CYP2B6 p.Ser259=
c.777C>T · rs45482602 · VCV3040512
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.43%, afr)
Conditions
1
CYP2B6-related disorder
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 -16 | |
| Overall | ||
| CADD | 0.288 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.43%
African / African-American · 314/72,962 alleles
Filtering AF
0.391%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.376%
Overall
0.0244%
386/1,580,934 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.43% | 232 |
| Remaining individualsnot grpmax-eligible | 0.0456% | 2,191 |
| Middle Eastern | 0.0168% | 5,950 |
| Admixed American | 0.0152% | 6,563 |
| South Asian | 0.00452% | 22,142 |
| European (non-Finnish) | 0.00251% | 39,819 |
| East Asian | 0.00225% | 44,480 |
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
- CYP2B6
- Protein
- p.Ser259=
- Coding
- c.777C>T
- MANE Select
- NM_000767
- dbSNP
- rs45482602
- Type
- single nucleotide variant
- Location
- chr19:41009350 (GRCh38)
- Gene constraint
- LOEUF 1.044 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.25 · 13 PDB
- Residue 259
- a UniProt-annotated variant site (in allele cyp2b6*3)
Disease context
CYP2B6-related disorder
Similar variants
- CYP2B6 p.Ser259Arg Likely benign ★ same residue
- CYP2B6 p.Val65Ile Uncertain significance ★ ⚠ same condition
- CYP2B6 p.Gln21Leu Likely benign same condition
- CYP2B6 p.Glu445= Likely benign same condition
- CYP2B6 p.Ile241= Likely benign same condition
- CYP2B6 p.Ile265= Likely benign same condition
- CYP2B6 p.Ile441= Likely benign same condition
- CYP2B6 p.Leu16= Likely benign 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/cyp2b6-p-ser259 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown