About CYP2C19
The CYP2C19 gene (Cytochrome P450 2C19) on chromosome 10q23 Polymorphisms define poor (*2/*3), intermediate, and ultrarapid (*17) metabolizer phenotypes with major pharmacogenomic implications. Key targets include Exons 1–9 for comprehensive mutation screening.
Mutations: *2 (rs4244285), *3 (rs4986893), *17 (rs12248560) | GC content: 58% | Target exons: Exons 1–9
CYP2C19 Primer Design Challenges
- Polymorphic star alleles: *2 (splice defect), *3 (premature stop), and *17 (promoter) require haplotype-specific primer designs
- High GC content (58%): Elevated GC content in exon 1 (68%) requires additive optimization for robust amplification
- Pseudogene CYP2C19P: Highly homologous pseudogene on chromosome 10 requires careful primer specificity verification
Recommended Primer Design Parameters for CYP2C19
| Parameter | Standard Exons | GC-Rich Regions (≥58%) |
|---|---|---|
| Primer length | 20–22 nt | 22–25 nt |
| GC content | 45–55% | 50–60% |
| Tm | 58–62°C | 60–65°C |
| Amplicon size | 150–300 bp | 180–350 bp |
| Annealing temp | 58–60°C | 60–64°C (touchdown) |
| PCR additive | Standard | Add 5–10% DMSO or betaine |
Recommended Primer Sequences for CYP2C19
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 5 (*2 site) | 5′-ACAACCAGAGCTTGGCATAT-3′ | 5′-CCTGGAATGTGCTGTGTTCT-3′ | 188 bp |
| Exon 9 (heme-binding) | 5′-CTGGGCCTGATGTTGGAACT-3′ | 5′-ACCCAGTTCACACTGCTTCA-3′ | 196 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing CYP2C19 primers, avoid these clinically significant variants:
- rs4244285 (*2 (splice)) — Exon 5 splice defect, poor metabolizer
- rs4986893 (*3 (stop)) — Exon 4 premature stop, poor metabolizer
- rs12248560 (*17 (promoter)) — Increased expression, ultrarapid metabolizer
Clinical Validation Required
All CYP2C19 primers designed with VigyanLLM are for research use only. Clinical diagnostic applications require additional wet-lab validation, Sanger sequencing confirmation, and regulatory approval before patient use.
Design CYP2C19 Primers Now
Pre-configured with CYP2C19-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.