ArticleMeta gene2014
In silico analysis of single nucleotide polymorphism (SNP) in human TNF-α gene.
Article in Meta gene, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 60 citations in OpenAlex.
- Computational association in parkinson's disease SNPs with brain structural and functional alterations.Neurogenetics · 2025Article
- Identification of candidate nsSNPs of the human FNDC5 gene and their structural and functional consequences using in silico analysis.Scientific reports · 2025Article
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- Investigation of pathogenic germline variants in gastric cancer and development of "GasCanBase" database.Cancer reports (Hoboken, N.J.) · 2023Article
- Single-Nucleotide Variants in microRNAs Sequences or in their Target Genes Might Influence the Risk of Epilepsy: A Review.Cellular and molecular neurobiology · 2022Review
- Identification of functional tumor necrosis factor-alpha promoter variants associated withWorld journal of gastroenterology · 2022Observational
- Screening of Pathogenic Missense Single Nucleotide Variants FromBioinformatics and biology insights · 2022Article
- BRCA1 gene polymorphism and finger dermatoglyphic patterns in Ghanaian breast cancer patients: a quantitative cross-sectional approach.The Pan African medical journal · 2022Article
- Exploring the Structural and Functional Effects of Nonsynonymous SNPs in the Human Serotonin Transporter Gene ThroughBioinformatics and biology insights · 2022Article
- TNF-α/HMGB1 inflammation signalling pathway regulates pyroptosis during liver failure and acute kidney injury.Cell proliferation · 2020Article
- Polymorphisms of TNF-BioMed research international · 2018Article
- Relationship of bovine TNF-α gene polymorphisms with the risk of bovine tuberculosis in Holstein cattle.The Journal of veterinary medical science · 2016Article
- In silico Analysis Revealed High-risk Single Nucleotide Polymorphisms in Human Pentraxin-3 Gene and their Impact on Innate Immune Response against Microbial Pathogens.Frontiers in microbiology · 2016Article
- A Single-Nucleotide Polymorphism of TaGS5 Gene Revealed its Association with Kernel Weight in Chinese Bread Wheat.Frontiers in plant science · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The TNF-α gene mutations are seen in many diseases especially inflammatory diseases. Hence, before planning a larger population study, it is advisable to sort out the possible functional SNPs. To accomplish this goal, data available in the dbSNP database and different computer programs can be used. Therefore, this study was undertaken to find the functional nsSNPs (non-synonymous single nucleotide polymorphisms) in TNF-α. Out of the total 169 SNPs, 48 were nsSNPs (non-synonymous single nucleotide polymorphisms), 23 occurred in the mRNA 3' UTR, 10 occurred in 5' UTR region, 41 occurred in intronic regions and the rest were other types of SNPs. SIFT and PolyPhen predicted 2 out of 48 nsSNPs as damaging. Among the predicted nsSNPs, rs4645843 and rs1800620 were identified as deleterious and damaging by the SIFT (Sorting Intolerant from Tolerant) and PolyPhen programs. Additionally, I-Mutant and nsSNPAnalyzer showed a decrease in stability for these nsSNPs upon mutation. Protein structural analysis with these amino acid variants was performed by using I-Mutant, Swiss PDB viewer, ANOLEA (Atomic Non-Local Environment Assessment), MUSTER (MUlti-Sources ThreadER) and NOMAD-Ref servers to check their molecular dynamics and energy minimization calculations. This study suggested that P84L and A94T variants of TNF-α could directly or indirectly destabilize the amino acid interactions and hydrogen bond networks thus explaining the functional deviations of protein to some extent.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.