CYP2A6 p.Pro413=
c.1239C>T · rs143336165 · VCV719052
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.25%, eas)
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 -11 | |
| Overall | ||
| CADD | 2.638 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.25%
East Asian · 542/43,394 alleles
Filtering AF
1.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.13%
Overall
0.0572%
922/1,611,738 alleles · low-frequency
exomes 806/1,460,240 · genomes 116/151,498 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.25% | 80 |
| Ashkenazi Jewishnot grpmax-eligible | 0.75% | 133 |
| Remaining individualsnot grpmax-eligible | 0.151% | 664 |
| South Asian | 0.0264% | 3,788 |
| Admixed American | 0.00667% | 14,992 |
| European (non-Finnish) | 0.00288% | 34,703 |
| African / African-American | 0.00268% | 37,355 |
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
- CYP2A6
- Protein
- p.Pro413=
- Coding
- c.1239C>T
- MANE Select
- NM_000762
- dbSNP
- rs143336165
- Type
- single nucleotide variant
- Location
- chr19:40844695 (GRCh38)
- Gene constraint
- LOEUF 0.879 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.70 · 11 PDB
- Residue 413
- an α-helix
Similar variants
- CYP2A6 p.Arg190Leu Likely benign ★★ same type
- CYP2A6 p.Asn418Asp Benign ★★ same type
- CYP2A6 p.Leu73= Likely benign ★★ same type
- CYP2A6 p.Met6Leu Benign ★★ same type
- CYP2A6 p.Ala159Pro Uncertain significance ★ ⚠ same type
- CYP2A6 p.Ala159Val Uncertain significance ★ ⚠ same type
- CYP2A6 p.Ala237Thr Uncertain significance ★ ⚠ same type
- CYP2A6 p.Ala86Val 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/cyp2a6-p-pro413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown