Table 2.
Pathogenicity prediction scores for the five genetic variants identified in the diabetic Tunisian patient.
| Pathogenicityprediction tools | Threshold score | BBS1-p.Pro245Leu | BBS4-p.Lys46Arg | TTC8-p.Asn297Asp | MKS1-p.Arg475Cys | CEP290-p.Arg1746Gln |
|---|---|---|---|---|---|---|
| Prediction | Prediction | Prediction | Prediction | Prediction | ||
| SIFT | <0.05 | Deleterious | Tolerated | Tolerated | Deleterious | Tolerated |
| Polyphen2_HDIV | >0.453 | Possibly damaging | Benign | Benign | Deleterious | Possibly damaging |
| Mutation assessor | >1.9 | Medium | Low | Neutral | Medium | Low |
| FATHMM | <0 | Tolerated | Tolerated | Tolerated | Tolerated | Tolerated |
| PROVEAN | < -2.5 | Deleterious | Neutral | Neutral | Deleterious | Neutral |
| VEST3 | >0.75 | Tolerated | Tolerated | Tolerated | Deleterious | Tolerated |
| MetaSVM | >0 | Deleterious | Tolerated | Tolerated | Deleterious | Tolerated |
| MetaLR | >0.5 | Deleterious | Tolerated | Tolerated | Deleterious | Tolerated |
| CADD | >20 | Deleterious | Deleterious | Tolerated | Deleterious | Deleterious |
| DANN | >0.8 | Deleterious | Deleterious | Tolerated | Deleterious | Deleterious |
| UMD predictor | >50 | Probably pathogenic | Polymorphism | Pathogenic | Pathogenic | Polymorphism |
| LRT | D, N, and U | – | Deleterious | Deleterious | Deleterious | Deleterious |
| Mutation taster | A, D, N, and P | Deleterious | Deleterious | Deleterious | Deleterious | Deleterious |
| M-CAP | D and N | Deleterious | – | Tolerated | Deleterious | – |
| Harmful/total prediction tools | 11/13 | 4/13 | 3/14 | 13/14 | 5/13 | |
Pathogenicity prediction tools with threshold score or categorical classification. Reported categorical classification stand for the following: A, disease causing automatic; D, deleterious; N, neutral; P, polymorphism-automatic; U, unknown.