About CSF1R
The CSF1R gene (Colony Stimulating Factor 1 Receptor) on chromosome 5q32 Mutations in CSF1R cause adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP), a fatal neurodegenerative disease. Key targets include Exons 12–22 (kinase domain) for comprehensive mutation screening.
Mutations: L301S, Y969C, M875T | GC content: 51% | Target exons: Exons 12–22 (kinase domain)
CSF1R Primer Design Challenges
- Kinase domain mutation burden: Missense mutations in the tyrosine kinase domain (exons 12–22) cluster near the ATP-binding pocket
- Moderate GC (51%): Balanced GC provides stable thermodynamics but requires verification against repetitive intronic elements
- Microglial expression specificity: Transcript variants with alternative 5' UTRs require promoter-aware primer design for expression analysis
Recommended Primer Design Parameters for CSF1R
| 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 CSF1R
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 12 (kinase insert) | 5′-GCCATCCTGACCTACTACGA-3′ | 5′-CACTGGCATGTCCAACATCT-3′ | 203 bp |
| Exon 21 (C-terminal) | 5′-GAGTCCAGCATGGAGTACCT-3′ | 5′-ACAGGCAGTTCATCCACATC-3′ | 188 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing CSF1R primers, avoid these clinically significant variants:
- rs121913301 (L301S) — Exon 7 extracellular domain mutation
- rs138554767 (Y969C) — Exon 21 kinase domain ALSP mutation
Clinical Validation Required
All CSF1R 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 CSF1R Primers Now
Pre-configured with CSF1R-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.