About HNF1A
The HNF1A gene (HNF1 Homeobox A) on chromosome 12q24 Mutations in HNF1A cause maturity-onset diabetes of the young type 3 (MODY3), the most common form of monogenic diabetes. Key targets include Exons 1–10 for comprehensive mutation screening.
Mutations: P291fsinsC, I27L, A98V, S142F | GC content: 48% | Target exons: Exons 1–10
HNF1A Primer Design Challenges
- P291 frameshift hotspot: The polyC tract in exon 4 is a mutational hotspot requiring careful polymerase selection to avoid slippage errors
- Low GC content (48%): AT-rich introns 2–4 affect primer binding and may require lower annealing temperatures
- MODY3 diagnosis specificity:>300 known mutations across all exons require complete exon coverage for clinical diagnostic panels
Recommended Primer Design Parameters for HNF1A
| 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 HNF1A
| Target Region | Forward Primer (5′→3′) | Reverse Primer (5′→3′) | Amplicon |
|---|---|---|---|
| Exon 4 (P291 region) | 5′-CACTTGCCCAGCTCTCTCTA-3′ | 5′-GACTCGGGAACAGAGGTGAC-3′ | 195 bp |
| Exon 1 (dimerization) | 5′-GTGCCAGGTGATCCATGTCT-3′ | 5′-AGGTGCCTTGCCTCTGATTG-3′ | 168 bp |
Key SNPs to Avoid in Primer Binding Sites
When designing HNF1A primers, avoid these clinically significant variants:
- rs137852835 (P291fsinsC) — Exon 4 polyC tract frameshift in MODY3
- rs1169288 (I27L) — Exon 1 common polymorphism
- rs121908448 (A98V) — Exon 1 missense in MODY diagnosis
Clinical Validation Required
All HNF1A 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 HNF1A Primers Now
Pre-configured with HNF1A-specific parameters. Use our primer design, Tm calculator, and GC content tools for optimal results.