Background: Hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome is an autosomal recessive inborn error of the urea cycle. It is caused by mutations in the SLC25A15 gene that codes the mitochondrial ornithine transporter. The aim of this study is to detect and identify the pathogenic SNPs in SLC25A15 gene through a combination set of bioinformatics tools and their effect on the structure and function of the protein. Methods:The deleterious SNPs in SLC25A15 are detected by various bioinformatics tools, with addition to identifying their effects on the structure and function of this gene.Results: 20 deleterious SNPs out 287of were found to have their own damaging effects on the structure and function of the SLC25A15 gene. Conclusion:This study is the first in silico analysis of SLC25A15 using a selection of bioinformatics tools to detect functional and structural effects of deleterious SNPs. Finding the pathogenic SNPs is a promising start to innovate new, useful SNP diagnostic markers for medical testing and for safer novel therapies specifically targeting mutant SLC25A15.
Background: Retinitis Pigmentosa (RP) refers to a group of inherited disorders characterized by the death of photoreceptor cells leading to blindness. The aim of this study is to identify the pathogenic SNPs in the IDH3A gene and their effect on the structure and function of the protein. Method: we used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein. Result: 20 deleterious SNPs out of 178 were found to have a damaging effect on the protein structure and function. Conclusion: this is the first in silico analysis of IDH3A gene and 20 novel mutations were found using different bioinformatics tools, and they could be used as diagnostic markers for Retinitis Pigmentosa.Keywords: Retinitis Pigmentosa (RP), IDH3A, SNP, in silico analysis, diagnostic markers.RP has three patterns of inheritance; autosomal dominant (adRP), autosomal recessive (arRP) and X-linked pattern (14,(20)(21)(22) and the most reported genes for each case are RHO gene, USH2A and RPGR respectively (4, 21-24) yet the gene we are working on, Isocitrate Dehydrogease 3, (IDH3A) is a novel gene identified as the cause of typical arRP (25) located in the human chromosome 15q25.1 (26). The IDH3A function is to catalyze the oxidative decarboxylation of isocitrate (27) which is the key rate-limiting step of the tricarboxylic acid cycle. It also plays a central role in the aerobic energy production and cellular respiration thus mutations in this gene will affect the nervous system (28, 29) and may cause cancer (30,31).Although the RP is the most common inherited disease of the retina (14, 32-36) there is still no effective therapeutic strategy and the exact pathogenesis and etiology of the disease is not clear (3,5,32,37).The aim of this study is to identify the pathogenic SNPs in the IDH3A gene and their effect on the structure and function of the protein, which might help in the overall understanding of the pathogenesis of the disease and could be used as diagnostic markers. This is the first in silico analysis in the coding region of IDH3A gene to prioritize SNPs for further genetic mapping studies. Utilization of in analysis softwares expedites the process of identifying the deleterious SNPs with no cost, and also facilitates future genetic studies. (38)
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