RAB3GAP2 p.Ile612=
c.1836C>A · rs794727209 · VCV194860
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | donor loss, 34 bp away · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.29 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP -1.1, phastCons 1 |
| Overall | ||
| CADD | 6.968 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- RAB3GAP2
- Protein
- p.Ile612=
- Coding
- c.1836C>A
- MANE Select
- NM_012414
- dbSNP
- rs794727209
- Type
- single nucleotide variant
- Location
- chr1:220185685 (GRCh38)
- Gene constraint
- LOEUF 0.535 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.77 · 1 PDB
Similar variants
- RAB3GAP2 p.Ile612Val Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-ile612 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown