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Table 1 Single nucleotide variants included in this study stratified according to the evidence supporting their impact on protein function

From: Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations

   Functional categories
Gene Total SNVs (n) Neutral (n) Non-neutral (n) Uncertain (n)
BRAF 54 0 23 31
BRCA1 505 61 20 424
BRCA2 837 50 12 775
DICER1 81 0 11 70
EGFR 131 0 33 98
ERBB2 75 5 33 37
ESR1 31 0 7 24
IDH1 19 0 1 18
IDH2 15 0 3 12
KIT 89 1 24 64
KRAS 41 0 25 16
MYOD1 11 0 1 10
PIK3CA 139 1 31 107
SF3B1 53 0 7 46
TP53 1,510 22 618 870
Total 3,591 140 849 2,602
  1. A total of 3,591 single nucleotide variants (SNVs) in six bona fide oncogenes, six new cancer genes and three bona fide tumor suppressor genes were assessed for the evidence supporting a functional role for each of the mutations. These SNVs were classified as non-neutral, neutral or uncertain based on direct experimental/functional data in the literature and/or on the basis of causation of Li-Fraumeni syndrome and Li-Fraumeni-like syndrome (for TP53) or early onset breast and ovarian cancer syndrome (for BRCA1 and BRCA2), as recorded in dedicated mutation databases [28-30]. For a detailed list, see Additional file 2.