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In silico analysis missense mutation

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https://www.readbyqxmd.com/read/29127258/homozygous-mutation-in-cep19-a-gene-mutated-in-morbid-obesity-in-bardet-biedl-syndrome-with-predominant-postaxial-polydactyly
#1
Esra Yıldız Bölükbaşı, Sara Mumtaz, Muhammad Afzal, Ute Woehlbier, Sajid Malik, Aslıhan Tolun
BACKGROUND: Bardet-Biedl syndrome (BBS) is a ciliopathy with extensive phenotypic variability and genetic heterogeneity. We aimed to discover the gene mutated in a consanguineous kindred with multiple cases of a BBS phenotype. METHODS: SNP genotype data were used for linkage analysis and exome sequencing to identify mutations. Modelling and in silico analysis were performed to predict mutation severity. RESULTS: Patients had postaxial polydactyly plus variable other clinical features including rod-cone dystrophy, obesity, intellectual disability, renal malformation, developmental delay, dental anomalies, speech disorder and enlarged fatty liver...
November 10, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29114575/prediction-of-a-highly-deleterious-mutation-e17k-in-akt-1-gene-an-in-silico-approach
#2
Imran Khan, Irfan A Ansari
The AKT1 (v-akt murine thymoma viral oncogene homologue 1) kinase is a member of most frequently activated proliferation and survival signaling pathway in cancer. Recently, hyperactivation of AKT1, due to functional point mutation in the pleckstrin homology (PH) domain of AKT1 gene, has been found to be associated with human colorectal, breast and ovarian cancer. Thus, considering its crucial role in cellular signaling pathway, a functional analysis of missense mutations of AKT1 gene was undertaken in this study...
July 2017: Biochemistry and Biophysics Reports
https://www.readbyqxmd.com/read/29047041/a-profound-computational-study-to-prioritize-the-disease-causing-mutations-in-prps1-gene
#3
Ashish Kumar Agrahari, P Sneha, C George Priya Doss, R Siva, Hatem Zayed
Charcot-Marie-Tooth disease (CMT) is one of the most commonly inherited congenital neurological disorders, affecting approximately 1 in 2500 in the US. About 80 genes were found to be in association with CMT. The phosphoribosyl pyrophosphate synthetase 1 (PRPS1) is an essential enzyme in the primary stage of de novo and salvage nucleotide synthesis. The mutations in the PRPS1 gene leads to X-linked Charcot-Marie-Tooth neuropathy type 5 (CMTX5), PRS super activity, Arts syndrome, X-linked deafness-1, breast cancer, and colorectal cancer...
October 18, 2017: Metabolic Brain Disease
https://www.readbyqxmd.com/read/28938448/autosomal-dominant-pth-gene-signal-sequence-mutation-in-a-family-with-familial-isolated-hypoparathyroidism
#4
Luigia Cinque, Angelo Sparaneo, Laura Penta, Amedea Mencarelli, Daniela Rogaia, Susanna Esposito, Federico Pio Fabrizio, Filomena Baorda, Alberto Verrotti, Alberto Falorni, Gabriela Stangoni, Geoffrey N Hendy, Vito Guarnieri, Paolo Prontera
Context: Familial isolated hypoparathyroidism (FIH) is a genetically heterogeneous disorder due to mutations of the calcium-sensing receptor (CASR), glial cells missing-2 (GCM2), guanine nucleotide binding protein α11 (GNA11), or parathyroid hormone (PTH) genes. Thus far, only four cases with homozygous and two cases with heterozygous mutations in the PTH gene have been reported. Objective: To clinically describe an FIH family and identify and characterize the causal gene mutation...
November 1, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28910730/pathogenic-and-likely-pathogenic-genetic-alterations-and-polymorphisms-in-growth-hormone-gene-gh1-and-growth-hormone-releasing-hormone-receptor-gene-ghrhr-in-a-cohort-of-isolated-growth-hormone-deficient-ighd-children-in-sri-lanka
#5
Tharmini Sundralingam, Kamani Hemamala Tennekoon, Shamya de Silva, Sumadee De Silva, Asanka Sudeshini Hewage
OBJECTIVE: Genetic alterations in GH1 and GHRHR genes are known to cause isolated growth hormone deficiency (IGHD). Of these, GHRHR codon 72 mutation has been reported to be highly prevalent in the Indian subcontinent, but among Sri Lankans its prevalence was low compared to reports from neighboring countries. The present study was therefore carried out to identify genetic alterations in the GH1 gene and rest of the GHRHR gene in a cohort of Sri Lankan IGHD patients who tested negative for GHRHR codon 72 mutation...
September 5, 2017: Growth Hormone & IGF Research
https://www.readbyqxmd.com/read/28900455/diverse-pattern-of-gap-junction-beta-2-and-gap-junction-beta-4-genes-mutations-and-lack-of-contribution-of-dfnb21-dfnb24-dfnb29-and-dfnb42-loci-in-autosomal-recessive-nonsyndromic-hearing-loss-patients-in-hormozgan-iran
#6
Masoud Akbarzadeh Laleh, Marzieh Naseri, Ali Akbar Poursadegh Zonouzi, Ahmad Poursadegh Zonouzi, Marjan Masoudi, Najmeh Ahangari, Leila Shams, Azim Nejatizadeh
BACKGROUND: We aimed to determine the contribution of four DFNB loci and mutation analysis of gap junction beta-2 (GJB2) and GJB4 genes in autosomal recessive nonsyndromic hearing loss (ARNSHL) in South of Iran. MATERIALS AND METHODS: A total of 36 large ARNSHL pedigrees with at least two affected subjects were enrolled in the current study. The GJB2 and GJB4 genes mutations were screened using direct sequencing method. The GJB2 and GJB4 negative families were analyzed for the linkage to DFNB21, DFNB24, DFNB29, and DFNB42 loci by genotyping the corresponding STR markers using polymerase chain reaction-PAGE method...
2017: Journal of Research in Medical Sciences: the Official Journal of Isfahan University of Medical Sciences
https://www.readbyqxmd.com/read/28875386/novel-spg20-mutation-in-an-extended-family-with-troyer-syndrome
#7
S Bizzari, A R Hamzeh, P Nair, M Mohamed, F Saif, G Aithala, M T Al-Ali, F Bastaki
Troyer Syndrome (TRS) is a rare autosomal recessive complicated spastic paraplegia disorder characterized by various neurological and musculoskeletal manifestations. Pathogenicity stems from mutations in SPG20 which encodes Spartin, a multifunctional protein that is thought to be essential for neuron viability. Here we report on the clinical and molecular characterization of TRS in five patients from an extended consanguineous family in the United Arab Emirates. Molecular analysis involved Whole Exome Sequencing and Sanger sequencing for identification and confirmation of the causative variant respectively...
December 2017: Metabolic Brain Disease
https://www.readbyqxmd.com/read/28808266/in-silico-analysis-of-glanzmann-variants-of-calf-1-domain-of-%C3%AE-iib%C3%AE-3-integrin-revealed-dynamic-allosteric-effect
#8
Matthieu Goguet, Tarun Jairaj Narwani, Rachel Petermann, Vincent Jallu, Alexandre G de Brevern
Integrin αIIbβ3 mediates platelet aggregation and thrombus formation. In a rare hereditary bleeding disorder, Glanzmann thrombasthenia (GT), αIIbβ3 expression / function are impaired. The impact of deleterious missense mutations on the complex structure remains unclear. Long independent molecular dynamics (MD) simulations were performed for 7 GT variants and reference structure of the Calf-1 domain of αIIb. Simulations were analysed using a structural alphabet to describe local protein conformations. Common and flexible regions as well as deformable zones were observed in all the structures...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28807866/brca1-2-missense-mutations-and-the-value-of-in-silico-analyses
#9
Carolin E Sadowski, Daniela Kohlstedt, Cornelia Meisel, Katja Keller, Kerstin Becker, Luisa Mackenroth, Andreas Rump, Evelin Schröck, Pauline Wimberger, Karin Kast
INTRODUCTION: The clinical implications of genetic variants in BRCA1/2 in healthy and affected individuals are considerable. Variant interpretation, however, is especially challenging for missense variants. The majority of them are classified as variants of unknown clinical significance (VUS). Computational (in-silico) predictive programs are easy to access, but represent only one tool out of a wide range of complemental approaches to classify VUS. With this single-center study, we aimed to evaluate the impact of in-silico analyses in a spectrum of different BRCA1/2 missense variants...
August 12, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28792652/mutations-in-the-novel-gene-fopv-are-associated-with-familial-autosomal-dominant-and-non-familial-obliterative-portal-venopathy
#10
Claude Besmond, Dominique Valla, Laurence Hubert, Karine Poirier, Brigitte Grosse, Catherine Guettier, Olivier Bernard, Emmanuel Gonzales, Emmanuel Jacquemin
BACKGROUND AND AIMS: Obliterative portal venopathy (OPV) is characterized by lesions of portal vein intrahepatic branches and is thought to be responsible for many cases of portal hypertension in absence of cirrhosis or obstruction of large portal or hepatic veins. In most cases the cause of OPV remains unknown. The aim was to identify a candidate gene of OPV. METHODS: Whole exome sequencing was performed in two families, including 6 patients with OPV. Identified mutations were confirmed by Sanger sequencing and expression of candidate gene transcript was studied by real time qPCR in human tissues...
August 9, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28780519/analysis-of-genetic-and-clinical-characteristics-of-a-chinese-kallmann-syndrome-cohort-with-anos1-mutations
#11
Min Nie, Hongli Xu, Rongrong Chen, Jiangfeng Mao, Xi Wang, Shuyu Xiong, Junjie Zheng, Bingqing Yu, Mingxuan Cui, Wanlu Ma, Qibin Huang, Hongbing Zhang, Xueyan Wu
OBJECTIVE: To analyze ANOS1 gene mutations in a large Chinese Kallmann syndrome (KS) cohort and to characterize the clinical presentation of the disease in patients with ANOS1 mutations. PATIENTS AND METHODS: Chinese patients with KS, including 187 sporadic and 23 pedigree cases were recruited. Patients' ANOS1 gene sequences were analyzed by direct sequencing of PCR-amplified products. In silico analysis was used to assess functional relevance of newly identified missense mutations...
October 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28770488/identification-and-characterization-of-functional-single-nucleotide-polymorphisms-snps-in-axin-1-gene-a-molecular-dynamics-approach
#12
Imran Khan, Irfan A Ansari, Pratichi Singh, J Febin Prabhu Dass, Fahad Khan
Wnt signaling pathway has been reported to play crucial role in intestinal crypt formation and deregulation of this pathway is responsible for colorectal cancer initiation and progression. Axin 1, a scaffold protein, play pivotal role in the regulation of Wnt/β-catenin signaling pathway and has been found to be mutated in several cancers; primarily in colon cancer. Considering its crucial role, a structural and functional analysis of missense mutations in Axin 1 gene was performed in this study. Initially, one hundred non-synonymous single nucleotide polymorphisms in the coding regions of Axin 1 gene were selected for in silico analysis...
