About FOXL2
The FOXL2 gene (Forkhead Box L2) on chromosome 3q22 The recurrent C134W mutation replaces cysteine with tryptophan in the forkhead domain and is present in>95% of adult granulosa cell tumors. Key targets include Exon 1 for comprehensive mutation screening.
Mutations: C134W (c.402C>G) | GC content: 59% | Target exons: Exon 1
FOXL2 Primer Design Challenges
- Single-exon gene: All pathogenic mutations reside in the single coding exon, simplifying but requiring high-resolution amplicon design for the GC-rich forkhead domain
- Single mutation dominance: C134W accounts for>95% of mutations, allowing focused locked nucleic acid (LNA) probe-based detection
- High GC content (59%): The forkhead domain shows elevated GC requiring 5–8% DMSO for optimal amplification
Recommended Primer Design Parameters for FOXL2
| 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 FOXL2
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 1 (C134W region) | 5′-GTACCCCCAGCACTCGTACA-3′ | 5′-GCTTGCCGTAGACGAGATGT-3′ | 167 bp |
| Exon 1 (forkhead domain) | 5′-CCCGGCATCAACGAGTACAT-3′ | 5′-GCTTGCCGTAGACGAGATGT-3′ | 198 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing FOXL2 primers, avoid these clinically significant variants:
- rs121909227 (C134W) — Single recurrent mutation in adult GCT
Clinical Validation Required
All FOXL2 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 FOXL2 Primers Now
Pre-configured with FOXL2-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.