About ALDH2
The ALDH2 gene (Aldehyde Dehydrogenase 2) on chromosome 12q24 The E504K variant (rs671) severely reduces ALDH2 activity and is carried by ~40% of East Asian populations, linking to cancer risk. Key targets include Exons 1–13 for comprehensive mutation screening.
Mutations: E504K (rs671), R475W | GC content: 61% | Target exons: Exons 1–13
ALDH2 Primer Design Challenges
- High GC content (61%): The ALDH2 gene has elevated overall GC content requiring denaturant optimization for robust amplification
- rs671 hotspot: The common E504K variant in exon 12 falls within primer binding regions requiring careful placement
- Homologous ALDH genes: ALDH1A1, ALDH1B1 paralogs share 65–70% sequence identity necessitating BLAST-based primer validation
Recommended Primer Design Parameters for ALDH2
| 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 ALDH2
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 2 (active site) | 5′-GTGGAGACCCATTCATCGGT-3′ | 5′-AGCTGGTACTCAGCATCGTG-3′ | 185 bp |
| Exon 12 (rs671 region) | 5′-CACTGCTGATGACAGGGCTG-3′ | 5′-CAACCTCCCATCAGCATGAG-3′ | 199 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing ALDH2 primers, avoid these clinically significant variants:
- rs671 (E504K) — Exon 12 variant affecting enzyme activity
- rs2228093 (R475W) — Exon 11 polymorphism in catalytic domain
Clinical Validation Required
All ALDH2 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 ALDH2 Primers Now
Pre-configured with ALDH2-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.