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In silico analysis missense mutation

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https://www.readbyqxmd.com/read/27914961/expanding-the-clinical-and-genetic-spectrum-of-g6pd-deficiency-the-occurrence-of-bcgitis-and-novel-missense-mutation
#1
Taj Ali Khan, Humaira Mazhar, Mehboob Nawaz, Kalsoom Kalsoom, Muhammad Ishfaq, Huma Asif, Hazir Rahman, Muhammad Qasim, Farkhanda Naz, Mubashir Hussain, Baharullah Khattak, Waheed Ullah, Otavio Cabral-Marques, Jawad Butt, Asif Iqbal
Glucose-6-phosphate dehydrogenase (G6PD) is a key enzyme in the pentose phosphate pathway that ensures sufficient production of coenzyme nicotinamide adenine dinucleotide phosphate (NADPH) by catalyzing the reduction of NADP+ to NADPH. Noteworthy, the latter mediates the production of reactive oxygen species (ROS) by phagocytic cells such as neutrophils and monocytes. Therefore, patients with severe forms of G6PD deficiency may present impaired NADPH oxidase activity and become susceptible to recurrent infections...
November 30, 2016: Microbial Pathogenesis
https://www.readbyqxmd.com/read/27905547/in-silico-mapping-of-protein-unfolding-mutations-for-inherited-disease
#2
Caitlyn L McCafferty, Yuri V Sergeev
The effect of disease-causing missense mutations on protein folding is difficult to evaluate. To understand this relationship, we developed the unfolding mutation screen (UMS) for in silico evaluation of the severity of genetic perturbations at the atomic level of protein structure. The program takes into account the protein-unfolding curve and generates propensities using calculated free energy changes for every possible missense mutation at once. These results are presented in a series of unfolding heat maps and a colored protein 3D structure to show the residues critical to the protein folding and are available for quick reference...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27882080/a-novel-krt5-mutation-associated-with-generalized-severe-epidermolysis-bullosa-simplex-in-a-2-year-old-chinese-boy
#3
Jia Zhang, Ming Yan, Jianying Liang, Ming Li, Zhirong Yao
Mutations in keratin 5 (KRT5) or KRT14 genes are responsible for the most severe form of epidermolysis bullosa simplex (EBS), which is EBS generalized severe (EBS-gen sev). To date, only four pathogenic mutations (p.Arg165Ser and p.Lys199Asn in KRT5; p.Arg125Cys and p.Arg125His in KRT14) have been reported to be responsible for EBS-gen sev in the Chinese population. In the present study, a 2-year-old Chinese boy was clinically suspected to suffer from EBS, and thus Sanger sequencing was performed in the extracted genomic DNA samples from the patient, his parents and 100 healthy controls...
November 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/27853304/genetic-epidemiology-of-glucose-6-dehydrogenase-deficiency-in-the-arab-world
#4
C George Priya Doss, Dima R Alasmar, Reem I Bux, P Sneha, Fadheela Dad Bakhsh, Iman Al-Azwani, Rajaa El Bekay, Hatem Zayed
A systematic search was implemented using four literature databases (PubMed, Embase, Science Direct and Web of Science) to capture all the causative mutations of Glucose-6-phosphate dehydrogenase (G6PD) deficiency (G6PDD) in the 22 Arab countries. Our search yielded 43 studies that captured 33 mutations (23 missense, one silent, two deletions, and seven intronic mutations), in 3,430 Arab patients with G6PDD. The 23 missense mutations were then subjected to phenotypic classification using in silico prediction tools, which were compared to the WHO pathogenicity scale as a reference...
November 17, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27826100/mutation-analysis-of-trps1-gene-including-core-promoter-5-utr-and-3-utr-regulatory-sequences-with-insight-into-their-organization
#5
Roman Solc, Michaela Klugerova, Josef Vcelak, Alice Baxova, Miloslav Kuklik, Jan Vseticka, Rastislav Beharka, Katerina Hirschfeldova
The TRPS1 protein is a potent regulator of proliferation, differentiation, and apoptosis. The TRPS1 gene aberrations are strongly associated with rare trichorhinophalangeal syndrome (TRPS) development. We have conducted MLPA analysis to capture deletion within the crucial 8q24.1 chromosomal region in combination with mutation analysis of TRPS1 gene including core promoter, 5'UTR, and 3'UTR sequences in nine TRPS patients. Low complexity or extent of untranslated regulatory sequences avoided them from analysis in previous studies...
