RAB2A p.Phe43=
c.129C>T · VCV3429128
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0184%, amr)
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 -3.3 | GERP -4.3 |
| Overall | ||
| CADD | 6.382 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0184%
Admixed American · 11/59,840 alleles
Filtering AF
0.0102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00797%
Overall
0.00591%
95/1,606,438 alleles · ultra-rare
exomes 83/1,454,466 · genomes 12/151,972 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0184% | 5,440 |
| African / African-American | 0.00938% | 10,667 |
| South Asian | 0.00771% | 12,964 |
| Remaining individualsnot grpmax-eligible | 0.00644% | 15,535 |
| European (non-Finnish) | 0.00562% | 17,800 |
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
- RAB2A
- Protein
- p.Phe43=
- Coding
- c.129C>T
- MANE Select
- NM_002865
- Type
- single nucleotide variant
- Location
- chr8:60572056 (GRCh38)
- Gene constraint
- LOEUF 1.024 · pLI 0.23 (gnomAD)
- Structure
- AlphaFold pLDDT 89.51 · 1 PDB
- Residue 43
- a β-strand
Similar variants
- RAB2A p.Ala199Gly Uncertain significance ★ ⚠ same type
- RAB2A p.Asn162Ser Uncertain significance ★ ⚠ same type
- RAB2A p.His107Tyr Uncertain significance ★ same type
- RAB2A p.His191Arg Uncertain significance ★ ⚠ same type
- RAB2A p.Ile144Val 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/rab2a-p-phe43 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown