1 PDB
Similar variants
- RAB3GAP2 c.713-2A>C Likely pathogenic ★★ same type
- RAB3GAP2 p.Arg1213Ter Pathogenic ★★ same type
- RAB3GAP2 p.Arg426Cys Pathogenic/Likely pathogenic ★★ same type
- RAB3GAP2 c.1631+8G>T Uncertain significance ★★ same type
- RAB3GAP2 c.*2171A>G Uncertain significance ★★ same type
- RAB3GAP2 p.Ala16Thr Uncertain significance ★★ ⚠ same type
- RAB3GAP2 p.Ala240Pro Uncertain significance ★★ ⚠ same type
- RAB3GAP2 p.Ala300Thr Uncertain significance ★★ ⚠ 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/rab3gap2-p-his356 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown