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Research Article Open access CC BY 4.0

Prediction by in silico Tools of Non-synonymous Single Nucleotide Polymorphisms (nsSNP) and 3-d Protein Structure Prediction in the Female MED12 Gene Associated with Uterine Leiomyomas

Bineta Keneme, Mbacke Sembene

Annual Research & Review in Biology · pp. 11–23 · Published 24 Dec 2023

10.9734/arrb/2023/v38i1030609

Abstract

Aims: Uterine leiomyomas are one of the most common benign gynecologic tumors, but the exact causes are not completely understood. Mutations at exon 2 MED12 gene was discovered in approximately 71% of uterine leiomyomas. Our recent studies confirmed the high frequency of MED12 exon 2 deleterious mutations in uterine leiomyoma in senegalese patients. In this context, molecular dynamics simulations of wild-type and non synonymous variants were conducted to access their structural dynamic and stability characteristics. Methodology: Tumour tissues were collected from 50 senegalese patients with uterine leiomyomas. We sequenced 226 bp for exon 2 region after DNA extraction and amplification. To understand the mutation’s role in this gene, we utilized computational tools based on different algorithms, including missense tools to predict pathogenic variants such as Alamut™ Visual Plus, ProtParam, Missense 3D; stability tools to analyze the impression of a mutated gene on the function of the protein like Dynamut2 and NetSurfP - 3.0, and post translational modifications using MutPred2. Results: Out of 50 patients with uterine fibroids, 88% have mutations in exon 2 of the MED12 gene. All this mutations are missense mutations. They are L36R, Q43P, G44C, GDDR, G44S, G44A, G44V, G44D, F45V, K60M and N61Y. A significant impact of the MED12 mutations has showed with a high frequency in codon 44. It was identified that all residues in codon 44 were identified to fall in disallowed regions. Our results show that all nsSNP except G44D, K60M and N61Y are associated with molecular mechanisms such as intrinsic disorder, altered disorder interface, gain or loss of helix, gain or loss of loop and post-translational modifications such as gain or loss of methylation, loss of ubiquitylation. Conclusion: Deleterious mutations identified in exon 2 MED12 gene show their implication in uterine leiomyomas. Given that the mutants identified are associated with protein instability, this opens up avenues for reflection on possible alterations of protein function in cases of uterine fibroids.

MED12 leiomyomas in silico tools 3D structure modeling

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