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An in silico approach to characterize nonsynonymous SNPs and regulatory SNPs in human TOX3 gene

Mehran Akhtar1, Tazkira Jamal, Jalal Ud Din

  • 1Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Pakistan. fazaljalil@awkum.edu.pk.

Journal of Genetics
|December 11, 2019
PubMed

Insights

This study identifies damaging single-nucleotide polymorphisms (SNPs) in the TOX3 gene linked to breast cancer. These genetic variations may impact protein function and gene regulation, offering potential for personalized medicine.

Area of Science:

  • Genetics
  • Molecular Biology
  • Bioinformatics

Background:

  • Cancer is a complex, multigene disease where single-nucleotide polymorphisms (SNPs) play a significant role.
  • The TOX3 gene is implicated in breast cancer, with previous research exploring SNP associations.

Purpose of the Study:

  • To computationally identify and analyze potentially damaging nonsynonymous SNPs (nsSNPs) in the TOX3 gene.
  • To investigate the functional and structural impact of these nsSNPs on TOX3 protein.
  • To characterize regulatory SNPs affecting TOX3 gene expression.

Main Methods:

  • Utilized in silico tools (PolyPhen2, SNP&GO, PhD-SNP, PROVEAN) to predict nsSNP deleteriousness.
  • Employed I-Mutant, MutPred1.2, and ConSurf to assess stability, functional, and structural effects.
  • Designed 3D protein models using I-TASSER for wild-type and mutant TOX3.

Main Results:

  • Identified rs368713418 (A266D), rs751141352 (P273S/T), and rs200878352 (A275T) as highly deleterious nsSNPs.
  • Found premature stop codon SNPs (e.g., Q527STOP) crucial for truncated protein formation.
  • Characterized nine regulatory SNPs with potential to affect TOX3 gene regulation.

Conclusions:

  • Identified specific nsSNPs and regulatory SNPs in TOX3 with significant implications for breast cancer.
  • These findings highlight the importance of studying these SNPs in model organisms and cell cultures.
  • The identified SNPs may hold potential for personalized medicine and gene therapy approaches in breast cancer treatment.

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