November 5, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/27824214/a-novel-missense-mutation-in-the-fgb-gene-p-gly302arg-leading-to-afibrinogenemia-predicted-structure-and-function-consequences
#6
V Ivaškevičius, H Rühl, G Detarsio, A Biswas, S Gupta, M Davoli, A Quartara, S Pérez, M Raviola, J Oldenburg
: Afibrinogenemia represents the rarest form of fibrinogen deficiency. Causative missense mutations occur rarely and may improve the understanding of fibrinogen structure and function. PATIENTS AND METHODS: The propositus was a 26-year-old Argentinian with afibrinogenemia. FGA, FGB and FGG exons and flanking regions were screened by sequencing and the mutant protein was analyzed in silico. RESULTS: A novel missense mutation in the FGB gene (Bbeta Gly272Arg, p...
November 8, 2016: Hämostaseologie
https://www.readbyqxmd.com/read/27814360/mutation-in-lim2-is-responsible-for-autosomal-recessive-congenital-cataracts
#7
Bushra Irum, Shahid Y Khan, Muhammad Ali, Haiba Kaul, Firoz Kabir, Bushra Rauf, Fareeha Fatima, Raheela Nadeem, Arif O Khan, Saif Al Obaisi, Muhammad Asif Naeem, Idrees A Nasir, Shaheen N Khan, Tayyab Husnain, Sheikh Riazuddin, Javed Akram, Allen O Eghrari, S Amer Riazuddin
PURPOSE: To identify the molecular basis of non-syndromic autosomal recessive congenital cataracts (arCC) in a consanguineous family. METHODS: All family members participating in the study received a comprehensive ophthalmic examination to determine their ocular phenotype and contributed a blood sample, from which genomic DNA was extracted. Available medical records and interviews with the family were used to compile the medical history of the family. The symptomatic history of the individuals exhibiting cataracts was confirmed by slit-lamp biomicroscopy...
2016: PloS One
https://www.readbyqxmd.com/read/27804176/comparison-of-bioinformatics-prediction-molecular-modeling-and-functional-analyses-of-foxc1-mutations-in-patients-with-axenfeld-rieger-syndrome
#8
Morteza Seifi, Tim Footz, Sherry A M Taylor, Michael A Walter
Mutations in the forkhead box C1 gene (FOXC1) cause Axenfeld-Rieger syndrome (ARS). Here, we investigated the effect of four ARS missense variants on FOXC1 structure and function, and examined the predictive value of four in silico programs for all 31 FOXC1 missense variants identified to date. Molecular modeling of the FOXC1 forkhead domain predicts that c.402G> A (p.C135Y) alters FOXC1's structure. In contrast, c.378A> G (p.H128R) and c.481A> G (p.M161V) are not predicted to change FOXC1's structure...
November 2, 2016: Human Mutation
https://www.readbyqxmd.com/read/27793474/clinical-imaging-pathological-and-biochemical-characterization-of-a-novel-presenilin-1-mutation-n135y-causing-alzheimer-s-disease
#9
Marissa Natelson Love, David G Clark, J Nicholas Cochran, Kyle A Den Beste, David S Geldmacher, Tammie L Benzinger, Brian A Gordon, John C Morris, Randall J Bateman, Erik D Roberson
We present 2 cases of early-onset Alzheimer's disease due to a novel N135Y mutation in PSEN1. The proband presented with memory and other cognitive symptoms at age 32. Detailed clinical characterization revealed initial deficits in memory with associated dysarthria, progressing to involve executive dysfunction, spastic gait, and episodic confusion with polyspike discharges on long-term electroencephalography. Amyloid- and FDG-PET scans showed typical results of Alzheimer's disease. By history, the proband's father had developed cognitive symptoms at age 42 and died at age 48...
October 3, 2016: Neurobiology of Aging
https://www.readbyqxmd.com/read/27755493/mutation-of-the-planar-cell-polarity-gene-vangl1-in-adolescent-idiopathic-scoliosis
#10
Malene Rask Andersen, Muhammad Farooq, Karen Koefoed, Klaus W Kjaer, Ane Simony, Sren Tvorup Christensen, Lars Allan Larsen
STUDY DESIGN: Mutation analysis of a candidate disease gene in a cohort of patients with moderate to severe Adolescent idiopathic scoliosis (AIS). OBJECTIVE: To investigate if damaging mutations in the planar cell polarity gene VANGL1 could be identified in AIS patients. SUMMARY OF BACKGROUND DATA: AIS is a spinal deformity which occurs in 1-3% of the population. The cause of AIS is often unknown, but genetic factors are important in the etiology...