August 2, 2017: Cell Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28765322/structural-basis-and-genotype-phenotype-correlations-of-insr-mutations-causing-severe-insulin-resistance
#13
Jun Hosoe, Hiroko Kadowaki, Fuyuki Miya, Katsuya Aizu, Tomoyuki Kawamura, Ichiro Miyata, Kenichi Satomura, Takeru Ito, Kazuo Hara, Masaki Tanaka, Hiroyuki Ishiura, Shoji Tsuji, Ken Suzuki, Minaka Takakura, Keith A Boroevich, Tatsuhiko Tsunoda, Toshimasa Yamauchi, Nobuhiro Shojima, Takashi Kadowaki
The insulin receptor (INSR) gene was analyzed in four patients with severe insulin resistance, revealing five novel mutations and a deletion that removed exon 2. A patient with Donohue syndrome (DS) had a novel p.V657F mutation in the second fibronectin type III domain (FnIII-2), which contains the α-β cleavage site and part of the insulin-binding site. The mutant INSR was expressed in Chinese hamster ovary cells, revealing that it reduced insulin proreceptor processing and impaired activation of downstream signaling cascades...
October 2017: Diabetes
https://www.readbyqxmd.com/read/28752769/mutation-spectrum-and-genotype-phenotype-analyses-in-a-pakistani-cohort-with-hemophilia-b
#14
Muhammad Tariq Masood Khan, Arshi Naz, Jawad Ahmed, Tahir Shamsi, Shariq Ahmed, Nisar Ahmed, Ayisha Imran, Nazish Farooq, Muhammad Tariq Hamayun Khan, Abid Sohail Taj
This study aimed to (1) identify F9 genetic alterations in patients with hemophilia B (HB) of Pakistani origin and (2) determine the genotype-phenotype relationships in these patients. Diagnosed cases of HB were identified through registries at designated tertiary health-care centers across the country. Consenting patients were enrolled into the study. The factor IX (FIX) coagulation activity (FIX:C) and key clinical features were recorded. Direct sequencing of F9 was carried out in all patients. All the variants identified were analyzed for functional consequences employing in silico analysis tools...
January 1, 2017: Clinical and Applied Thrombosis/hemostasis
https://www.readbyqxmd.com/read/28718531/next-generation-sequencing-for-patients-with-non-obstructive-azoospermia-implications-for-significant-roles-of-monogenic-oligogenic-mutations
#15
S Nakamura, M Miyado, K Saito, M Katsumi, A Nakamura, Y Kobori, Y Tanaka, H Ishikawa, A Yoshida, H Okada, K Hata, K Nakabayashi, K Okamura, H Ogata, Y Matsubara, T Ogata, H Nakai, M Fukami
Azoospermia affects up to 1% of adult men. Non-obstructive azoospermia is a multifactorial disorder whose molecular basis remains largely unknown. To date, mutations in several genes and multiple submicroscopic copy-number variations (CNVs) have been identified in patients with non-obstructive azoospermia. The aim of this study was to clarify the contribution of nucleotide substitutions in known causative genes and submicroscopic CNVs in the genome to the development of non-obstructive azoospermia. To this end, we conducted sequence analysis of 25 known disease-associated genes using next-generation sequencing and genome-wide copy-number analysis using array-based comparative genomic hybridization...
July 2017: Andrology
https://www.readbyqxmd.com/read/28716744/a-heterozygous-mutation-in-got1-is-associated-with-familial-macro-aspartate-aminotransferase
#16
Maria Kulecka, Aldona Wierzbicka, Agnieszka Paziewska, Michal Mikula, Andrzej Habior, Wojciech Janczyk, Michalina Dabrowska, Jakub Karczmarski, Michal Lazniewski, Krzysztof Ginalski, Anna Czlonkowska, Piotr Socha, Jerzy Ostrowski
BACKGROUND & AIMS: Macro-aspartate aminotransferase (macro-AST) manifests as a persistent elevation of AST levels, because of association of the protein with immunoglobulins in the circulation. Macro-AST is a rare, benign condition without a previously confirmed genetic basis. METHODS: Whole exome sequencing (WES)-based screening was performed on 32 participants with suspected familial macro-AST, while validation of variants was performed on an extended cohort of 92 probands and 1,644 healthy controls using Taqman genotyping...
