Identification of deleterious nsSNPs in human HGF gene: in silico approach

Abstract

HGF is a protein that binds to the hepatocyte growth factor receptor to regulate cell growth, cell motility and morphogenesis in different cells and tissues. Several bioinformatics tools and in silico methods were used to identify most deleterious nsSNPs that might change the structure and function of HGF protein. The in silico tools such as SIFT, SNP&GO and PolyPhen2 were used to distinguish deleterious nsSNPs from neutral ones. Protein stability is analysed by I‐Mutant, MUpro and iStable. The functional and structural effects are predicted by other tools like MutPred2, Maestro, DUET etc. Analysis of structure was performed by HOPE and Mutation3D. SWISS-MODEL. server, was used for wild type and mutant proteins 3‐D Modelling. Gene–gene and protein–protein interaction were predicted by GeneMANIA and STRING, respectively. The wildtype HGF protein and these three variants were independently docked with their close interactor protein MET by the use of ClusPro. Our study suggested that out of 392 missense nsSNPs of the HGF gene, five nsSNPs (D358G, G648R, I550N, N175S and R220Q), are the most deleterious in HGF gene. Gene–gene interactions showed relation of HGF with other genes depicting its importance in several pathways and co‐expressions. The protein–protein interacting network is composed of 11 nodes. Analysis of protein stability by different tools indicated that the five nsSNPS decreased the stability of the protein. Anyway these nsSNPs need a confirmation analysis by experimental investigation and GWAS studies

Communicated by Ramaswamy H. Sarma

Keywords:

• Bioinformatic tools
• mutations
• protein stability
• gene–gene interaction
• 3D homology modelling

Data availability statement

All data generated or analyzed during this study are included in this published article.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Ethics approval and consent to participate

This article does not contain any studies with human participants or animals performed by any of the authors.

Funding

This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.