Analysis of evolutionary pressure and pathogenicity of missense variations

Background and aims: Gene and protein sequences are subject to variation upon reproduction where favorable alleles are expressed in further generations by positive selection and bad alleles are being eliminated by means of purifying selection. Thus, selective pressures acting on sequences can result positive or negative selection upon evolution. Ka/Ks ratio is the ratio of non-synonymous and synonymous substitution rate. Calculation of Ka/Ks ratio returns selective evolutionary pressure acting on a particular gene. However, codon wise site specific Ka/Ks ratios calculated for each amino acid differ from the overall selective pressure active on the respective gene. This study was aimed to calculate site specific evolutionary pressure of specific human missense variations of both neutral and pathogenic type and to retrieve hidden facts underlying in it. In addition, analysis of pathogenicity of variants was also another major aspect in this research. Methods: Variation data were obtained from VariBench database. Gene and respective protein sequences reported in the dataset were downloaded along with their orthologs to calculate site specific evolutionary pressures. After that, Ka/Ks values were calculated by Selecton software for each amino acid. Finally, statistical analyses were performed with R to examine selective pressure distribution separately for pathogenic and neutral variations. In addition, pathogenicity was also calculated for individual amino acids and for different amino acid groups. Results: Overall distribution of Ka/Ks values was found to be lower for pathogenic variations than neutral ones. Means, medians, and quartiles were also lower for pathogenic variations for each amino acid and for different amino acid groups. Cysteine, glycine, and tryptophan are among the amino acids which were most likely substituted into pathogenic variants whereas threonine, aspargine and isoleucine were more frequent to result neutral variants. Conclusion: Overall Ka/Ks distribution was lower for pathogenic variants. Neutral variants were less conserved in comparison with the pathogenic type. Moreover, aromatic amino acids were most likely to be converted into pathogenic variations and hence can be marked as having highest pathogenicity. In contrast, negatively charged acidic amino acids showed least pathogenicity