PTENpred: A Designer Protein Impact Predictor for PTEN-related Disorders

J Comput Biol. 2016 Dec;23(12):969-975. doi: 10.1089/cmb.2016.0058. Epub 2016 Jun 16.


Connecting a genotype with a phenotype can provide immediate advantages in the context of modern medicine. Especially useful would be an algorithm for predicting the impact of nonsynonymous single-nucleotide polymorphisms in the gene for PTEN, a protein that is implicated in most human cancers and connected to germline disorders that include autism. We have developed a protein impact predictor, PTENpred, that integrates data from multiple analyses using a support vector machine algorithm. PTENpred can predict phenotypes related to a human PTEN mutation with high accuracy. The output of PTENpred is designed for use by biologists, clinicians, and laymen, and features an interactive display of the three-dimensional structure of PTEN. Using knowledge about the structure of proteins, in general, and the PTEN protein, in particular, enables the prediction of consequences from damage to the human PTEN gene. This algorithm, which can be accessed online, could facilitate the implementation of effective therapeutic regimens for cancer and other diseases.

Keywords: autism; cancer; mutation; phosphatase and tensin homolog deleted from chromosome ten; support vector machine algorithm..

MeSH terms

  • Algorithms*
  • Autistic Disorder / genetics
  • Autistic Disorder / pathology*
  • Humans
  • Mutation
  • Neoplasms / genetics
  • Neoplasms / pathology*
  • PTEN Phosphohydrolase / genetics*
  • PTEN Phosphohydrolase / metabolism
  • Phenotype
  • Polymorphism, Single Nucleotide*
  • Predictive Value of Tests
  • Software*
  • Support Vector Machine


  • PTEN Phosphohydrolase
  • PTEN protein, human