About ATM
The ATM gene (ATM Serine/Threonine Kinase) on chromosome 11q22 Biallelic ATM mutations cause ataxia-telangiectasia, while monoallelic loss increases breast and pancreatic cancer risk. Key targets include Exons 2–63 (PI3K-like kinase domain in exons 39–63) for comprehensive mutation screening.
Mutations: Truncating, missense mutations | GC content: 44% | Target exons: Exons 2–63 (PI3K-like kinase domain in exons 39–63)
ATM Primer Design Challenges
- Very large gene (62 exons): ATM spans ~150 kb with 62 coding exons requiring extensive tiled primer panels
- Low GC content (44%): AT-rich regions near intron 8 affect primer annealing, requiring higher Tm primers
- High SNP density: The large coding region contains numerous benign polymorphisms requiring frequent primer repositioning
Recommended Primer Design Parameters for ATM
| Parameter | Standard Exons | Low-GC / AT-Rich 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 | Longer primers (24–28 nt), lower annealing Tₘ |
Recommended Primer Sequences for ATM
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 24 (FAT domain) | 5′-GCTGTGAACAGCTTGAGACG-3′ | 5′-CCAAACTCCCTTGTCTGCAT-3′ | 176 bp |
| Exon 39 (PI3K domain) | 5′-TGCATGTATCTTGCCATCCT-3′ | 5′-ACATGGCGTGAACTCACTGT-3′ | 201 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing ATM primers, avoid these clinically significant variants:
- rs1800057 (P1054R) — Exon 24 missense variant
- rs121434379 (R3047X) — Truncating mutation in kinase domain
Clinical Validation Required
All ATM 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 ATM Primers Now
Pre-configured with ATM-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.