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Numerous disease-causing and neutral variations have been identified in several genes and proteins. To gain insight into the total number of harmful variations we have performed protein-wide predictions for Bruton tyrosine kinase (BTK) involved in primary immunodeficiency and mismatch repair (MMR) system proteins in gastric cancers. Mutation rates have been measured and estimated for certain proteins, however, are not very useful in this respect as the rates are known to vary by 100 fold depending on the gene.
We developed dedicated predictors both for the BTK, called PONBTK (1), and for four MMR proteins, called PON-MMR2 (2). The methods were carefully evaluated before used for the analyses. They both have very good performance according to several measures. In the case of BTK kinase domain we found that altogether two thirds of all the possible single-nucleotide substitution-caused amino acid variations (SNAVs) are harmful. In the case of the MMR proteins, where all the possible substitutions i.e. 19 per position, were investigated the ratios are somewhat smaller than for BTK and different for individual proteins. Predictions with PON-P2 (3), a generic pathogenicity predictor, indicate very different ratios of harmful variants in proteins. PON-P2 is very suitable for this kind of analysis due to its high performance and ability to distinguish harmful variants. We have applied this approach to all the 22 mitochondrial tRNA molecules by using our novel PON-mt-tRNA predictor (4). Several mechanisms are behind the harmful variants. When developing a new predictor for protein solubility affecting variants (PON-Sol, 4), we tested the method on interleukin 1-β and found structure context dependent distribution differences for the solubility increasing and decreasing variants.
Knowledge about harmful variants in genes and proteins allows deeper insight into diseases and when combined with other information, such as protein structures, understanding the mechanisms behind diseases due to variants.
All the tools mentioned are freely available at http://structure.bmc.lu.se/
1. Väliaho, J., Faisal, I., Ortutay, C., Smith, C. I. E. and Vihinen, M. (2015) Characterization of all possible single-nucleotide change caused amino acid substitutions in the kinase domain of Bruton tyrosine kinase. Hum. Mutat. 36, 638-647.
2. Niroula, A. and Vihinen, M. (2015) Classification of amino acid substitutions in mismatch repair proteins using PON-MMR2.
3. Niroula, A., Urolagin, S. and Vihinen, M. (2015) PON-P2: Prediction method for fast and reliable identification of harmful variants. PLoS ONE 10(2):e0117380.
4. Niroula, A. and Vihinen, M. (2016) PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations. Nucleic Acids Res. 44, 2020-2027.
5. Yang, Y., Niroula, A., Shen, B., and Vihinen, M. PON-Sol: prediction of effects of variants on protein solubility. Bioinf. (in press).