Abstract—The ability to distinguish missense nucleotide substitutions that contribute to harmful effect from those that do not is a difficult problem usually accomplished through functional in vivo analyses. In this study, instead current biochemical methods, the effects of missense mutations upon protein structure and function were assayed by means of computational methods and information from the databases. For this order, the effects of new missense mutations in exon 5 of PTEN gene upon protein structure and function were examined. The gene coding for PTEN was identified and localized on chromosome region 10q23.3 as the tumor suppressor gene. The utilization of these methods were shown that c.319G>A and c.341T>G missense mutations that were recognized in patients with breast cancer and Cowden disease, could be pathogenic. This method could be use for analysis of missense mutation in others genes. Keywords—Bioinformatics, missense mutations, PTEN tumor suppressor gene. I. INTRODUCTION HE word of mutation was primarily used by De Vries to describe a method for genesis of new species, though it is quite different than the current definition. Many different types of mutations are in the human genome and they are classified in two main group including major gene rearrangements and point mutations. Point mutations are single substitutions of specific bases in DNA including adenine, guanine, cytosine, and thymine. Alterations in the DNA sequence can result in an alteration of the protein sequence, expression or function. Point mutations within a gene that results a substitution of one amino acid to another in a protein were called missense mutations. The effects of missense mutations range from early lethality in fetal development to no observable phenotypic changes [1]. The effects of mutations on a proteins structures and functions have until recently only been assigned by laborious biochemical characterization of the mutant proteins. In these days computational methods and wide range of information from the databases containing information on DNA and I. Nasseri is with the National Institute of Biochemistry and Biophysics (IBB), Tehran, Iran (phone: +98-915-9157100; fax: (+9821) 66404680; e- mail: Isar.nassiri@ibb.ut.ac.ir). B. Goliaei is now with the National Institute of Biochemistry and Biophysics (IBB), Tehran, Iran (phone: +98-21 6111-3356/6649-8672; fax: (+9821) 66404680; e-mail: goliaei@ibb.ut.ac.ir). M. Tavassoli is with the Molecular Genetics, Division of Genetics, Dept of Biology, Faculty of Science, The University of Isfahan (e-mail: manoochehr@biol.ui.ac.ir). protein sequences and on protein structure and function are exploited in order to the assessment of the effects of mutation on the protein structure and function [2]. In this study computational methods were used to examine the effects of new missense mutations in exon 5 of PTEN tumor suppressor gene upon protein structure and function. The gene coding for PTEN (Phosphatase and Tensin homolog deleted on chromosome TEN), also called MMAC1 (Mutated in Multiple Advanced Cancers) was identified and localized to chromosome region 10q23.3 as the tumour suppressor gene [3,4] responsible for susceptibility to Cowden (CD) [5], Lhemitte-Duclos (LDD) and to Bannayan-Zonana syndromes (BZS) [6]. PTEN contains 9 exons and encodes a 403 amino acid lipid phosphatase that dephosphorylates D3 of phosphatidylinositol (3,4,5) trisphosphate (PtdIns(3,4,5)P3) in opposition to phosphatidylinositol 3 kinase (PI3K) activity. PTEN is a member of the large PTP (protein tyrosine phosphatase) family [7]. The structure of PTEN consists of an N terminal phosphatase domain followed by an associated C terminal C2 domain [8]. The phosphatase domain contains the active site which carries out the enzymatic function of the protein. C- terminal tail contains a cluster of serine and threonine residues (PEST sequence) that become phosphorylated in many cells, and a binding site for a group of PDZ domain containing proteins. The C2 domain allows PTEN bind to the phospholipid membrane and dephosphorylation of PI3P [9]. The purpose of this study was assessment of the pathogenicity of amino acids substitution in phosphatase domain of PTEN protein by computational methods and information from the databases. II. MATERIALS AND METHODS The studied material comprised of 2 new missense mutation and 34 single nucleotide polymorphism in coding and noncoding regions of PTEN gene. For traditional sequencing, PCR products were amplified from genomic DNA extracted from somatic cell. Sequence reactions were done using conventional Sanger sequencing methods for sense directions. Traces were analyzed using Sequencher (Gene Codes, Ann Arbor, MI). At the first step of study, in a order to establish the novelty of mutations the databases NIEHS (National institute of environmental health science) and COSMIC (Catalogue of Somatic Mutations in Cancer) were searched [10, 11]. Bioinformatics Profiling of Missense Mutations I. Nassiri, B. Goliaei, and M. Tavassoli T World Academy of Science, Engineering and Technology 52 2009 207