scholarly journals The Association between SLC25A15 Gene Polymorphisms and Hyperornithinemia-hyperammonemia-homocitrullinuria Syndrome: Using In Silico Analysis

2019 ◽  
Author(s):  
Nuha A. Mahmoud ◽  
Dina T. Ahmed ◽  
Zainab O. Mohammed ◽  
Fatima A. Altyeb ◽  
Mujahed I. Mustafa ◽  
...  
Keyword(s):  
In Silico ◽  
Autosomal Recessive ◽  
Urea Cycle ◽  
In Silico Analysis ◽  
Structure And Function ◽  
Medical Testing ◽  
Bioinformatics Tools ◽  
And Function ◽  
Silico Analysis ◽  
Selection Of

BackgroundHyperornithinemia-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.MethodsThe deleterious SNPs in SLC25A15 are detected by various bioinformatics tools, with addition to identifying their effects on the structure and function of this gene.Results20 deleterious SNPs out 287of were found to have their own damaging effects on the structure and function of the SLC25A15 gene.ConclusionThis 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.

scholarly journals In silico analysis ofIDH3Agene revealed Novel mutations associated with Retinitis Pigmentosa

2019 ◽  
Author(s):  
Thwayba A. Mahmoud ◽  
Abdelrahman H. Abdelmoneim ◽  
Naseem S. Murshed ◽  
Zainab O. Mohammed ◽  
Dina T. Ahmed ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
In Silico ◽  
In Silico Analysis ◽  
Photoreceptor Cells ◽  
Structure And Function ◽  
Novel Mutations ◽  
Inherited Disorders ◽  
Bioinformatics Tools ◽  
And Function ◽  
Silico Analysis

AbstractBackgroundRetinitis 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.Methodwe used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein.Result20 deleterious SNPs out of 178 were found to have a damaging effect on the protein structure and function.Conclusionthis 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.

scholarly journals In Silico Analysis and Modeling of Novel Pathogenic Single Nucleotide Polymorphisms (SNPs) in Human CD40LG Gene

2019 ◽  
Author(s):  
Abdelrahman H. Abdelmoneim ◽  
Mujahed I. Mustafa ◽  
Thwayba A. Mahmoud ◽  
Naseem S. Murshed ◽  
Mohamed A. Hassan
Keyword(s):  
In Silico ◽  
Elevated Serum ◽  
In Silico Analysis ◽  
Structure And Function ◽  
Immunoglobulin M ◽  
Hyper Igm Syndrome ◽  
Bioinformatics Tools ◽  
Hyper Igm ◽  
And Function ◽  
Silico Analysis

Abstract:Background:The X-linked hyper-immunoglobulin M syndrome (XHIGM) is a rare, inherited immune deficiency disorder. It is more common in males. Characterized by elevated serum IgM levels and low to undetectable levels of serum IgG, IgA and IgE. Hyper-IgM syndrome is caused by mutations in the CD40LG gene. Located in human Xq26. CD40LG acts as an immune modulator in activated T cells.Method:We used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein.Result:8 novel SNPs out of 233 were found to have most deleterious effect on the protein structure and function. While modeling of nsSNPs was studied by Project HOPE software.Conclusion:Better understanding of Hyper-IgM syndrome caused by mutations in CD40LG gene was achieved using in silico analysis. This is the first in silico functional analysis of CD40LG gene and 8 novel mutations were found using different bioinformatics tools, and they could be used as diagnostic markers for hyper-IgM syndrome. These 8 novel SNPs may be important candidates for the cause of different types of human diseases by CD40LG gene.

scholarly journals Comprehensive in silico Analysis of IKBKAP gene that could potentially cause Familial dysautonomia

2018 ◽  
Author(s):  
Mujahed I. Mustafa ◽  
Enas A. Osman ◽  
Abdelrahman H. Abdelmoneiom ◽  
Dania M. Hassn ◽  
Hadeel M. Yousif ◽  
...  
Keyword(s):  
In Silico ◽  
Genetic Disorder ◽  
In Silico Analysis ◽  
Familial Dysautonomia ◽  
Structural Effect ◽  
Structure And Function ◽  
Genetic Studies ◽  
And Function ◽  
Silico Analysis

AbstractBackgroundFamilial dysautonomia (FD) is a rare neurodevelopmental genetic disorder within the larger classification of hereditary sensory and autonomic neuropathies. We aimed to identify the pathogenic SNPs in IKBKAP gene by computational analysis software’s, and to determine the structure, function and regulation of their respective proteins.Materials and MethodsWe carried out in silico analysis of structural effect of each SNP using different bioinformatics tools to predict SNPs influence on protein structure and function.Result41 novel mutations out of 973 nsSNPs that are found be deleterious effect on the IKBKAP structure and function.ConclusionThis is the first in silico analysis in IKBKAP gene to prioritize SNPs for further genetic studies.

scholarly journals In silicoanalysis of coding SNPs and 3′-UTR associated miRNAs inDCAF17gene that may affect the regulation and pathogenesis of Woodhouse-Sakati Syndrome

2019 ◽  
Author(s):  
Abdelrahman H. Abdelmoneim ◽  
Asia M. Elrashied ◽  
Alaa I. Mohammed ◽  
Sara A. Mirghani ◽  
Rania E. Osman ◽  
...  
Keyword(s):  
Diabetes Mellitus ◽  
Protein Structure ◽  
In Silico Analysis ◽  
Structure And Function ◽  
Novel Mutations ◽  
Inherited Disorders ◽  
Bioinformatics Tools ◽  
Extrapyramidal Signs ◽  
And Function ◽  
Silico Analysis

AbstractBackgroundWoodhouse-Sakati Syndrome refers to a group of inherited disorders characterized by alopecia, hypogonadism, diabetes mellitus, hypothyroidism and progressive extrapyramidal signs. The aim of this study is to identify the pathogenic SNPs in theDCAF17gene with their related mciroRNAs and their effect on the structure and function of the protein.Material and MethodsWe used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein. After that we defined the miRNAs founded in the 3′-UTR region on theDCAF17gene and studied the annotations relative to it.ResultsTen deleterious SNPs out of 339 were found to have a damaging effect on the protein structure and function, with one significant micoRNA in the 3′-UTR region.ConclusionThis was the first in silico analysis ofDCAF17gene, in which 10 novel mutations were found using different bioinformatics tools that could be used as a diagnostic markers for Woodhouse-Sakati syndrome, with one relevant microRNA that can regulate the function of the protein.

scholarly journals Novel mutations within PRSS1 Gene that could potentially cause hereditary pancreatitis: Using Comprehensive in silico Approach

2019 ◽  
Author(s):  
Mujahed I. Mustafa ◽  
Abdelrahman H. Abdelmoneim ◽  
Nafisa M. Elfadol ◽  
Soada A. osman ◽  
Tebyan A. Abdelhameed ◽  
...  
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Structure And Function ◽  
Incomplete Penetrance ◽  
Nucleotide Polymorphisms ◽  
Hereditary Pancreatitis ◽  
Novel Mutations ◽  
Autosomal Dominant Disorder ◽  
And Function ◽  
Silico Analysis

AbstractBackgroundHereditary pancreatitis (HP) is an autosomal dominant disorder with incomplete penetrance characterized by recurring episodes of severe abdominal pain often presenting in childhood. The comprehensive in silico analysis of coding SNPs, and their functional impacts on protein level, still remains unknown. In this study, we aimed to identify the pathogenic SNPs in PRSS1 gene by computational analysis approach.Materials and MethodsWe carried out in silico analysis of structural effect of each SNP using different bioinformatics tools to predict Single-nucleotide polymorphisms influence on protein structure and function.ResultTwo novel mutations out of 339 nsSNPs that are found be deleterious effect on the PRSS1 structure and function.ConclusionThis is the first in silico analysis in PRSS1 gene, which will be a valuable resource for future targeted mechanistic and population-based studies.

