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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.
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Orphanet Journal of Rare Diseases

ISSN: 1750-1172