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In silico analysis missense mutation

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https://www.readbyqxmd.com/read/28792652/mutations-in-the-novel-gene-fopv-are-associated-with-familial-autosomal-dominant-and-non-familial-obliterative-portal-venopathy
#1
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
#2
Min Nie, Hongli Xu, Rongrong Chen, Jiangfeng Mao, Xi Wang, Shuyu Xiong, Junjie Zheng, Bingqing Yu, Mingxuan Cui, Wanlu Ma, Qibing 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...
August 5, 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
#3
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
#4
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 5 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...
August 1, 2017: Diabetes
https://www.readbyqxmd.com/read/28752769/mutation-spectrum-and-genotype-phenotype-analyses-in-a-pakistani-cohort-with-hemophilia-b
#5
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
#6
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
#7
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 persistent elevation of AST levels, due to 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 variants validation was performed on an extended cohort of 90 probands and 1644 healthy controls using Taqman genotyping...
July 14, 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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28676128/phenotype-prediction-for-mucopolysaccharidosis-type-i-by-in-silico-analysis
#12
Li Ou, Michael J Przybilla, Chester B Whitley
BACKGROUND: Mucopolysaccharidosis type I (MPS I) is an autosomal recessive disease due to deficiency of α-L-iduronidase (IDUA), a lysosomal enzyme that degrades glycosaminoglycans (GAG) heparan and dermatan sulfate. To achieve optimal clinical outcomes, early and proper treatment is essential, which requires early diagnosis and phenotype severity prediction. RESULTS: To establish a genotype/phenotype correlation of MPS I disease, a combination of bioinformatics tools including SIFT, PolyPhen, I-Mutant, PROVEAN, PANTHER, SNPs&GO and PHD-SNP are utilized...
July 4, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28670533/mutational-analysis-of-androgen-receptor-gene-in-two-families-with-androgen-insensitivity
#13
Radha Ramadevi Akella
BACKGROUND: Androgen insensitivity syndrome (AIS) is a rare X-linked disorder due to mutations in the androgen receptor (AR) gene causing end-organ resistance to the androgenic hormone. SUBJECTS AND METHODS: Genetic studies were carried out in two families by karyotype and targeted exome sequencing of the AR gene. RESULTS: Two novel missense mutations were identified, p.L822P and p.P392S, in two families with complete androgen insensitivity (CAIS) and partial androgen insensitivity (PAIS), respectively...
July 2017: Indian Journal of Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28664505/ssadh-deficiency-in-an-italian-family-a-novel-aldh5a1-gene-mutation-affecting-the-succinic-semialdehyde-substrate-binding-site
#14
Sara Leo, Concetta Capo, Bianca Maria Ciminelli, Federico Iacovelli, Giovanna Menduti, Silvia Funghini, Maria Alice Donati, Mattia Falconi, Luisa Rossi, Patrizia Malaspina
SSADH deficiency (SSADHD) is a rare autosomal recessively inherited metabolic disorder. It is associated with mutations of ALDH5A1 gene, coding for the homotetrameric enzyme SSADH. This enzyme is involved in γ-aminobutyric acid (GABA) catabolism, since it oxidizes succinic semialdehyde (SSA) to succinate. Mutations in ALDH5A1 gene result in the abnormal accumulation of γ-hydroxybutyrate (GHB), which is pathognomonic of SSADHD. In the present report, diagnosis of SSADHD in a three-month-old female was achieved by detection of high levels of GHB in urine...
June 29, 2017: Metabolic Brain Disease
https://www.readbyqxmd.com/read/28662348/abnormal-wnt5a-signaling-causes-mandibular-hypoplasia-in-robinow-syndrome
#15
S Hosseini-Farahabadi, S J Gignac, A Danescu, K Fu, J M Richman
The study of rare genetic diseases provides valuable insights into human gene function. Here, we investigate dominant Robinow syndrome (RS), which affects the WNT5A signaling pathway. Autosomal dominant RS is caused by missense mutations in WNT5A or nonsense mutations in the adaptor protein DVL1 or DVL3. The recessive form of the disease is caused by loss-of-function mutations in the receptor ROR2. RS is characterized by hypertelorism, midface, and mandibular hypoplasia. Here, we focus on the missense mutations in WNT5A, since the impact on function is difficult to predict from in silico analysis...
June 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28660537/in-silico-analysis-of-nssnps-of-carp-tlr22-gene-affecting-its-binding-ability-with-poly-i-c
#16
Vemulawada Chakrapani, Kiran D Rasal, Sunil Kumar, Shibani D Mohapatra, Jitendra K Sundaray, Pallipuram Jayasankar, Hirak K Barman
Immune response mediated by toll-like receptor 22 (TLR22), only found in teleost/amphibians, is triggered by double-stranded RNA binding to its LRR (leucine-rich repeats) ecto-domain. Accumulated evidences suggested that missense mutations in TLR genes affect its function. However, information on mutation linked pathogen recognition for TLR22 was lacking. The present study was commenced for predicting the effect of non-synonymous single-nucleotide polymorphisms (nsSNPs) on the pathogen recognizable LRR domain of TLR22 of farmed carp, Labeo rohita...
June 28, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28645778/whole-genome-sequencing-of-monozygotic-twins-discordant-for-schizophrenia-indicates-multiple-genetic-risk-factors-for-schizophrenia
#17
Jinsong Tang, Yu Fan, Hong Li, Qun Xiang, Deng-Feng Zhang, Zongchang Li, Ying He, Yanhui Liao, Ya Wang, Fan He, Fengyu Zhang, Yin Yao Shugart, Chunyu Liu, Yanqing Tang, Raymond C K Chan, Chuan-Yue Wang, Yong-Gang Yao, Xiaogang Chen
Schizophrenia is a common disorder with a high heritability, but its genetic architecture is still elusive. We implemented whole-genome sequencing (WGS) analysis of 8 families with monozygotic (MZ) twin pairs discordant for schizophrenia to assess potential association of de novo mutations (DNMs) or inherited variants with susceptibility to schizophrenia. Eight nonsynonymous DNMs (including one splicing site) were identified and shared by twins, which were either located in previously reported schizophrenia risk genes (p...
June 8, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28644346/twelve-novel-mutations-in-the-slc26a3-gene-in-17-sporadic-cases-of-congenital-chloride-diarrhea
#18
Felice Amato, Giuseppe Cardillo, Renato Liguori, Manuela Scorza, Marika Comegna, Ausilia Elce, Sonia Giordano, Laura Lucaccioni, Licia Lugli, Sabrina Cardile, Claudio Romano, Vincenza Pezzella, Giuseppe Castaldo, Roberto Berni Canani
OBJECTIVES: We aimed to improve the knowledge of pathogenic mutations in sporadic cases of congenital chloride diarrhea (CCD) and emphasize the importance of functional studies to define the effect of novel mutations. METHODS: All member 3 of solute carrier family 26 (SLC26A3) coding regions were sequenced in 17 sporadic patients with CCD. Moreover, the minigene system was used to analyze the effect of 2 novel splicing mutations. RESULTS: We defined the SLC26A3 genotype of all 17 patients with CCD and identified 12 novel mutations...
July 2017: Journal of Pediatric Gastroenterology and Nutrition
https://www.readbyqxmd.com/read/28644047/mutational-analysis-of-galt-gene-in-greek-patients-with-galactosaemia-identification-of-two-novel-mutations-and-clinical-evaluation
#19
Kleopatra H Schulpis, Georgia Thodi, Konstantinos Iakovou, Maria Chatzidaki, Yannis Dotsikas, Elina Molou, Olga Triantafylli, Yannis L Loukas
Classical galactosaemia is an inborn error of metabolism due to the deficiency of the enzyme galactose-1-phosphate uridylyltransferase (GALT). The aim of the study was to identify the underlying mutations in Greek patients with GALT deficiency and evaluate their psychomotor and speech development. Patients with GALT deficiency (n = 17) were picked up through neonatal screening. Mutational analysis was conducted via Sanger sequencing, while in silico analysis was used in the cases of novel missense mutations...
June 23, 2017: Scandinavian Journal of Clinical and Laboratory Investigation
https://www.readbyqxmd.com/read/28631565/genetic-and-epigenetic-alterations-affecting-park-2-expression-in-cervical-neoplasm-among-north-indian-patients
#20
Afreen Naseem, Zafar Iqbal Bhat, Ponnusamy Kalaiarasan, Bhupender Kumar, Gauri Gandhi, M Moshahid Alam Rizvi
The recent investigation on PARK-2, a putative tumor suppressor gene, has found that it has been altered in multiple human malignancies. However, the clinical impact of PARK-2 alteration in uterine cervix carcinoma has not yet been studied. Therefore, we aimed to examine mutations, promoter hypermethylation, and protein expression of PARK-2 among the North Indian patients and their association with clinical parameters to evaluate the implication of PARK-2 in the genesis of cervical cancer. A total of 168 patient samples were processed for mutational analysis by single-strand conformation polymorphism, sequencing, and further in silico analysis of the identified mutations...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
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