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Related Concept Videos

Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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Related Experiment Video

Updated: Sep 10, 2025

In Vivo Modeling of the Morbid Human Genome using Danio rerio
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Computational insights into PKCθ non-synonymous SNPs: from structural changes to functional implications.

Amna Hafeez1, Andleeb Farooq1, Maria Shabbir1

  • 1Department of Bioscience, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan.

Journal of Biomolecular Structure & Dynamics
|August 23, 2025
PubMed
Summary

This study identifies six highly pathogenic single-nucleotide polymorphisms (SNPs) in the PRKCQ gene, linked to cancer. These variants impact protein kinase C theta (PKCθ) stability and function, suggesting new therapeutic targets.

Keywords:
PKCθ’Single nucleotide polymorphismsbioinformatic toolscancermolecular dynamics simulations

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Area of Science:

  • Genetics and Molecular Biology
  • Bioinformatics
  • Cancer Research

Background:

  • Single-nucleotide polymorphisms (SNPs) are key to individual genetic variation, evolution, and disease susceptibility, including cancer and diabetes.
  • The PRKCQ gene encodes protein kinase C theta (PKCθ), a crucial enzyme in immune responses and cancer development.

Purpose of the Study:

  • To identify and characterize pathogenic non-synonymous SNPs (nsSNPs) in the PRKCQ gene.
  • To assess the impact of these nsSNPs on PKCθ protein structure, stability, and function.
  • To explore the implications of these findings for PRKCQ-associated diseases and personalized medicine.

Main Methods:

  • Utilized multiple bioinformatics tools for pathogenicity assessment of nsSNPs.
  • Performed structural predictions, domain analysis, and conservation profiling of PKCθ.
  • Conducted stability analyses and molecular dynamics (MD) simulations for selected nsSNPs.

Main Results:

  • Identified six highly pathogenic and oncogenic nsSNPs in PRKCQ (rs1838691533 R6W, rs145984477 P27L, rs1248923790 C29Y, rs1837738907 R145C, rs1837738573 R146W, rs1403981107 L495P).
  • Found variants located in critical functional domains of PKCθ, affecting membrane binding and catalytic activity.
  • Demonstrated that most nsSNPs decrease protein stability and significantly alter PKCθ conformation and dynamics.

Conclusions:

  • Pathogenic nsSNPs in PRKCQ can critically impact PKCθ function, contributing to oncogenic signaling.
  • These findings highlight the role of PRKCQ in cancer and suggest potential for targeted therapies.
  • The study supports personalized medicine approaches for diseases associated with PRKCQ variations.