October 17, 2016: Spine
https://www.readbyqxmd.com/read/27746904/using-diverse-u-s-beef-cattle-genomes-to-identify-missense-mutations-in-epas1-a-gene-associated-with-high-altitude-pulmonary-hypertension
#11
Michael P Heaton, Timothy P L Smith, Jacky K Carnahan, Veronica Basnayake, Jiansheng Qiu, Barry Simpson, Theodore S Kalbfleisch
The availability of whole genome sequence (WGS) data has made it possible to discover protein variants in silico. However, existing bovine WGS databases do not show data in a form conducive to protein variant analysis, and tend to under represent the breadth of genetic diversity in U.S. beef cattle. Thus, our first aim was to use 96 beef sires, sharing minimal pedigree relationships, to create a searchable and publicly viewable set of mapped genomes relevant for 19 popular breeds of U.S. cattle. Our second aim was to identify protein variants encoded by the bovine endothelial PAS domain-containing protein 1 gene ( EPAS1), a gene associated with high-altitude pulmonary hypertension in Angus cattle...
2016: F1000Research
https://www.readbyqxmd.com/read/27724896/genome-wide-association-study-for-hereditary-ataxia-in-the-parson-russell-terrier-and-dna-testing-for-ataxia-associated-mutations-in-the-parson-and-jack-russell-terrier
#12
Alana Christina Gast, Julia Metzger, Andrea Tipold, Ottmar Distl
BACKGROUND: Spinocerebellar ataxia also referred to as hereditary ataxia comprises different forms of progressive neurodegenerative diseases. A complex mode of inheritance was most likely in Parson Russell Terriers (PRT) and in Jack Russell Terriers (JRT). Recently, the missense mutation KCNJ10:c.627C > G was shown to be associated with the spinocerebellar ataxia (SCA) in JRT and related Russell group of terriers, whereas the missense mutation CAPN1:c.344G > A was associated with late onset ataxia (LOA) in PRT...
October 10, 2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27676246/a-comprehensive-functional-analysis-of-ntrk1-missense-mutations-causing-hereditary-sensory-and-autonomic-neuropathy-type-iv-hsan-iv
#13
Samiha S Shaikh, Ya-Chun Chen, Sally-Anne Halsall, Michael S Nahorski, Kiyoyuki Omoto, Gareth T Young, Anne Phelan, Christopher Geoffrey Woods
Hereditary sensory and autonomic neuropathy type IV (HSAN IV) is an autosomal recessive disorder characterized by a complete lack of pain perception and anhidrosis. Here, we studied a cohort of seven patients with HSAN IV and describe a comprehensive functional analysis of seven novel NTRK1 missense mutations, c.1550G>A, c.1565G>A, c.1970T>C, c.2096T>C, c.2254T>A, c.2288G>C, c.2311C>T, corresponding to p.G517E, p.G522E, p.L657P, p.I699T, p.C752S, p.C763S and p.R771C, all of which were predicted pathogenic by in-silico analysis...
September 27, 2016: Human Mutation
https://www.readbyqxmd.com/read/27620667/structural-impact-analysis-of-missense-snps-present-in-the-uroguanylin-gene-by-long-term-molecular-dynamics-simulations
#14
Antonio C S Marcolino, William F Porto, Állan S Pires, Octavio L Franco, Sérgio A Alencar
The guanylate cyclase activator 2B, also known as uroguanylin, is part of the guanylin peptide family, which includes peptides such as guanylin and lymphoguanylin. The guanylin peptides could be related to sodium absorption inhibition and water secretion induction and their dysfunction may be related to various pathologies such as chronic renal failure, congestive heart failure and nephrotic syndrome. Besides, uroguanylin point mutations have been associated with essential hypertension. However, currently there are no studies on the impact of missense SNPs on uroguanylin structure...
September 9, 2016: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27581627/role-of-e542-and-e545-missense-mutations-of-pik3ca-in-breast-cancer-a-comparative-computational-approach
#15
D Thirumal Kumar, C George Priya Doss
Recent statistics describe breast cancer as the leading cause of death among women across the world with varied causes and reasons. Lifestyle, diet, genetic and environmental factors introduce their generous contributions towards breast cancer, among which genetic factors have lately become one of the most important aspects in understanding the mechanism. Although various genes have already been reported in causing breast cancer, PIK3CA stands second on the list. Mutations observed in this gene have the ability to trigger the different activities of the cell, thereby bypassing the regular cellular cycle...
