Table 2 Summary of pathogenicity and LOF of reclassified variants
HGMD | |||
Reclassification criteria | Total reclassified | Pathogenicity prediction (SIFT, PolyPhen, MutationTaster, metaSVM, CADD) | LOF (stop-gain, frameshift, splicing) |
Criteria1: > = 0.05 (Additional file 1: Table S1) | 255 | 9, 24, 16, 5, 77 | 13, 7, 15 (13.3%) |
Criteria 2: > = 0.05 in SGP (and < 0.05 in PublicDB) (Additional file 3: Table S3) | 16 | 5, 3, 8, 5, 12 | 2, 0, 1 (18%) |
Criteria 3: > = 0.01 in SGP (at least 1 hom) (Additional file 5: Table S5) | 607 | 97, 127, 149, 66, 288 | 34, 0, 16 (8.2%) |
Criteria 4: <0.01, hom in SGP, no association with disease (Additional file 7: Table S7) | 215 | 58, 84, 105, 60, 141 | 7, 0, 5 (5.5%) |
Total = 1093 | |||
ClinVar | |||
Reclassification criteria | Total reclassified | Pathogenicity prediction (SIFT, PolyPhen, MutationTaster, metaSVM, CADD) | LOF (stop-gain, frameshift, splicing) |
Criteria1 > = 0.05 (Additional file 2: Table S2) | 334 | 23, 35, 11, 9, 65 | 2, 1, 6 (2.7%) |
Criteria 2: > = 0.05 in SGP (and < 0.05 in PublicDB) (Additional file 4: Table S4) | 10 | 1, 2, 4, 1, 6 | 0, 0, 1 (10%) |
Criteria 3: > = 0.01 in SGP (at least 1 hom) (Additional file 6: Table S6) | 484 | 69, 86, 70, 41, 165 | 3, 0, 5 (1.65%) |
Criteria 4: <0.01, hom in SGP, no association with disease (Additional file 8: Table S8) | 70 | 17, 25, 27, 21, 41 | 1, 0, 0 (1.4%) |
Total = 898 | |||