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Table 2 Predictions of 3,591 functionally validated single nucleotide variants by 15 mutation effect prediction algorithms

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

Prediction algorithm Prediction class Functional categories Total
Neutral Non-neutral Uncertain
(n = 140) (n = 849) (n = 2,602) (n = 3,591)
CHASM (breast) Driver 27 764 1,085 1,876
Passenger 113 85 1,517 1,715
CHASM (lung) Driver 32 783 1,155 1,970
Passenger 108 66 1,447 1,621
CHASM (melanoma) Driver 48 795 1,440 2,283
Passenger 92 54 1,162 1,308
FATHMM (cancer) CANCER 71 831 1,655 2,557
PASSENGER/OTHER 69 18 947 1,034
FATHMM (missense) Damaging 69 745 1,416 2,230
Tolerated 71 104 1,167 1,342
No weights 0 0 19 19
Mutation Assessor High 2 71 97 170
Medium 50 579 1,053 1,682
Low 51 129 919 1,099
Neutral 37 69 527 633
N/A 0 1 6 7
MutationTaster Disease_causing 34 740 1,313 2,087
Disease_causing_automatic 1 31 4 36
Polymorphism 99 78 1,285 1,462
Polymorphism_automatic 6 0 0 6
PolyPhen-2 Probably damaging 40 600 920 1,560
Possibly damaging 26 115 478 619
Benign 74 134 1,204 1,412
PROVEAN Deleterious 43 632 955 1,630
Neutral 97 217 1,647 1,961
SIFT Damaging 70 731 1,469 2,270
Tolerated 70 118 1,133 1,321
VEST Functional 100 702 1,663 2,465
Neutral 40 147 939 1,126
CanDrA (breast) Driver 140 805 2,423 3,368
Passenger 0 39 140 179
No-call 0 5 39 44
CanDrA (lung) Driver 24 767 1,150 1,941
Passenger 102 59 1,282 1,443
No-call 14 23 170 207
CanDrA (melanoma) Driver 28 734 1,147 1,909
Passenger 97 75 1,260 1,432
No-call 15 40 195 250
Condel Deleterious 77 786 1,741 2,604
Neutral 63 63 861 987
  1. Single nucleotide variants (SNVs) were classified as non-neutral, neutral or uncertain based on functional/experimental data from the literature or mutation databases [28-30]. Each SNV was classified by each of the mutation effect prediction algorithms independently.