APOBEC2 p.Phe184=
c.552C>T · VCV3417126
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
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 5.9 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 14.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,084 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.00031%
5/1,614,204 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,361 |
| East Asian | 0.00223% | 44,882 |
| European (non-Finnish) | 8.47e-05% | 1,180,036 |
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
- APOBEC2
- Protein
- p.Phe184=
- Coding
- c.552C>T
- MANE Select
- NM_006789
- Type
- single nucleotide variant
- Location
- chr6:41061748 (GRCh38)
- Gene constraint
- LOEUF 1.085 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.10 · 1 PDB
- Residue 184
- an α-helix
Similar variants
- APOBEC2 p.Ala2Asp Uncertain significance ★ ⚠ same type
- APOBEC2 p.Ala8Val Uncertain significance ★ ⚠ same type
- APOBEC2 p.Ala95Val Uncertain significance ★ ⚠ same type
- APOBEC2 p.Arg116Trp Uncertain significance ★ ⚠ same type
- APOBEC2 p.Arg46Gln Uncertain significance ★ ⚠ same type
- APOBEC2 p.Arg46Trp Uncertain significance ★ ⚠ same type
- APOBEC2 p.Arg57Trp Uncertain significance ★ ⚠ same type
- APOBEC2 p.Arg87Trp 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/apobec2-p-phe184 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown