title: In silico analysis of functional nsSNPs in human TRPC6 gene associated with steroid resistant nephrotic syndrome.
abstract: The aim of the present study is to identify functional non-synonymous SNPs of TRPC6 gene using various in silico approaches. These SNPs are believed to have a direct impact on protein stability through conformation changes. Transient receptor potential cation channel-6 (TRPC6) is one of the proteins that plays a key role causing focal segmental glomerulosclerosis (FSGS) associated with the steroid-resistant nephritic syndrome (SRNS). Data of TRPC6 was collected from dbSNP and further used to investigate a damaging effect using SIFT, PolyPhen, PROVEAN, and PANTHER. The comparative analysis predicted that two functional SNPs "rs35857503 at position N157T and rs36111323 at position A404V" showed a damaging effect (score of 0.096-1.00).We modeled the 3D structure of TRPC6 using a SWISS-MODEL workspace and validated it via PROCHECK to get a Ramachandran plot (83.0% residues in the most favored region, 12.7% in additionally allowed regions, 2.3% in a generously allowed region and 2.0% were in a disallowed region). QMEAN (0.311) and MUSTER (10.06) scores were under acceptable limits. Putative functional SNPs that may possibly undergo post-translation modifications were also identified in TRPC6 protein. It was found that mutation at N157T can lead to alteration in glycation whereas mutation at A404V was present at a ligand binding site. Additionally, I-Mutant showed a decrease in stability for these nsSNPs upon mutation, thus suggesting that the N157T and A404V variants of TRPC6 could directly or indirectly destabilize the amino acid interactions causing functional deviations of protein to some extent.
authors.affiliation: Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), affiliated to Sardar Patel University, Vallabh Vidyanagar, Gujarat 388120, India.
authors.forename: Bhoomi B
authors.initials: BB
authors.lastname: Joshi
authors.affiliation: College of Veterinary Sciences and Animal Husbandary, Anand Agricutural University, India.
authors.forename: Prakash G
authors.initials: PG
authors.lastname: Koringa
authors.affiliation: Ashok and Rita Patel Institute of Integrated Study and Research in Biotechnology and Allied Sciences (ARIBAS), affiliated to Sardar Patel University, Vallabh Vidyanagar, Gujarat 388120, India. Electronic address: kinnarimistry@aribas.edu.in.
authors.forename: Kinnari N
authors.initials: KN
authors.lastname: Mistry
authors.affiliation: College of Veterinary Sciences and Animal Husbandary, Anand Agricutural University, India.
authors.forename: Amrut K
authors.initials: AK
authors.lastname: Patel
authors.affiliation: Muljibhai Patel Urological Hospital, Dr. V.V. Desai Road, Nadiad 387 001, Gujarat, India.
authors.forename: Sishir
authors.initials: S
authors.lastname: Gang
authors.affiliation: College of Veterinary Sciences and Animal Husbandary, Anand Agricutural University, India.
authors.forename: Chaitanya G
authors.initials: CG
authors.lastname: Joshi
mesh_terms: D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D001665:Binding Sites / Q000235:genetics; D003198:Computer Simulation; D017124:Conserved Sequence; D030541:Databases, Genetic; D004351:Drug Resistance; D005923:Glomerulosclerosis, Focal Segmental / Q000235:genetics; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009404:Nephrotic Syndrome / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D017354:Point Mutation; D020641:Polymorphism, Single Nucleotide; D011487:Protein Conformation; D011499:Protein Processing, Post-Translational; D055550:Protein Stability; D012984:Software; D013256:Steroids / Q000494:pharmacology; D050052:TRPC Cation Channels / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D000074287:TRPC6 Cation Channel
chemical_list: D008024:Ligands; D013256:Steroids; D050052:TRPC Cation Channels; D000074287:TRPC6 Cation Channel; C117032:TRPC6 protein, human
keywords: Genomic variants; In silico analysis; Ligand binding sites; Modeled structure; Post translational modification; TRPC6 gene