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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