A panoramic review and in silico analysis of IL-11 structure and function

2016 ◽  
Vol 32 ◽  
pp. 41-61 ◽  
Author(s):  
Manica Negahdaripour ◽  
Navid Nezafat ◽  
Younes Ghasemi
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Structure And Function ◽  
And Function ◽  
Silico Analysis

scholarly journals In silico analysis of Missense Variants in Human MPL Gene Associated with Essential Thrombocythemia

2019 ◽  
Author(s):  
Sahar G. Elbager ◽  
Abier A. Makkawi ◽  
Hadeel A. Mohamed ◽  
Fauzia A. Abdelrahman ◽  
Lamia H. Osman ◽  
...  
Keyword(s):  
Essential Thrombocythemia ◽  
In Silico ◽  
Association Studies ◽  
In Silico Analysis ◽  
Structure And Function ◽  
Janus Kinase ◽  
Hematopoietic Stem ◽  
Missense Variants ◽  
And Function ◽  
Silico Analysis

AbstractIntroductionThe proto-oncogene (MPL) gen encodes the receptor for thrombopoietin (TPO-R), a member of hematopoietic receptor superfamily. Thrombopoietin (TPO), the primary cytokine regulating self-renewal of hematopoietic stem cells, thrombopoiesis and megakaryocytopoiesis. TPO binding to TPO-R induces activation of Janus Kinase 2 (JAK2). Activated JAK2 triggers the activation of downstream positive signaling pathways, leading to the survival, proliferation, and differentiation of hematopoietic cells. Mutations in MPL gene possibly will alter the normal regulatory mechanisms. Numerous MPL mutations have been observed in various hematopoietic cancers such as essential thrombocythemia and primary myelofibrosis and leukemias. In this study, we performed a comprehensive in silico analysis of the functional and structural impact of non-synonymous (nsSNP) that are deleterious to TPO-R structure and function.MethodologyThe data on human MPL gene was retrieved from dbSNP/NCBI. Nine prediction algorithms; SIFT, Polyphen, PROVEAN, SNAP2, Condel, PhD-SNP, I-Mutant, Mutpred. RaptorX and Chimera were used to analyzing the effect of nsSNPs on functions and structure of the TPO-R. STRING and KEGG database were used for TPO-R protein-protein interaction.Results and DiscussionAs per dbSNP database, the human MPL gene contained 445 missense mutations. A total 5 nsSNPs (D295G, R257C, Y252H, R537W and D128Y) were predicted to have the most damaging effects on TPO-R structure and function. STRING and KEGG revealed that MPL had strong interactions with proteins that involved in cell growth, apoptosis, signal transduction pathway, some cancers pathways such as colorectal cancer, lung cancer, pancreas cancers, and skin cancer. A literature search revealed that Y252H has contribute to the development of essential thrombocythemia.ConclusionThese in silico predictions will provide useful information in selecting the target SNPs that are likely to have functional impact on the TPO-R and moreover could act as potential targets in genetic association studies. Keywords: In Silico analyses; JAK2; Missense Variants; MPL gene; Thrombopoietin (TPO); Single nucleotide polymorphism (SNP).

scholarly journals Novel deleterious nsSNPs within MEFV gene that could be used as Diagnostic Markers to Predict Hereditary Familial Mediterranean Fever: Using bioinformatics analysis

2018 ◽  
Author(s):  
Mujahed I. Mustafa ◽  
Tebyan A Abdelhameed ◽  
Fatima A. Abdelrhman ◽  
Soada Ahmed Osman ◽  
Mohamed A. Hassan
Keyword(s):  
Familial Mediterranean Fever ◽  
In Silico ◽  
Mediterranean Basin ◽  
Mefv Gene ◽  
Structure And Function ◽  
Diagnostic Markers ◽  
Novel Mutations ◽  
Bioinformatics Tools ◽  
Mediterranean Fever ◽  
And Function

AbstractBackgroundFamilial Mediterranean Fever (FMF) is the most common auto inflammatory disease (AID) affecting mainly the ethnic groups originating from Mediterranean basin, we aimed to identify the pathogenic SNPs in MEFV by computational analysis software.MethodsWe carried out in silico prediction of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structure and function.Result23 novel mutations out of 857 nsSNPs that are found to be deleterious effect on the MEFV structure and function.ConclusionThis is the first in silico analysis in MEFV gene to prioritize SNPs for further genetic mapping studies. After using multiple bioinformatics tools to compare and rely on the results predicted, we found 23 novel mutations that may cause FMF disease and it could be used as diagnostic markers for Mediterranean basin populations.

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