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In silico analysis missense mutation

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https://www.readbyqxmd.com/read/28072499/in-silico-analysis-of-the-deleterious-nssnp-s-missense-in-the-homeobox-domain-of-human-hoxb13-gene-responsible-for-hereditary-prostate-cancer
#1
Gopalakrishnan Chandrasekaran, Eu Chang Hwang, Taek Won Kang, Dongdeuk Kwon, Kwangsung Park, Je-Jung Lee, Vinoth-Kumar Lakshmanan
The human HOXB13 gene encodes a transcription factor containing a DNA-binding homeobox domain and a HoxA13 N-terminal domain. SNP is considered to be the primary genetic cause for hereditary prostate cancer (PCa). The study of functional nsSNP's would give an insight into the exact cause underlying the onset of hereditary PCa and possible methodologies for the cure or early management of the disease. Several in silico tools were used to screen and map the deleterious nsSNP's to the protein structure for predicting the structure-function effects...
January 10, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28061825/new-cdh3-mutation-in-the-first-spanish-case-of-hypotrichosis-with-juvenile-macular-dystrophy-a-case-report
#2
Fiona Blanco-Kelly, Luciana Rodrigues-Jacy da Silva, Iker Sanchez-Navarro, Rosa Riveiro-Alvarez, Miguel Angel Lopez-Martinez, Marta Corton, Carmen Ayuso
BACKGROUND: CDH3 on 16q22.1 is responsible for two rare autosomal recessive disorders with hypotrichosis and progressive macular dystrophy: Hypotrichosis with Juvenile Macular Dystrophy and Ectodermal Dysplasia, Ectrodactyly and Macular Dystrophy. We present a new case of Hypotrichosis with Juvenile Macular Dystrophy. CASE PRESENTATION: A Spanish male born in 1998 from non-consanguineous healthy parents with a suspected diagnosis of Keratosis Follicularis Spinulosa Decalvans and Retinitis Pigmentosa Inversa referred to our Genetics Department (IIS-Fundación Jiménez Díaz)...
January 7, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28028996/genetic-profiles-of-korean-patients-with-glucose-6-phosphate-dehydrogenase-deficiency
#3
Jaewoong Lee, Joonhong Park, Hayoung Choi, Jiyeon Kim, Ahlm Kwon, Woori Jang, Hyojin Chae, Myungshin Kim, Yonggoo Kim, Jae Wook Lee, Nack Gyun Chung, Bin Cho
BACKGROUND: We describe the genetic profiles of Korean patients with glucose-6-phosphate dehydrogenase (G6PD) deficiencies and the effects of G6PD mutations on protein stability and enzyme activity on the basis of in silico analysis. METHODS: In parallel with a genetic analysis, the pathogenicity of G6PD mutations detected in Korean patients was predicted in silico. The simulated effects of G6PD mutations were compared to the WHO classes based on G6PD enzyme activity...
March 2017: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/28000143/update-on-novel-ccm-gene-mutations-in-patients-with-cerebral-cavernous-malformations
#4
Concetta Scimone, Placido Bramanti, Concetta Alafaci, Francesca Granata, Francesco Piva, Carmela Rinaldi, Luigi Donato, Federica Greco, Antonina Sidoti, Rosalia D'Angelo
Cerebral cavernous malformations (CCMs) are lesions affecting brain microvessels. The pathogenesis is not clearly understood. Conventional classification criterion is based on genetics, and thus, familial and sporadic forms can be distinguished; however, classification of sporadic cases with multiple lesions still remains uncertain. To date, three CCM causative genes have been identified: CCM1/KRIT1, CCM2/MGC4607 and CCM3/PDCD10. In our previous mutation screening, performed in a cohort of 95 Italian patients, with both sporadic and familial cases, we identified several mutations in CCM genes...
December 20, 2016: Journal of Molecular Neuroscience: MN
https://www.readbyqxmd.com/read/27989988/novel-mutations-and-structural-deletions-in-tubb8-expanding-mutational-and-phenotypic-spectrum-of-patients-with-arrest-in-oocyte-maturation-fertilization-or-early-embryonic-development
#5
Biaobang Chen, Bin Li, Da Li, Zheng Yan, Xiaoyan Mao, Yao Xu, Jian Mu, Qiaoli Li, Li Jin, Lin He, Yanping Kuang, Qing Sang, Lei Wang
STUDY QUESTION: Are there any new type of mutations and novel phenotypes in patients with arrest in oocyte maturation, fertilization or early embryonic development having tubulin beta eight class VIII (TUBB8) mutations? SUMMARY ANSWER: We identified new types of mutations in TUBB8 associated with maturation, fertilization and developmental arrest. WHAT IS KNOWN ALREADY: We previously found heterozygous mutations and a homozygous frameshift/internal seven amino acid deletion in TUBB8 that are responsible for oocyte maturation arrest...
December 17, 2016: Human Reproduction
https://www.readbyqxmd.com/read/27928163/tbcd-may-be-a-causal-gene-in-progressive-neurodegenerative-encephalopathy-with-atypical-infantile-spinal-muscular-atrophy
#6
Toshio Ikeda, Akihiko Nakahara, Rie Nagano, Maiko Utoyama, Megumi Obara, Hiroshi Moritake, Tamayo Uechi, Jun Mitsui, Hiroyuki Ishiura, Jun Yoshimura, Koichiro Doi, Naoya Kenmochi, Shinichi Morishita, Ichizo Nishino, Shoji Tsuji, Hiroyuki Nunoi
Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disorder caused by survival motor neuron gene mutations. Variant forms of SMA accompanied by additional clinical presentations have been classified as atypical SMA and are thought to be caused by variants in as yet unidentified causative genes. Here, we presented the clinical findings of two siblings with an SMA variant followed by progressive cerebral atrophy, and the results of whole-exome sequencing analyses of the family quartet that was performed to identify potential causative variants...
December 8, 2016: Journal of Human Genetics
https://www.readbyqxmd.com/read/27914961/expanding-the-clinical-and-genetic-spectrum-of-g6pd-deficiency-the-occurrence-of-bcgitis-and-novel-missense-mutation
#7
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...
January 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/27905547/in-silico-mapping-of-protein-unfolding-mutations-for-inherited-disease
#8
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
#9
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
#10
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
#11
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...
January 2017: 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
#12
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
#13
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
#14
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...
February 2017: 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
#15
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...
January 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/27755493/mutation-of-the-planar-cell-polarity-gene-vangl1-in-adolescent-idiopathic-scoliosis
#16
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
#17
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
#18
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
#19
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, and 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...
January 2017: 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
#20
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
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