Biology subjects

Abdelhameed, T. A.

Publications and source records attributed to Abdelhameed, T. A..

7 recordsLinked to original sources

bioRxiv2019

Comprehensive Analysis of HEXB Protein Reveal Forty Two Novel nsSNPs That May Lead to Sandhoff disease (SD) Using Bioinformatics

BackgroundSingle Nucleotide Polymorphisms (SNPs) in the HEXB gene are associated with a neurodegenerative disorder called Sandhoff disease (SD) (GM2 gangliosidosis-O variant). This study aimed to predict the possible pathogenic SNPs of this gene and their impact on the protein using different bioinformatics tools. MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms collectively predicted the effect of single nucleotide substitution on both structure and function of beta subunit beta subunit of both hexosaminidase A and hexosaminidase B proteins. ResultsForty nine mutations were found to be extremely damaging to the structure and function of the HEXB gene protein. ConclusionAccording to this study, forty two novel nsSNP in HEXB are predicted to have possible role in Sandhoff disease using different bioinformatics tools, beside two SNPs found to have effect on miRNAs binding site affecting expression of HEXB gene. Our findings may assist in genetic study and diagnosis of Sandhoff disease.

bioinformatics↗

bioRxiv2019

Insilico Analysis Reveal Three novel nsSNPs May effect on GM2A protein Leading to AB variant of GM2 gangliosidosis

BackgroundAB variant of GM2 gangliosidosis caused as a result of mutations in GM2 activator gene (GM2A) which is regarded as neurodegenerative disorder. This study aimed to predict the possible damaging SNPs of this gene and their impact on the protein using different bioinformatics tools. MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different tools collectively predicted the effect of single nucleotide substitution on both structure and function of GM2 activator. ResultsThree novel mutations were found to be highly damaging to the structure and function of the GM2A gene. ConclusionFour SNPs were found to be highly damaging SNPs that affect function, structure and stability of GM2A protein, which they are: C99Y, C112F, C138S and C138R, three of them are novel SNPs (C99Y, C112F and C138S). Also 46 SNPs were predicted to affect miRNAs binding sites on 3UTR leading to abnormal expression of the resulting protein. These SNPs should be considered as important candidates in causing AB variant of GM2 gangliosidosis and may help in diagnosis and genetic screening of the disease.

bioinformatics↗

bioRxiv2019

Thirty two novel nsSNPs May effect on HEXA protein Leading to Tay-Sachs disease (TSD) Using a Computational Approach

BackgroundGenetic polymorphisms in the HEXA gene are associated with a neurodegenerative disorder called Tay-Sachs disease (TSD) (GM2 gangliosidosis type 1). This study aimed to predict the possible pathogenic SNPs of this gene and their impact on the protein using different bioinformatics tools.\n\nMethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms collectively predicted the effect of single nucleotide substitution on both structure and function of the hexosaminidase A protein.\n\nResultsFifty nine mutations were found to be highly damaging to the structure and function of the HEXA gene protein.\n\nConclusionAccording to this study, thirty two novel nsSNP in HEXA are predicted to have possible role in Tay-Saches Disease using different bioinformatics tools. Our findings could help in genetic study and diagnosis of Tay-Saches Disease.

bioinformatics↗

bioRxiv2019

Thirty five novel nsSNPs may effect on ADAMTS13 protein leading to Thrombotic thrombocytopenic purpura (TTP) using bioinformatics approach

BackgroundGenetic polymorphisms in the ADAMTS13 gene are associated with thrombotic thrombocytopenic purpura or TTP, a life-threatening microangiopathic disorder. This study aims to predict the possible pathogenic SNPs of this gene and their impact on the protein structure and function using insilico methods.\n\nMethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms applied collectively to predictthe effect of single nucleotide substitution on both structure and function of the ADAMTS13 protein.\n\nResultsFifty one mutations were found to be highly damaging to the structure and function of the protein. Of those, thirty five were novel nsSNPs not previously reported in the literature.\n\nConclusionAccording to our analysis we found thirty five nsSNPs effects on ADAMTS13 protein leading to thrombotic thrombocytopenic purpura using computational approach. Bioinformatics tools are vital in prediction analysis, making use of increasingly voluminous biomedical data thereby providing markers for screening or for genetic mapping studies.

bioinformatics↗

bioRxiv2019

Computational Analysis Revealed Five Novel Mutations in Human IL2RG gene Related to X-SCID

BackgroundX linked severe combined immunodeficiency (X-SCID) is a life-threatening disorder. It is due to mutation of the interleukin two receptor gamma-chain (IL2RG) gene. Nonsynonymous SNPs (nsSNPs) are the most common polymorphism, known to be deleterious or disease-causing variations because they alter protein sequence, structure, and function. Objective: is to reveal the effect of harmful SNPs in the function and structure of IL2RG protein. MethodData on IL2RG was investigated from dbSNP/NCBI database. Prediction of damaging effect was done using sift, polyphen, provean and SNAP2.more software were used for more analysis: phd-snp, and and go, Pmut, Imutant.modeling was done using chimera and project hope. Gene interaction was done by gene mania.3UTR prediction was done using polymiRTS software. ResultThe in-silico prediction identified 1479 SNPs within IL2RG gene out of which 253 were coding SNPs, 50 took place in the miRNA 3 UTR, 21 occurred in 5 UTR region and 921 occurred in intronic regions. a total of 12 missense nsSNPs were found to be damaging by both a sequence homology-based tool (SIFT) and a structural homology-based method (PolyPhen), Five of them were novel; rs1322436793(G305R), rs1064794027(C182Y), rs111033620(G114D), rs193922347 (Y105C) and rs1293196743(Y91C), Two SNPs(Rs144075871 and rs191726889) out of 50 in the 3UTR region were predicted to disrupt miRNAs binding sites and affect the gene expression. ConclusionsComputational analysis of SNPs has become a very valuable tool in order to discriminate neutral SNPs from damaging SNPs. This study revealed 5 novel nsSNPs in the IL2RG gene by using different software and 21 SNPs in 3UTR. These SNPs could be considered as important candidates in causing diseases related to IL2RG mutation and could be used as diagnostic markers.

bioinformatics↗

bioRxiv2019

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

BackgroundHereditary 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.\n\nMaterials 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.\n\nResultTwo novel mutations out of 339 nsSNPs that are found be deleterious effect on the PRSS1 structure and function.\n\nConclusionThis is the first in silico analysis in PRSS1 gene, which will be a valuable resource for future targeted mechanistic and population-based studies.

bioinformatics↗

bioRxiv2018

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

BackgroundFamilial 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 softwares, and to determine the structure, function and regulation of their respective proteins.\n\nMaterials 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.\n\nResult41 novel mutations out of 973 nsSNPs that are found be deleterious effect on the IKBKAP structure and function.\n\nConclusionThis is the first in silico analysis in IKBKAP gene to prioritize SNPs for further genetic studies.

bioinformatics↗