CYP3A5 p.Pro397=
c.1191A>C · rs200628208 · VCV3040536
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, nfe)
Conditions
1
CYP3A5-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 -2.4 | GERP -1 |
| Overall | ||
| CADD | 2.786 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
European (non-Finnish) · 174/1,179,988 alleles
Filtering AF
0.0129%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0123%
Overall
0.0115%
186/1,613,988 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0147% | 6,782 |
| African / African-American | 0.00935% | 10,701 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,598 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
| Admixed American | 0.00167% | 59,996 |
| Finnishnot grpmax-eligible | 0.00156% | 64,040 |
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
- CYP3A5
- Protein
- p.Pro397=
- Coding
- c.1191A>C
- MANE Select
- NM_000777
- dbSNP
- rs200628208
- Type
- single nucleotide variant
- Location
- chr7:99652615 (GRCh38)
- Gene constraint
- LOEUF 1.028 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.52 · 6 PDB
Disease context
CYP3A5-related disorder
Similar variants
- CYP3A5 c.219-235A>G Uncertain significance ★ same condition
- CYP3A5 c.72-111C>T Benign same condition
- CYP3A5 c.72-152T>C Likely benign same condition
- CYP3A5 c.799-127G>A Likely benign same condition
- CYP3A5 c.-74C>T Likely benign same condition
- CYP3A5 c.-86G>A Likely benign same condition
- CYP3A5 p.Lys208= Likely benign same condition
- CYP3A5 p.Ser100Tyr 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/cyp3a5-p-pro397 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown