About HRAS
The HRAS gene (HRas Proto-Oncogene) on chromosome 11p15 Activating mutations at codons 12, 13, and 61 occur in Costello syndrome (germline) and bladder, thyroid, and head and neck cancers (somatic). Key targets include Exons 1–6 (G domain in exons 1–4) for comprehensive mutation screening.
Mutations: G12V, G12S, G13R, Q61R, Q61L | GC content: 55% | Target exons: Exons 1–6 (G domain in exons 1–4)
HRAS Primer Design Challenges
- Hotspot codons 12/13/G61: The entire mutation spectrum spans <100 bp in exons 2–3, enabling single-amplicon coverage for most mutations
- Moderate GC (55%): Balanced GC content with a GC-rich stretch in exon 1 requiring touchdown PCR optimization
- HRAS-specific pseudogene: Processed HRAS pseudogene on chromosome 5 requires careful primer specificity BLAST verification
Recommended Primer Design Parameters for HRAS
| 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 HRAS
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 2 (G12/G13) | 5′-GACGAATACGACCCCACTAT-3′ | 5′-GGTCCTGCACCAGTAATGTG-3′ | 175 bp |
| Exon 3 (Q61) | 5′-GACTCCTACCGGAAGCAGGT-3′ | 5′-CATGGTGGGTCACTGTATGG-3′ | 182 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing HRAS primers, avoid these clinically significant variants:
- rs104894228 (G12V) — Exon 2 transforming mutation in bladder cancer
- rs121913514 (Q61R) — Exon 3 activating mutation in head and neck cancer
Clinical Validation Required
All HRAS 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 HRAS Primers Now
Pre-configured with HRAS-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.