Skip to main content

Table 6 Results from the three different analysis programs used to predict the pathogenicity of novel missense changes

From: Mutational screening of the USH2A gene in Spanish USH patients reveals 23 novel pathogenic mutations

  SIFT PolyPhen PMUT
p.G44R Affect (Score 0.01) Probably damaging Pathogenic (NN output 0.5113)
p.N2377S Tolerated (Score 0.44) Possibly damaging Neutral (NN output 0.2372)
p.N2394K Tolerated (Score 0.23) Possibly damaging Neutral (NN output 0.5113)
p.G3546R Affect (Score 0.01) Probably damaging Pathogenic (NN output 0.1799)
p.N3894D Tolerated (Score 0.05) Probably damaging Neutral (NN output 0.0522)
p.E4921K Tolerated (Score 0.85) Benign Neutral (NN output 0.3130)
  1. SIFT: SIFT Score ranges from 0 to 1. The amino acid substitution is predicted to be damaging if the score is < 0.05, and tolerated if the score is 0/> 0.05.
  2. PolyPhen: "Probably damaging" (it is believed most likely to affect protein function or structure), "Possibly damaging" (it is believed to affect protein function or structure), "Benign" (most likely lacking any phenotypic effect).
  3. PMUT: NN output is the original output from the neural network for this mutation and its parameters. If that output is bigger than 0.5 it is predicted as pathogenic, otherwise as neutral.