July 15, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28716533/novel-ubqln2-mutations-linked-to-amyotrophic-lateral-sclerosis-and-atypical-hereditary-spastic-paraplegia-phenotype-through-defective-hsp70-mediated-proteolysis
#17
Elisa Teyssou, Laura Chartier, Maria-Del-Mar Amador, Roselina Lam, Géraldine Lautrette, Marie Nicol, Selma Machat, Sandra Da Barroca, Carine Moigneu, Mathilde Mairey, Thierry Larmonier, Safaa Saker, Christelle Dussert, Sylvie Forlani, Bertrand Fontaine, Danielle Seilhean, Delphine Bohl, Séverine Boillée, Vincent Meininger, Philippe Couratier, François Salachas, Giovanni Stevanin, Stéphanie Millecamps
Mutations in UBQLN2 have been associated with rare cases of X-linked juvenile and adult forms of amyotrophic lateral sclerosis (ALS) and ALS linked to frontotemporal dementia (FTD). Here, we report 1 known (c.1489C>T, p.Pro497Ser, P497S) and 3 novel (c.1481C>T, p.Pro494Leu, P494L; c.1498C>T, p.Pro500Ser, P500S; and c.1516C>G, p.Pro506Ala, P506A) missense mutations in the PXX domain of UBQLN2 in familial motor neuron diseases including ALS and spastic paraplegia (SP). A novel missense mutation (c...
June 24, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28697396/novel-mutations-in-the-exon-5-intron-2-and-3-utr-regions-of-il-12b-gene-were-observed-in-clinically-proven-tuberculosis-patients-of-south-india
#18
Pallipamu Prakash Babu, Pasupuleti Santhosh Kumar, Alladi Mohan, Bhattaram Siddhartha Kumar, Potukuchi Venkata Gurunadha Krishna Sarma
Interleukin-12 (IL-12) is formed by the interaction of IL-12p35 and IL-12p40 expressed independently from IL-12A and IL-12B genes. This interleukin plays prominent role in the T-helper type-1 (Th1) response against intracellular pathogens. Variations in IL-12B gene causes disruption of various activities one of them is suppression of Th1 response and is one of the characteristic features observed in patients with active tuberculosis. Hence, in the present study IL-12B gene status was evaluated in 50 new sputum smear-positive pulmonary tuberculosis patients (NSP-PTB) as identified by Ziehl-Nielsen (ZN) staining and 50 apparently healthy control subjects (HCS) who were sputum smear-negative...
July 8, 2017: Cytokine
https://www.readbyqxmd.com/read/28687848/screening-of-best1-gene-in-a-chinese-cohort-with-best-vitelliform-macular-dystrophy-or-autosomal-recessive-bestrophinopathy
#19
Lu Tian, Tengyang Sun, Ke Xu, Xiaohui Zhang, Xiaoyan Peng, Yang Li
Purpose: Mutations in the BEST1 gene can cause Best vitelliform macular dystrophy (BVMD) and autosomal recessive bestrophinopathy (ARB). The aim of the current study was to establish the BEST1 mutation spectrum in Chinese patients with BVMD and ARB and to describe the phenotypic characteristics of patients carrying BEST1 mutations. Methods: A total of 37 probands with a clinical diagnosis of BVMD (17 patients) or ARB (20 patients) were recruited for genetic analysis; of these, only 5 probands had a family history...
July 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28677912/analysis-of-kera-in-four-families-with-cornea-plana-identifies-two-novel-mutations
#20
Lubica Dudakova, Jang Hee J Vercruyssen, Irina Balikova, Lavina Postolache, Bart P Leroy, Pavlina Skalicka, Petra Liskova
PURPOSE: To identify the molecular genetic cause in four families of various ethnic backgrounds with cornea plana. METHODS: Detailed ophthalmological examination and direct sequencing of the KERA coding region in five patients of Czech and Turkish origin and their available family members. RESULTS: Compound heterozygosity for a novel missense mutation c.209C>T; p.(Pro70Leu) and a novel splice site mutation c.887-1G>A in KERA were detected in two affected siblings of Czech origin...
July 5, 2017: Acta Ophthalmologica
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