title: Genetic association of KCNJ10 rs1130183 with seizure susceptibility and computational analysis of deleterious non-synonymous SNPs of KCNJ10 gene.
abstract: Establishing genetic basis of Idiopathic generalized epilepsies (IGE) is challenging because of their complex inheritance pattern and genetic heterogeneity. Kir4.1 inwardly rectifying channel (KCNJ10) is one of the independent genes reported to be associated with seizure susceptibility. In the current study we have performed a comprehensive in silico analysis of genetic variants in KCNJ10 gene at functional and structural level along with a case-control analysis for the association of rs1130183 (R271C) polymorphism in Indian patients with IGE. Age and sex matched 108 epileptic patients and normal healthy controls were examined. Genotyping of KCNJ10rs1130183 variation was performed using PCR-RFLP method. The risk association was determined by using odds ratio and 95% confidence interval. Functional effects of non-synonymous SNPs (nsSNPs) in KCNJ10 gene were analyzed using SIFT PolyPhen-2, I-Mutant 2.0, PANTHER and FASTSNP. Subsequently, homology modeling of protein three dimensional (3D) structures was performed using Modeller tool (9.10v) and compared the native protein with mutant for assessment of structure and stability. SIFT, PolyPhen-2, I-Mutant 2.0 and PANTHER collectively showed rs1130183, rs1130182 and rs137853073 SNPs inKCNJ10 gene affect protein structure and function. There was a considerable variation in the Root Mean Square Deviation (RMSD) value between the native and mutant structure (1.17Ǻ). Association analysis indicate KCNJ10rs1130183 did not contribute to risk of seizure susceptibility in Indian patients with IGE (OR- 0.38; 95%CI, 0.07-2.05) and T allele frequency (0.02%) was in concordance with dbSNP reports. This study identifies potential SNPs that may contribute to seizure susceptibility and further studies with the selected SNPs in larger number of samples and their functional analysis is required for understanding the variants of KCNJ10 with seizure susceptibility.
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal-576104, India.
authors.forename: Nagaraja M
authors.initials: NM
authors.lastname: Phani
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal-576104, India.
authors.forename: Shreeshakala
authors.initials: S
authors.lastname: Acharya
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal-576104, India.
authors.forename: Seethu
authors.initials: S
authors.lastname: Xavy
authors.affiliation: Department of Pediatrics, Kasturba Medical College, Manipal University, Manipal-576104 India.
authors.forename: Nalini
authors.initials: N
authors.lastname: Bhaskaranand
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal-576104, India.
authors.forename: Manoj K
authors.initials: MK
authors.lastname: Bhat
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal-576104, India.
authors.forename: Aditya
authors.initials: A
authors.lastname: Jain
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal-576104, India. Electronic address: padmalatha.rai@manipal.edu.
authors.forename: Padmalatha S
authors.initials: PS
authors.lastname: Rai
authors.forename: Kapaettu
authors.initials: K
authors.lastname: Satyamoorthy
authors.affiliation: Division of Biotechnology, School of Life Sciences, Manipal University, Manipal-576104, India.
authors.forename: Satyamoorthy
authors.initials: S
authors.lastname: Kapaettu
mesh_terms: D016022:Case-Control Studies; D005787:Gene Frequency / Q000235:genetics; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D005838:Genotype; D006801:Humans; D009154:Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D024661:Potassium Channels, Inwardly Rectifying / Q000235:genetics*; D012640:Seizures / Q000209:etiology / Q000235:genetics*; D000098854:Kcnj10 Channel
chemical_list: D000098854:Kcnj10 Channel; D024661:Potassium Channels, Inwardly Rectifying
keywords: CI; CNS; Central nervous system; Computational prediction tools; Confidence interval; Epilepsy; FASTSNP; Functional analysis and selection tool for single nucleotide polymorphisms; HMM; Hidden Markov Model; Hp; Hydrophobicity; IGE; Idiopathic generalized epilepsy; KCNJ10 rs1130183 (R271C) polymorphism; LRO; Long range order; MSA; Multiple sequence alignment; NCBI; National Centre for Biotechnology Information; Non synonymous single nucleotide polymorphisms; OR; Odds ratios; PANTHER; PDB; PSIC; PolyPhen-2; Polymorphism phenotyping-2; Position specific independent counts; Protein analysis through evolutionary relationships; Protein data bank; QTL; Quantitative trait loci; RMSD; RSA; Relative solvent accessibility; Root mean square deviation; SABLE; SC; SIFT; SNPs; SRs; SVM; Seizure; Single nucleotide polymorphisms; Solvent Accessibilities; Sorting intolerant from tolerant; Stabilizing center; Stabilizing residues; Substitution position specific evolutionary conservation; Support vector machine; TI; TIFAC-CORE; Technology Information Forecasting and Assessment Council - Centre of Relevance and Excellence; Tolerance index; UTR; Untranslated region; nsSNPs; subPSEC