About CEBPA
The CEBPA gene (CCAAT Enhancer Binding Protein Alpha) on chromosome 19q13 Biallelic CEBPA mutations (N-terminal frameshift + C-terminal in-frame) define a distinct acute myeloid leukemia subtype with favorable prognosis. Key targets include Exons 1–2 for comprehensive mutation screening.
Mutations: N-terminal frameshift, C-terminal bZIP mutations | GC content: 66% | Target exons: Exons 1–2
CEBPA Primer Design Challenges
- Highest GC content (66%): CEBPA has extremely high GC content, especially in the N-terminal region requiring optimized PCR with DMSO/betaine
- Only 2 coding exons: Compact gene structure but with complex mutation patterns requiring careful primer placement around repetitive GC tracts
- Biallelic mutation detection: N-terminal and C-terminal mutations occur on different alleles requiring long-range or allele-specific genotyping
Recommended Primer Design Parameters for CEBPA
| 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 CEBPA
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 1 (N-term) | 5′-ACCTGCGGATCTCCACCTT-3′ | 5′-CGTTCGTCCCCTCCTTCTCT-3′ | 195 bp |
| Exon 2 (bZIP domain) | 5′-TGAAGCCGAAGCAAAACAG-3′ | 5′-CCTTTCCACTGGGTCTGCT-3′ | 180 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing CEBPA primers, avoid these clinically significant variants:
- rs121913001 (N-term frameshift) — Exon 1 18 bp duplication in AML
- rs1555408753 (C-term bZIP) — Exon 2 in-frame mutation
Clinical Validation Required
All CEBPA 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 CEBPA Primers Now
Pre-configured with CEBPA-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.