September 27, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27544631/three-novel-mutations-and-genetic-epidemiology-analysis-of-the-gap-junction-beta-1-gjb1-gene-among-hungarian-charcot-marie-tooth-disease-patients
#16
Gyorgy Mate Milley, Edina Timea Varga, Zoltan Grosz, Benjamin Bereznai, Zsuzsanna Aranyi, Judit Boczan, Peter Dioszeghy, Bernadette Kálmán, Aniko Gal, Maria Judit Molnar
Pathogenic variants of the gap junction beta 1 (GJB1) gene are responsible for the Charcot-Marie-Tooth neuropathy X type 1 (CMTX1). In this study, we report the mutation frequency of GJB1 in 210 Hungarian CMT patients and the phenotype comparison between male and female CMTX1 patients. Altogether, 13 missense substitutions were found in the GJB1 gene. Among them, 10 have been previously described as pathogenic variants (p.Arg15Trp, p.Val63Ile, p.Leu89Val, p.Ala96Gly, p.Arg107Trp, p.Arg142Gln, p.Arg164Trp, p...
October 2016: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/27435880/next-generation-semiconductor-based-sequencing-of-bitter-taste-receptor-genes-in-different-pig-populations-and-association-analysis-using-a-selective-dna-pool-seq-approach
#17
A Ribani, F Bertolini, G Schiavo, E Scotti, V J Utzeri, S Dall'Olio, P Trevisi, P Bosi, L Fontanesi
Taste perception in animals affects feed intake and may influence production traits. In particular, bitter is sensed by receptors encoded by the family of TAS2R genes. In this research, using a DNA pool-seq approach coupled with next generation semiconductor based target resequencing, we analysed nine porcine TAS2R genes (TAS2R1, TAS2R3, TAS2R4, TAS2R7, TAS2R9, TAS2R10, TAS2R16, TAS2R38 and TAS2R39) to identify variability and, at the same time, estimate single nucleotide polymorphism (SNP) allele frequencies in several populations and testing differences in an association analysis...
July 20, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27430550/a-dominant-negative-mutation-at-the-atp-binding-domain-of-amhr2-is-associated-with-a-defective-anti-m%C3%A3-llerian-hormone-signaling-pathway
#18
Lin Li, Xueya Zhou, Xi Wang, Jing Wang, Wei Zhang, Binbin Wang, Yunxia Cao, Kehkooi Kee
STUDY QUESTION: Does a heterozygous mutation in AMHR2, identified in whole-exome sequencings (WES) of patients with primary ovarian insufficiency (POI), cause a defect in anti-Müllerian hormone (AMH) signaling? SUMMARY ANSWER: The I209N mutation at the adenosine triphosphate binding domain of AMHR2 exerts dominant negative defects in the AMH signaling pathway. WHAT IS KNOWN ALREADY: Previous studies have demonstrated the associations of several sequence variants in AMH or AMHR2 with POI, but no functional assay has been performed to verify whether there was any defect on AMH signaling...
September 2016: Molecular Human Reproduction
https://www.readbyqxmd.com/read/27421141/in-silico-predicted-structural-and-functional-insights-of-all-missense-mutations-on-2b-domain-of-k1-k10-causing-genodermatoses
#19
Santasree Banerjee, Qian Wu, Yuyi Ying, Yanni Li, Matsuyuki Shirota, Dante Neculai, Chen Li
The K1 and K10 associated genodermatoses are characterized by clinical symptoms of mild to severe redness, blistering and hypertrophy of the skin. In this paper, we set out to computationally investigate the structural and functional effects of missense mutations on the 2B domain of K1/K10 heterodimer and its consequences in disease phenotype. We modeled the structure of the K1/K10 heterodimer based on crystal structures for the human homolog K5/K14 heterodimer, and identified that the missense mutations exert their effects on stability and assembly competence of the heterodimer by altering physico-chemical properties, interatomic interactions, and inter-residue atomic contacts...
July 13, 2016: Oncotarget
https://www.readbyqxmd.com/read/27405681/genetic-analysis-of-bleeding-disorders
#20
E Edison, B A Konkle, A C Goodeve
Molecular genetic analysis of inherited bleeding disorders has been practised for over 30 years. Technological changes have enabled advances, from analyses using extragenic linked markers to next-generation DNA sequencing and microarray analysis. Two approaches for genetic analysis are described, each suiting their environment. The Christian Medical Centre in Vellore, India, uses conformation-sensitive gel electrophoresis mutation screening of multiplexed PCR products to identify candidate mutations, followed by Sanger sequencing confirmation of variants identified...
July 2016: Haemophilia: the Official Journal of the World Federation of Hemophilia
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