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 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 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 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.

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 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.

Novel ABCD1 gene mutations in Iranian pedigrees with X-linked adrenoleukodystrophy

2019 ◽  
Vol 32 (11) ◽  
pp. 1207-1215
Author(s):  
Babak Emamalizadeh ◽  
Yousef Daneshmandpour ◽  
Abbas Tafakhori ◽  
Sakineh Ranji-Burachaloo ◽  
Sajad Shafiee ◽  
...  
Keyword(s):  
Protein Structure ◽  
Direct Sequencing ◽  
Gene Mutations ◽  
Protein Product ◽  
Structure And Function ◽  
Novel Mutations ◽  
Chain Reaction ◽  
Abcd1 Gene ◽  
Polymerase Chain ◽  
And Function

Abstract Background X-linked adrenoleukodystrophy (X-ALD), the most common peroxisomal disorder, is caused by mutations in the ABCD1 gene located on Xq28. X-ALD is characterized by a spectrum of different manifestations varying in patients and families. Methods Four pedigrees with X-ALD consisting of patients and healthy members were selected for investigation of ABCD1 gene mutations. The mutation analysis was performed by polymerase chain reaction (PCR) followed by direct sequencing of all exons. The identified mutations were investigated using bioinformatics tools to predict their effects on the protein product and also to compare the mutated sequence with close species. Results One previously known missense mutation (c.1978 C > T) and three novel mutations (c.1797dupT, c.879delC, c.1218 C > G) were identified in the ABCD1 gene, each in one family. Predicting the effects of the mutations on protein structure and function indicated the probable damaging effect for them with significant alterations in the protein structure. We found three novel mutations in the ABCD1 gene with damaging effects on its protein product and responsible for X-ALD.

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 Novel Deleterious nsSNPs within MEFV Gene that Could Be Used as Diagnostic Markers to Predict Hereditary Familial Mediterranean Fever: Using Bioinformatics Analysis

2019 ◽  
Vol 2019 ◽  
pp. 1-13
Author(s):  
Mujahed I. Mustafa ◽  
Tebyan A. Abdelhameed ◽  
Fatima A. Abdelrhman ◽  
Soada A. 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

Background. Familial Mediterranean Fever (FMF) is the most common autoinflammatory disease (AID) affecting mainly the ethnic groups originating from Mediterranean basin. We aimed to identify the pathogenic SNPs in MEFV by computational analysis software. Methods. We carried out in silico prediction of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structure and function. Result. 23 novel mutations out of 857 nsSNPs are found to have deleterious effect on the MEFV structure and function. Conclusion. This is the first in silico analysis of 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.

scholarly journals Unmasking of novel mutations within XK gene that could be used as Diagnostic Markers to Predict McLeod syndrome: Using in silico analysis

2019 ◽  
Author(s):  
Mujahed I. Mustafa ◽  
Mohamed A. Hassan
Keyword(s):  
In Silico ◽  
In Silico Analysis ◽  
Structural Effect ◽  
Novel Mutations ◽  
Multisystem Disorder ◽  
Functional Studies ◽  
Central Nervous Systems ◽  
The One ◽  
And Function ◽  
Silico Analysis

AbstractBackgroundMcLeod neuroacanthocytosis syndrome is a rare X-linked recessive multisystem disorder affecting the peripheral and central nervous systems, red blood cells, and internal organs.MethodsWe carried out in silico analysis of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structural and functional level.Result2 novel mutations out of 104 nsSNPs that are found to be deleterious effect on the XK structure and function.ConclusionThe present study provided a novel insight into the understanding of McLeod syndrome, SNPs occurring in coding and non-coding regions, may lead to RNA alterations and should be systematically verified. Functional studies can gain from a preliminary multi-step approach, such as the one proposed here; we prioritize SNPs for further genetic mapping studies. This will be a valuable resource for neurologists, hematologists, and clinical geneticists on this rare and debilitating disease.

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