Table 4 In silico prediction of variants pathogenicity
Variant prediction | I-Mutant 3.0 | |||||
|---|---|---|---|---|---|---|
Variant | CADD_PHRED | SIFT | PolyPhen | UMD_Prediction | DDG Value prediction | SVM3 prediction effect |
ROBO1: p.Val610Ile | 25.3 | Deleterious | Probably_damaging | Probably pathogenic | − 0.07 kcal/mol | Large decrease |
ROBO2: p.Asp213Glu | 20.7 | Tolerated | Benign | Probably pathogenic | − 0.24 kcal/mol | Large increase |
ROBO2: p.Arg811Trp | 31 | Deleterious | Probably_damaging | Pathogenic | − 0.31 kcal/mol | Neutral |
ROBO3: p.Thr323Met | 25.4 | Deleterious | Probably_damaging | Pathogenic | − 1.73 kcal/mol | Large decrease |
ROBO3: p.Arg539Trp | 23.7 | Deleterious | Probably_damaging | Pathogenic | − 0.03 kcal/mol | Neutral |
ROBO3: p.Pro859Gln | 32 | Deleterious | Probably_damaging | Pathogenic | − 1.33 kcal/mol | Large decrease |
ROBO3: p.Gly998Val | 24.8 | Deleterious | Benign | Pathogenic | − 0.46 kcal/mol | Large decrease |
ROBO3: p.Pro1160Ser | 26.1 | Deleterious | Probably_damaging | Pathogenic | − 1.06 kcal/mol | Large decrease |
ROBO4: p.Ala303Asp | 14.37 | Tolerated | Benign | Pathogenic | − 0,52 kcal/mol | Neutral |
ROBO4: p.Ala446Asp | 23 | Deleterious | Benign | Probably pathogenic | − 0.61 kcal/mol | Large decrease |
ROBO4: p.Arg776Cys | 22.9 | Tolerated | Benign | Probably pathogenic | − 0.59 kcal/mol | Neutral |
ROBO4: p.Arg908Gln | 16.15 | Tolerated | Benign | Pathogenic | − 0.67 kcal/mol | Neutral |
ROBO4: c.3001 + 3G > A | – | – | – | – | – | – |
SLIT1: p.Pro149Leu | 24.7 | Deleterious | Probably_damaging | Pathogenic | − 0.30 kcal/mol | Neutral |
SLIT1: p.Cys263Ter | 36 | – | – | Pathogenic | – | – |
SLIT1: p.Arg455Ser | 27.1 | Deleterious | Probably_damaging | Pathogenic | − 1.30 kcal/mol | Large decrease |
SLIT1: p.Ala1253Thr | 19.47 | Tolerated | Benign | Probably pathogenic | − 0.78 kcal/mol | Large decrease |
SLIT1: p.Glu1340Asp | 15.21 | Tolerated | Benign | Probably pathogenic | − 0.29 kcal/mol | Large decrease |
SLIT1: p.His1382Arg | 14.47 | Tolerated | Benign | Probably pathogenic | 0.11 kcal/mol | Neutral |
SLIT1: p.Cys1401Phe | 29.9 | Deleterious | Probably_damaging | Pathogenic | − 0.35 kcal/mol | Large decrease |
SLIT2: p.Leu1293Met | 24.8 | Deleterious | Probably_damaging | Probably pathogenic | − 1.17 kcal/mol | Large decrease |
SLIT3: p.Arg494Thr | 23.3 | Deleterious | Probably_damaging | Pathogenic | − 1.10 kcal/mol | Large decrease |
SLIT3: p.Ser629Asn | 21.8 | Tolerated | Benign | Pathogenic | − 0.75 kcal/mol | Neutral |
SLIT3: p.Cys1355Ter | 42 | – | – | Pathogenic | – | – |