Table 3.
In silico identification of mutations in patients
| Patient | Mutated gene | DNA sequence change | SIFT | Mutation taster | LRT | PROVEAN | CADD phred score | Predicted pathogenicity* |
|---|---|---|---|---|---|---|---|---|
| 1 | PIK3CA | c.1636C > A | Tolerated | Disease causing | Deleterious | Neutral | 25.2 | Pathogenic |
| 2 | PIK3CA | c.2740G > A | Deleterious | Disease causing | Deleterious | Deleterious | 31 | Pathogenic |
| 3 | PIK3CA | c.1345C > A | Deleterious | Disease causing | Deleterious | Deleterious | 28.4 | Likely pathogenic |
| 4 | PIK3CA | c.1633G > A | Deleterious | Disease causing | Deleterious | Deleterious | 33 | Pathogenic |
| 5 | PIK3CA | c.1357G > A | Tolerated | Disease causing | Deleterious | Neutral | 32 | Likely pathogenic |
| 6 | PIK3CA | c.3073A > G | Tolerated | Disease causing | Deleterious | Deleterious | 23.2 | Likely pathogenic |
| 7 | PIK3CA | c.2908G > A | Tolerated | Disease causing | Neutral | Neutral | 22.8 | Likely pathogenic |
| 8 | KRAS | c.35G > A | Deleterious | Disease causing | Deleterious | Deleterious | 25.3 | Pathogenic |
| 9 | KRAS | c.35G > A | Deleterious | Disease causing | Deleterious | Deleterious | 25.3 | Pathogenic |
| 10 | PTEN | c.755A > T | Deleterious | Disease causing | Deleterious | Deleterious | 27.3 | Likely pathogenic |
| 11 | MAP2K3 | c.696 + 1G > A | – | Disease causing | – | – | 26.8 | VUS |
| 12 | GNAQ | c.548G > A | Deleterious | Disease causing | Deleterious | Deleterious | 35 | Pathogenic |
| 13 | TBC1D4 | c.667G > A | Deleterious | Disease causing | Deleterious | Deleterious | 34 | VUS |
| 14 | TEK | c.3324_3334del | – | – | – | – | Pathogenic |
SIFT, Sorting Intolerant For Tolerant; LRT, Likelihood Ratio Test; PROVEAN, Protein Variation Effect Analyzer; CADD, Combined Annotation Dependent Depletion; VUS, variant of unknown significance;*, As presented in the consensus statement of the ACMG (American College of Medical Genetics)