CYP1A2 p.Pro131=
c.393G>A · rs34153904 · VCV713008
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0981%, 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 -20 | GERP -4.6 |
| Overall | ||
| CADD | 0.013 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0981%
East Asian · 44/44,874 alleles
Filtering AF
0.075%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0669%
Overall
0.00787%
127/1,614,040 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0981% | 1,020 |
| South Asian | 0.0582% | 1,718 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,290 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.00167% | 60,020 |
| Finnishnot grpmax-eligible | 0.00156% | 63,902 |
| African / African-American | 0.00133% | 75,042 |
| European (non-Finnish) | 0.000593% | 168,577 |
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
- CYP1A2
- Protein
- p.Pro131=
- Coding
- c.393G>A
- MANE Select
- NM_000761
- dbSNP
- rs34153904
- Type
- single nucleotide variant
- Location
- chr15:74750131 (GRCh38)
- Gene constraint
- LOEUF 1.355 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.66 · 1 PDB
- Residue 131
- an α-helix
Similar variants
- CYP1A2 c.-9-154C>A Likely benign ★★ same type
- CYP1A2 p.Arg281Trp Likely benign ★★ ⚠ same type
- CYP1A2 p.Ala134Val Uncertain significance ★ ⚠ same type
- CYP1A2 p.Ala154Thr Uncertain significance ★ ⚠ same type
- CYP1A2 p.Ala202Val Uncertain significance ★ ⚠ same type
- CYP1A2 p.Ala230Pro Uncertain significance ★ ⚠ same type
- CYP1A2 p.Arg362Lys Uncertain significance ★ ⚠ same type
- CYP1A2 p.Arg428Leu 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/cyp1a2-p-pro131 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown