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In silico analysis missense mutation

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https://www.readbyqxmd.com/read/29331980/dmc1-mutation-that-causes-human-non-obstructive-azoospermia-and-premature-ovarian-insufficiency-identified-by-whole-exome-sequencing
#1
Wen-Bin He, Chao-Feng Tu, Qiang Liu, Lan-Lan Meng, Shi-Min Yuan, Ai-Xiang Luo, Fu-Sheng He, Juan Shen, Wen Li, Juan Du, Chang-Gao Zhong, Guang-Xiu Lu, Ge Lin, Li-Qing Fan, Yue-Qiu Tan
BACKGROUND: The genetic causes of the majority of male and female infertility caused by human non-obstructive azoospermia (NOA) and premature ovarian insufficiency (POI) with meiotic arrest are unknown. OBJECTIVE: To identify the genetic cause of NOA and POI in two affected members from a consanguineous Chinese family. METHODS: We performed whole-exome sequencing of DNA from both affected patients. The identified candidate causative gene was further verified by Sanger sequencing for pedigree analysis in this family...
January 13, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/29317596/rare-loss-of-function-mutations-in-n-methyl-d-aspartate-glutamate-receptors-and-their-contributions-to-schizophrenia-susceptibility
#2
Yanjie Yu, Yingni Lin, Yuto Takasaki, Chenyao Wang, Hiroki Kimura, Jingrui Xing, Kanako Ishizuka, Miho Toyama, Itaru Kushima, Daisuke Mori, Yuko Arioka, Yota Uno, Tomoko Shiino, Yukako Nakamura, Takashi Okada, Mako Morikawa, Masashi Ikeda, Nakao Iwata, Yuko Okahisa, Manabu Takaki, Shinji Sakamoto, Toshiyuki Someya, Jun Egawa, Masahide Usami, Masaki Kodaira, Akira Yoshimi, Tomoko Oya-Ito, Branko Aleksic, Kinji Ohno, Norio Ozaki
In schizophrenia (SCZ) and autism spectrum disorder (ASD), the dysregulation of glutamate transmission through N-methyl-D-aspartate receptors (NMDARs) has been implicated as a potential etiological mechanism. Previous studies have accumulated evidence supporting NMDAR-encoding genes' role in etiology of SCZ and ASD. We performed a screening study for exonic regions of GRIN1, GRIN2A, GRIN2C, GRIN2D, GRIN3A, and GRIN3B, which encode NMDAR subunits, in 562 participates (370 SCZ and 192 ASD). Forty rare variants were identified including 38 missense, 1 frameshift mutation in GRIN2C and 1 splice site mutation in GRIN2D...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29304759/a-novel-compound-heterozygous-variant-identified-in-gldc-gene-in-a-chinese-family-with-non-ketotic-hyperglycinemia
#3
Yiming Lin, Zhenzhu Zheng, Wenjia Sun, Qingliu Fu
BACKGROUND: Non-ketotic hyperglycinemia (NKH) is a rare, devastating autosomal recessive disorder of glycine metabolism with a very poor prognosis. Currently, few studies have reported genetic profiling of Chinese NKH patients. This study aimed to identify the genetic mutations in a Chinese family with NKH. METHODS: A Chinese family of Han ethnicity, with three siblings with NKH was studied. Sanger sequencing and multiplex ligation-dependent probe amplification combined with SYBR green real-time quantitative PCR was used to identify potential mutations in the GLDC, AMT and GCSH genes...
January 5, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29290829/genetic-variation-in-n-and-c-terminal-regions-of-bovine-dnaja1-heat-shock-protein-gene-in-african-asian-and-american-cattle
#4
Oyeyemi O Ajayi, Sunday O Peters, Marcos De Donato, F Denis Mujibi, Waqas A Khan, Tanveer Hussain, Masroor E Babar, Ikhide G Imumorin, Bolaji N Thomas
DNAJA1 or heat shock protein 40 (Hsp40) is associated with heat adaptation in various organisms. We amplified and sequenced a total of 1,142 bp of bovine Hsp40 gene representing the critical N-terminal (NTR) and C-terminal (CTR) regions in representative samples of African, Asian and American cattle breeds. Eleven and 9 different haplotypes were observed in the NTR in Asian and African breeds respectively while in American Brangus, only two mutations were observed resulting in two haplotypes. The CTR appears to be highly conserved between cattle and yak...
2018: Journal of Genomics
https://www.readbyqxmd.com/read/29247561/protein-altering-variants-of-ptpn2-in-childhood-onset-type-1a-diabetes
#5
M Okuno, T Ayabe, I Yokota, I Musha, K Shiga, T Kikuchi, N Kikuchi, A Ohtake, A Nakamura, K Nakabayashi, K Okamura, Y Momozawa, M Kubo, J Suzuki, T Urakami, T Kawamura, S Amemiya, T Ogata, S Sugihara, M Fukami
AIM: To conduct PTPN2 mutation analysis in Japanese people with childhood-onset Type 1A diabetes in order to examine whether PTPN2 variants contribute to the risk of this condition. METHODS: PTPN2 mutation analysis was carried out for 169 unrelated Japanese people with childhood-onset Type 1A diabetes. We searched for coding variants that were absent or extremely rare in the general population and were scored as damaging by multiple in silico programs. We performed mRNA analysis and three-dimensional structural prediction of the detected variants, when possible...
December 16, 2017: Diabetic Medicine: a Journal of the British Diabetic Association
https://www.readbyqxmd.com/read/29230161/a-homozygous-missense-variant-in-inpp5e-associated-with-joubert-syndrome-and-related-disorders
#6
Mitesh Shetty, Nimmy Ramdas, Shubhi Sahni, Nandita Mullapudi, Sridevi Hegde
Joubert syndrome and related disorders (JSRD; ORPHA 140874) is a complex set of neurodevelopmental disorders with multiple organ involvement. JSRD is a type of ciliopathy which is caused by the presence of defective primary cilia in an individual. JSRD is commonly inherited in an autosomal recessive pattern, and more than 23 genes are known to be associated with JSRD. We report a novel homozygous mutation identified in the INPP5E gene, c.1303C>T, which leads to a change of an amino acid from arginine to tryptophan at residue 435 in the protein chain...
November 2017: Molecular Syndromology
https://www.readbyqxmd.com/read/29197658/utilizing-the-genome-aggregation-database-computational-pathogenicity-prediction-tools-and-patch-clamp-heterologous-expression-studies-to-demote-previously-published-type-1-long-qt-syndrome-mutations-from-pathogenic-to-benign
#7
Daniel J Clemens, Anne R Lentino, Jamie D Kapplinger, Dan Ye, Wei Zhou, David J Tester, Michael J Ackerman
BACKGROUND: Mutations in the KCNQ1-encoded Kv7.1 potassium channel cause type 1 long QT syndrome (LQT1). It has been suggested that ∼10-20% of rare LQTS case-derived variants in the literature may have been published erroneously as LQT1-causative mutations and may be "false positives." OBJECTIVE: To determine which previously published KCNQ1 case variants are likely false positives. METHODS: A list of all published, case-derived KCNQ1 missense variants (MVs) was compiled...
November 29, 2017: Heart Rhythm: the Official Journal of the Heart Rhythm Society
https://www.readbyqxmd.com/read/29172679/in-silico-approach-to-investigate-the-structural-and-functional-attributes-of-familial-hypercholesterolemia-variants-reported-in-the-saudi-population
#8
Fatima A Morad, Omran M Rashidi, Saida S Sadath, Faisal A Al-Allaf, Mohammad Athar, Mohamed N Alama, Sherif E Edris, Nabeel S Bondagji, Noor A Shaik, Babajan Banaganapalli, Zuhier Awan
Familial hypercholesterolemia (FH) is a metabolic disorder that leads primarily to premature cardiovascular diseases, the main cause of mortality in Saudi Arabia (SA). FH is underreported and underdiagnosed in SA with statistical evidence of high expected prevalence in such a consanguineous community. Lacking knowledge of which and how these alterations are actually impacting lipid metabolism is one of the main reasons why FH is insufficiently diagnosed in the region. The aim of this study was to develop a fast prediction approach using an integrated bioinformatics method for future screening of the potential causative variants from national registries...
November 27, 2017: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29159838/eys-mutation-update-in-silico-assessment-of-271-reported-and-26-novel-variants-in-patients-with-retinitis-pigmentosa
#9
Muriël Messchaert, Lonneke Haer-Wigman, Muhammad I Khan, Frans P M Cremers, Rob W J Collin
Mutations in Eyes shut homolog (EYS) are one of the most common causes of autosomal recessive (ar) retinitis pigmentosa (RP), a progressive blinding disorder. The exact function of the EYS protein and the pathogenic mechanisms underlying EYS-associated RP are still poorly understood, which hampers the interpretation of the causality of many EYS variants discovered to date. We collected all reported EYS variants present in 377 arRP index cases published before June 2017, and uploaded them in the Leiden Open Variation Database (www...
November 21, 2017: Human Mutation
https://www.readbyqxmd.com/read/29127258/homozygous-mutation-in-cep19-a-gene-mutated-in-morbid-obesity-in-bardet-biedl-syndrome-with-predominant-postaxial-polydactyly
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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