Prediction of deleterious single nucleotide polymorphisms and their effect on the sequence and structure of the human CCND1 gene

Abstract

Objective The CCND1 gene expresses a protein, G1/S-specific cyclin, that regulates the G1/S transition in the cell cycle and also inhibits retinoblastoma (RB) proteins. Overexpression or rearrangements of this gene can result in various tumours. This study aimed to identify possible deleterious non-synonymous single nucleotide polymorphisms (SNP's) of CCND1 using computational methods. Methods SNPs in the human CCND1 gene were retrieved from dbSNP. These SNPs were screened by the Sorting Intolerant From Tolerant (SIFT) algorithm and the PredictSNP classification. Mutants with deleterious SNPs were built using Discovery Studio 3.5, and dynamics studies were performed on native and mutant varieties. Results In Homo sapiens , 1194 SNPs were found, of which 94 were missense and 2 were nonsense SNPs. Three SNPs were found to be deleterious. Molecular dynamics and trajectory analysis showed that there was a significant deviation of the root mean square deviation (RMSD) values in the N216K mutant from the values of the native protein. Conclusion Based on this study, we propose that the SNP with SNP ID rs112525097 (NM_053056.2:c.648C>G) might cause aberrations in CCND1 , which might lead to a change in the function of the G1/S-specific cyclin protein. This, in turn, may lead to the development of acute myeloid leukaemia (AML).

Finding Pathogenic nsSNP’s and their structural effect on COPS2 using Molecular Dynamic Approach

“…The QMEAN scores were also calculated for the mutated structures using SWISS-MODEL QMEAN tool [31] with the score of -3.29, -3.24, -3.28, -3.2, -3.27 and -3.38 respectively. Which is all below the threshold of -4.0. therefore considered as a significant [32].…”