title: Path to facilitate the prediction of functional amino acid substitutions in red blood cell disorders--a computational approach.
abstract: BACKGROUND
  A major area of effort in current genomics is to distinguish mutations that are functionally neutral from those that contribute to disease. Single Nucleotide Polymorphisms (SNPs) are amino acid substitutions that currently account for approximately half of the known gene lesions responsible for human inherited diseases. As a result, the prediction of non-synonymous SNPs (nsSNPs) that affect protein functions and relate to disease is an important task.
  
  
  RESULTS
  In this study, we performed a comprehensive analysis of deleterious SNPs at both functional and structural level in the respective genes associated with red blood cell metabolism disorders using bioinformatics tools. We analyzed the variants in Glucose-6-phosphate dehydrogenase (G6PD) and isoforms of Pyruvate Kinase (PKLR & PKM2) genes responsible for major red blood cell disorders. Deleterious nsSNPs were categorized based on empirical rule and support vector machine based methods to predict the impact on protein functions. Furthermore, we modeled mutant proteins and compared them with the native protein for evaluation of protein structure stability.
  
  
  CONCLUSIONS
  We argue here that bioinformatics tools can play an important role in addressing the complexity of the underlying genetic basis of Red Blood Cell disorders. Based on our investigation, we report here the potential candidate SNPs, for future studies in human Red Blood Cell disorders. Current study also demonstrates the presence of other deleterious mutations and also endorses with in vivo experimental studies. Our approach will present the application of computational tools in understanding functional variation from the perspective of structure, expression, evolution and phenotype.
authors.affiliation: Medical Biotechnology Division, Center for Nanobiotechnology, School of Biosciences and Technology, Vellore Institute of Technology University, Vellore, Tamil Nadu, India.
authors.forename: Rajith
authors.initials: R
authors.lastname: B
authors.forename: George Priya Doss
authors.initials: GP
authors.lastname: C
mesh_terms: D000740:Anemia / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D017353:Gene Deletion; D005954:Glucosephosphate Dehydrogenase / Q000235:genetics; D005955:Glucosephosphate Dehydrogenase Deficiency / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D009154:Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D020033:Protein Isoforms; D011770:Pyruvate Kinase / Q000737:chemistry / Q000235:genetics; D012984:Software
chemical_list: D020033:Protein Isoforms; D005954:Glucosephosphate Dehydrogenase; D011770:Pyruvate Kinase