Table 4 Example of prediction tools used for assessment of pathogenicity of identified rare variants
From: Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta
Pat. No. | Gene | ClinVar significance | Polyphen-2 prediction | Polyphen score | SIFT prediction | SIFT score | Minor allele frequency |
|---|---|---|---|---|---|---|---|
1 | AXIN2 | Likely benign | Probably damaging | 1.0 | Tolerated | 0.21 | 0.003 |
1 | FZR1 | None | None | None | 0.00994087453707 | ||
1 | TGFA | None | None | None | 0.000338868180278 | ||
1 | MKKS | Uncertain, pathogenic | Probably damaging | 0.952 | Deleterious | 0.01 | 0.00972556485506 |
1 | PTCH1 | None | Probably damaging | 0.95 | Deleterious | 0.0 | −1.0 |
1 | KDM6A | Benign | None | None | |||
2 | HOXB1 | None | None | None | −1.0 | ||
2 | COL3A1 | Likely benign | None | None | 0.0079 | ||
2 | COL3A1 | Likely benign, other | Possibly damaging | 0.632 | None | 0.0069 | |
2 | GLI3 | None | Possibly damaging | 0.504 | Deleterious | 0.01 | 8.98580243216e-05 |
2 | SMO | None | Benign | 0.017 | Deleterious low confidence | 0.0 | 0.002 |
2 | RECQL4 | None | None | None | 0.00532454361055 | ||
3 | TCOF1 | Likely benign | Benign | 0.012 | None | 0.003 | |
4 | CDH1 | None | Probably damaging | 0.992 | Tolerated | 0.05 | 1.50001500015e-05 |
4 | NSD1 | Uncertain | Benign | 0.007 | Tolerated low confidence | 0.14 | 0.00049447091612 |
4 | EVC2 | Uncertain, benign | Possibly damaging | 0.876 | Deleterious | 0.0 | 0.0089 |
4 | PITX2 | Likely benign, other | Benign | 0.02 | Tolerated | 0.61 | 0.00612416864787 |
5 | EVC | Likely benign, other | Possibly damaging | 0.786 | Tolerated | 0.1 | 0.00930071821378 |
6 | TBX3 | None | Benign | 0.004 | Tolerated | 0.84 | 0.002 |
6 | MSX2 | None | Benign | 0.005 | Tolerated | 0.06 | 0.0002457002457 |
7,8 | SEMA3F | None | Probably damaging | 1.0 | Deleterious | 0.02 | −1.0 |
7,8 | FLNB | Likely benign | None | None | 0.0082 | ||
7,8 | EVC | Uncertain | Possibly damaging | 0.655 | Tolerated low confidence | 0.38 | 0.0 |
9 | KMT2D | None | Unknown | 0.0 | None | 0.001 | |
9 | SATB2 | None | Probably damaging | 0.987 | Tolerated | 0.12 | 2.99733237419e-05 |
10 | OFD1 | Benign | Benign | 0.066 | Tolerated | 0.49 | 0.00845140442456 |