About IDH2
The IDH2 gene (Isocitrate Dehydrogenase (NADP(+)) 2) on chromosome 15q26 R140Q and R172 hotspot mutations produce 2-hydroxyglutarate and occur in AML, glioma, and cholangiocarcinoma with prognostic significance. Key targets include Exons 4–11 (active site in exons 4, 11) for comprehensive mutation screening.
Mutations: R140Q, R172K, R172M, R172S | GC content: 56% | Target exons: Exons 4–11 (active site in exons 4, 11)
IDH2 Primer Design Challenges
- Dual hotspot exons: R140 mutations in exon 4 (AML) and R172 in exon 11 (glioma/cholangiocarcinoma) require two separate targeted amplicons
- Elevated GC (56%): Balanced GC with elevated regions in exon 4 requiring standard additive optimization
- Mitochondrial targeting: The mitochondrial localization signal in exon 1 requires careful 5' primer placement for full-length amplification
Recommended Primer Design Parameters for IDH2
| 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 IDH2
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 4 (R140) | 5′-GACTGCCTGTCCCTTGTCTT-3′ | 5′-TCCTGACCAAGACCATCACC-3′ | 193 bp |
| Exon 11 (R172) | 5′-CTAGCCTGTCCCCATCTCTC-3′ | 5′-GCAGGACACGGTTTTGATCT-3′ | 208 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing IDH2 primers, avoid these clinically significant variants:
- rs121913504 (R140Q) — Exon 4 AML hotspot mutation
- rs121913503 (R172K) — Exon 11 glioma/cholangiocarcinoma hotspot
Clinical Validation Required
All IDH2 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 IDH2 Primers Now
Pre-configured with IDH2-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.