Consideration of pathogenicity of nsSNVs in CDKN2A gene, as a new tumor marker for leukemia, using bioinformatics methods

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Farzaneh Ghasemi¹, Mohammad Mehdi Heidari², Mehri Khatami³, Yuriy L. Orlov^4
1Department of Biology, Faculty of science,Yazd University, Yazd, Iran, heidarimm@yazd.ac.ir
²Department of Biology, Faculty of science,Yazd University, Yazd, Iran, heidarimm@yazd.ac.ir
³Department of Biology, Faculty of science,Yazd University, Yazd, Iran, heidarimm@yazd.ac.ir
⁴I.M.Sechenov First Moscow State Medical University, Moscow, Russia, orlov@bionet.nsc.ru

CDKN2A as a tumor suppressor gene (TSG) encodes p14 and p16 that they are tumor suppressor proteins and cell cycle regulators. Downregulation of these proteins causes various cancers. Sequence deletions or promoter hypermethylation lead to downregulation of these proteins. Also, point mutations can be caused malfunction or dysfunction of proteins. The aim of this study is definition of pathogenicity of non-synonymous single nucleotide variants (nsSNVs). We study three nsSNVs including rs104894095, rs786204195 and rs104894098 from NCBI/dbSNP databank. Then, these nsSNVs are considered by bioinformatics tools such as SIFT, PolyPhen-2, I-Mutant2.0, PANTHER, P-Mut, ExPASy/ProtScale, PEPTIDE 2.0 web server and PyMOL software. Plot of hydrophobicity of rs104894098 (V126D) is significantly changed. Also, we study hydrogen bonds length and atom distances in Aspartic acid substituted Valine in position 126 by PyMOL software. These parameters are compared with wild type protein. Finally, we find that rs786204195 and rs104894095 have destructive effects. But, rs104894098 (V126D) is deleterious because polar contacts, protein stability and hydrophobicity are changed in mutant form. This theory should be proved with experimental studies.