ArticleJournal of biomedical science2009
Investigation on the role of nsSNPs in HNPCC genes--a bioinformatics approach.
Article in Journal of biomedical science, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 56 citations in OpenAlex.
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- Investigation of pathogenic germline variants in gastric cancer and development of "GasCanBase" database.Cancer reports (Hoboken, N.J.) · 2023Article
- Neonatal congenital leukemia caused by several missense mutations and AFF1-KMT2A fusion: A case report.Oncology letters · 2022Article
- Do non-pathogenic variants of DNA mismatch repair genes modify neurofibroma load in neurofibromatosis type 1?Child's nervous system : ChNS : official journal of the International Society for Pediatric Neurosurgery · 2022Review
- Increased diagnostic yield in a cohort of hearing loss families using a comprehensive stepwise strategy of molecular testing.Frontiers in genetics · 2022Article
- Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays.Scientific reports · 2021Article
- DNA Mismatch Repair Gene Variants in Sporadic Solid Cancers.International journal of molecular sciences · 2020Review
- Prediction of Deleterious Non-synonymous SNPs of Human STK11 Gene by Combining Algorithms, Molecular Docking, and Molecular Dynamics Simulation.Scientific reports · 2019Article
- Computational insights of K1444N substitution in GAP-related domain of NF1 gene associated with neurofibromatosis type 1 disease: a molecular modeling and dynamics approach.Metabolic brain disease · 2018Article
- A profound computational study to prioritize the disease-causing mutations in PRPS1 gene.Metabolic brain disease · 2018Article
- Assessment of in silico protein sequence analysis in the clinical classification of variants in cancer risk genes.Journal of community genetics · 2017Article
- Targeted next-generation sequencing of 22 mismatch repair genes identifies Lynch syndrome families.Cancer medicine · 2016Article
- Functional and Structural Consequences of Damaging Single Nucleotide Polymorphisms in Human Prostate Cancer Predisposition Gene RNASEL.BioMed research international · 2015Article
- Evaluation and identification of damaged single nucleotide polymorphisms in COL1A1 gene involved in osteoporosis.Archives of medical science : AMS · 2013Article
- Article
- Computational refinement of functional single nucleotide polymorphisms associated with ATM gene.PloS one · 2012Article
- Identification of functional SNPs in BARD1 gene and in silico analysis of damaging SNPs: based on data procured from dbSNP database.PloS one · 2012Article
- Screening and structural evaluation of deleterious Non-Synonymous SNPs of ePHA2 gene involved in susceptibility to cataract formation.Bioinformation · 2012Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA central focus of cancer genetics is the study of mutations that are causally implicated in tumorigenesis. The identification of such causal mutations not only provides insight into cancer biology but also presents anticancer therapeutic targets and diagnostic markers. Missense mutations are nucleotide substitutions that change an amino acid in a protein, the deleterious effects of these mutations are commonly attributed to their impact on primary amino acid sequence and protein structure.
methodsThe method to identify functional SNPs from a pool, containing both functional and neutral SNPs is challenging by experimental protocols. To explore possible relationships between genetic mutation and phenotypic variation, we employed different bioinformatics algorithms like Sorting Intolerant from Tolerant (SIFT), Polymorphism Phenotyping (PolyPhen), and PupaSuite to predict the impact of these amino acid substitutions on protein activity of mismatch repair (MMR) genes causing hereditary nonpolyposis colorectal cancer (HNPCC).
resultsSIFT classified 22 of 125 variants (18%) as 'Intolerant." PolyPhen classified 40 of 125 amino acid substitutions (32%) as "Probably or possibly damaging". The PupaSuite predicted the phenotypic effect of SNPs on the structure and function of the affected protein. Based on the PolyPhen scores and availability of three-dimensional structures, structure analysis was carried out with the major mutations that occurred in the native protein coded by MSH2 and MSH6 genes. The amino acid residues in the native and mutant model protein were further analyzed for solvent accessibility and secondary structure to check the stability of the proteins.
conclusionBased on this approach, we have shown that four nsSNPs, which were predicted to have functional consequences (MSH2-Y43C, MSH6-Y538S, MSH6-S580L, and MSH6-K854M), were already found to be associated with cancer risk. Our study demonstrates the presence of other deleterious mutations and also endorses with in vivo experimental studies.
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