Table 1 In vitro observed and in silico predicted mRNA splicing phenotypes associated with the two canonical splice site variants and four intronic variants prioritized for quantitative RT-PCR analysis
From: In silico prioritization and further functional characterization of SPINK1 intronic variants
Intron | SPINK1 variant | SpliceSiteFinder-like (0–100) | MaxEntScan (0–12) | NNSPLICE (0–1) | Human Splicing Finder (0–100) | In vitro observed mRNA splicing phenotypea |
|---|---|---|---|---|---|---|
Canonical splice donor site variants | ||||||
2 | c.87 + 1G > A | dss 79.8 → 0 | dss 8.3 → 0 | dss 0.9 → 0 | dss 84.1 → 0 | Complete exon 2 skipping |
3 | c.194 + 2T > C | dss 82.6 → 72.3 | dss 11.1 → 0 | dss 1.0 → 0 | dss 92.1 → 0 | Partial exon 3 skipping |
Variants prioritized for quantitative RT-PCR analysis | ||||||
2 | c.87 + 363A > G | − | − | − | dss 0 → 65.5 | Normal |
ass 0 → 83.3 | ||||||
3 | c.194 + 13T > G | dss 0 → 82.0 | dss 0 → 9.5 | dss 0 → 0.9 | dss 0 → 86.9 | Normal |
3 | c.194 + 1504A > G | dss 0 → 77.2 | − | dss 0 → 0.7 | dss 0 → 83.2 | Normal |
3 | c.195-323C > T | − | dss 0 → 6.3 | dss 0 → 0.7 | dss 0 → 75.1 | Normal |