About CHEK2
The CHEK2 gene (Checkpoint Kinase 2) on chromosome 22q12 The hypomorphic 1100delC truncating mutation increases breast cancer risk ~2-fold and is present in ~1% of the European population. Key targets include Exons 2–15 for comprehensive mutation screening.
Mutations: 1100delC, I157T, S428F, del5395 | GC content: 52% | Target exons: Exons 2–15
CHEK2 Primer Design Challenges
- Founder mutation 1100delC: The 1100delC frameshift in exon 10 causes premature truncation requiring specific genotyping primers
- Multiple splice variants: Alternative splicing generates isoforms lacking kinase domain or FHA domain, requiring transcript awareness
- Pseudogene interference: Processed pseudogene on chromosome 15 shares homology with CHEK2 exons 10–15
Recommended Primer Design Parameters for CHEK2
| Parameter | Standard Exons | Optimized Regions |
|---|---|---|
| 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 | Optional 3–5% DMSO for problematic regions |
Recommended Primer Sequences for CHEK2
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 10 (1100delC) | 5′-CAATATTGCTGTGGGAGTGC-3′ | 5′-CCTGAGTCCACCTGTCCTTC-3′ | 192 bp |
| Exon 3 (FHA domain) | 5′-GCCCAGACCATGTGTAAGGA-3′ | 5′-ACAGGTTCATCATCGCAACA-3′ | 167 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing CHEK2 primers, avoid these clinically significant variants:
- rs555607708 (1100delC) — Exon 10 founder frameshift, breast cancer risk
- rs17879961 (I157T) — Exon 3 missense, reduced kinase activity
Clinical Validation Required
All CHEK2 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 CHEK2 Primers Now
Pre-configured with CHEK2-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.