Table 3. In silico pathogenicity prediction of the coding HOXB13 variants.
| cDNA change, Protein change | PolyPhen2 | Provean | SIFT | Mutation Taster (Probability values) | MutPred (Probability of deleterious mutation) | Mutation Assessor (FI score) | ESEfinder 3.0 |
|---|---|---|---|---|---|---|---|
| c.383C>A, p.(Ala128Asp) | Probably damaging (1.000) | Deleterious (-4.27) | Damaging (0.000) | Disease causing (≈1.0) | 0.239 | Medium (2.525) | Weak alteration (SRSF2) |
| c.720C>A, p.(Phe240Leu) | Probably damaging (0.999) | Deleterious (-5.09) | Damaging (0.001) | Disease causing (≈1.0) | 0.590 | Medium (2.79) | ESE disruption (SRSF6) |
| c.96T>A, p. (=) | N/A | Neutral (0) | Tolerated (0.48) | Disease causing (≈1.0) | N/A | N/A | ESE creation (SRSF1, SRSF1:IgM-BRCA1 and SRSF5) and weak alteration (SRSF1:IgM-BRCA1) |
| c.330C>A, p. (=) | N/A | Neutral (0) | Tolerated (0.566) | Disease causing (≈1.0) | N/A | N/A | ESE disruption (SRSF1:IgM-BRCA1) and weak alteration (SRSF1, SRSF1:IgM-BRCA1, SRSF2 and SRSF6) |
FI score–Functional impact combined score; N/A–not applicable; p. (=) –protein has not been analyzed, but no change is expected.