Single nucleotide polymorphisms (SNPs) are variations in a single nucleotide base within the DNA sequence that occur in at least 1 % of the population. SNPs are found throughout the genome and could be the cause of differences in how individuals respond to diseases, drugs, and environmental factors. Deleterious SNPs predispose individuals to various diseases and by studying genetic variations in individuals, it is possible to develop personalized medicine. SNPs can occur in the coding regions of the gene producing a change in the amino acid (nonsynonymous) or can be silent without causing a change in the amino acid (synonymous), or can occur in the non-coding regions (5’ untranslated region (UTR), 3’UTR, and introns). Missense nonsynonymous SNPs (nsSNPs) cause variations in the amino acid sequence and have the potential to affect the structure and function of a protein thereby impacting the pathogenesis and progression of diseases in individuals. SNPs can also influence gene expression and translational efficiency by affecting promoter activity, conformation and stability of messenger RNA (mRNA).
Author(s) Details:
Harini Venkata Subbiah
Human Genetics Research Centre, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, 600100, India.
Usha Subbiah
Human Genetics Research Centre, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, Tamil Nadu, 600100, India.
Recent Global Research Developments in In Silico Analysis of Single Nucleotide Polymorphisms (SNPs) in the Human GCH1 Gene
In Silico Analysis of Single Nucleotide Polymorphisms in Human β-Globin Gene: This study used various in silico tools to analyze SNPs in the β-globin gene, which is crucial for understanding hemoglobinopathies. Tools like SIFT, PolyPhen, and Pupa Suite were used to predict the impact of SNPs on protein function and structure [1] .
Determination of Deleterious Single-Nucleotide Polymorphisms of Human LYZ C Gene: This research focused on identifying deleterious SNPs in the LYZ C gene using computational methods. Tools like SIFT, PolyPhen, and I-Mutant 3.0 were employed to predict the impact of SNPs on protein stability and function [2] .
In Silico Analysis of Functional Single Nucleotide Polymorphisms in the Human GCH1 Gene: This study specifically analyzed SNPs in the GCH1 gene using in silico algorithms like PolyPhen-2, SIFT, and nsSNP Analyzer. The research aimed to identify high-risk nsSNPs that could affect protein function [3] .
Single-Nucleotide Polymorphisms (SNP) Mining and Their Impact on Gene Expression: This research explored the impact of SNPs located in the 5’-untranslated region (UTR) or 3’-UTR on transcription factor binding sites and alternative splicing regulatory motifs. The study used FASTSNP to assess the risk associated with these SNPs [4] .
In Silico Analysis of Single Nucleotide Polymorphisms in Human Genes: This comprehensive study analyzed SNPs across various human genes, including GCH1, using multiple in silico tools to predict their functional impact. The research highlighted the importance of computational methods in understanding genetic variations [2] .
References
- Alanazi, M., Abduljaleel, Z., Khan, W., Warsy, A. S., Elrobh, M., Khan, Z., … & Bazzi, M. D. (2011). In silico analysis of single nucleotide polymorphism (SNPs) in human β-globin gene. PloS one, 6(10), e25876.
- Venkata Subbiah, H., Ramesh Babu, P. & Subbiah, U. Determination of deleterious single-nucleotide polymorphisms of human LYZ C gene: an in silico study. J Genet Eng Biotechnol 20, 92 (2022). https://doi.org/10.1186/s43141-022-00383-8
- Kelly, J. N., & Barr, S. D. (2014). In silico analysis of functional single nucleotide polymorphisms in the human TRIM22 gene. PLoS One, 9(7), e101436.
- Vallejos-Vidal E, Reyes-Cerpa S, Rivas-Pardo JA, Maisey K, Yáñez JM, Valenzuela H, Cea PA, Castro-Fernandez V, Tort L, Sandino AM, Imarai M and Reyes-López FE (2020) Single-Nucleotide Polymorphisms (SNP) Mining and Their Effect on the Tridimensional Protein Structure Prediction in a Set of Immunity-Related Expressed Sequence Tags (EST) in Atlantic Salmon (Salmo salar). Front. Genet. 10:1406. doi: 10.3389/fgene.2019.01406
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