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In silico analysis missense mutation

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https://www.readbyqxmd.com/read/28422960/predicting-the-impact-of-lynch-syndrome-causing-missense-mutations-from-structural-calculations
#1
Sofie V Nielsen, Amelie Stein, Alexander B Dinitzen, Elena Papaleo, Michael H Tatham, Esben G Poulsen, Maher M Kassem, Lene J Rasmussen, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen
Accurate methods to assess the pathogenicity of mutations are needed to fully leverage the possibilities of genome sequencing in diagnosis. Current data-driven and bioinformatics approaches are, however, limited by the large number of new variations found in each newly sequenced genome, and often do not provide direct mechanistic insight. Here we demonstrate, for the first time, that saturation mutagenesis, biophysical modeling and co-variation analysis, performed in silico, can predict the abundance, metabolic stability, and function of proteins inside living cells...
April 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28410400/inherited-variants-in-genes-somatically-mutated-in-thyroid-cancer
#2
Chiara Campo, Aleksandra Köhler, Gisella Figlioli, Rossella Elisei, Cristina Romei, Monica Cipollini, Franco Bambi, Kari Hemminki, Federica Gemignani, Stefano Landi, Asta Försti
BACKGROUND: Tumour suppressor genes when mutated in the germline cause various cancers, but they can also be somatically mutated in sporadic tumours. We hypothesized that there may also be cancer-related germline variants in the genes commonly mutated in sporadic well-differentiated thyroid cancer (WDTC). METHODS: We performed a two-stage case-control association study with a total of 2214 cases and 2108 healthy controls from an Italian population. By genotyping 34 single nucleotide polymorphisms (SNPs), we covered a total of 59 missense SNPs and SNPs located in the 5' and 3' untranslated regions (UTRs) of 10 different genes...
2017: PloS One
https://www.readbyqxmd.com/read/28410371/determining-the-role-of-missense-mutations-in-the-pou-domain-of-hnf1a-that-reduce-the-dna-binding-affinity-a-computational-approach
#3
Sneha P, Thirumal Kumar D, George Priya Doss C, Siva R, Hatem Zayed
Maturity-onset diabetes of the young type 3 (MODY3) is a non-ketotic form of diabetes associated with poor insulin secretion. Over the past years, several studies have reported the association of missense mutations in the Hepatocyte Nuclear Factor 1 Alpha (HNF1A) with MODY3. Missense mutations in the POU homeodomain (POUH) of HNF1A hinder binding to the DNA, thereby leading to a dysfunctional protein. Missense mutations of the HNF1A were retrieved from public databases and subjected to a three-step computational mutational analysis to identify the underlying mechanism...
2017: PloS One
https://www.readbyqxmd.com/read/28399682/clinical-molecular-and-computational-analysis-in-patients-with-a-novel-double-mutation-and-a-new-synonymous-variant-in-mecp2-report-of-the-first-missense-mutation-within-the-at-hook1-cluster-in-rett-syndrome
#4
Marwa Kharrat, Yosra Kamoun, Fatma Kamoun, Emna Ellouze, Marwa Maalej, Nourhene Fendri-Kriaa, Leila Ammar-Keskes, Neila Belghith, Ali Gargouri, Chahnez Triki, Faiza Fakhfakh
Rett syndrome is an X-linked neurodevelopmental disorder, primarily caused by MECP2 mutations. In this study, clinical, molecular and bioinformatics analyses were performed in Rett patients to understand the relationship between MECP2 mutation type and the clinical severity. Two double MeCP2 mutations were detected: a novel one (p.G185 V in cis with p.R255X) in P1 and a known one (p.P179 S in cis with p.R255X) in P2. Besides, a novel synonymous mutation (c.807C>T; p.G269G), which could affect mRNA splicing, was identified in P3...
January 1, 2017: Journal of Child Neurology
https://www.readbyqxmd.com/read/28391651/identification-of-a-heterozygous-p-gly568val-missense-mutation-in-the-trpv3-gene-in-a-japanese-patient-with-olmsted-syndrome-in-silico-analysis-of-trpv3
#5
Hiroshi Nagai, Yutaka Takaoka, Aki Sugano, Yuji Nakamachi, Seiji Kawano, Chikako Nishigori
Olmsted syndrome is a very rare congenital disorder, characterized by palmoplantar keratoderma and periorificial keratotic lesions. Recently, TRPV3 was reported to be a causative gene of Olmsted syndrome. We identified a heterozygous missense mutation of TRPV3, c.1703G>T, p.Gly568Val, in a Japanese patient with Olmsted syndrome. To the best of our knowledge, this is the first report of a Japanese patient with Olmsted syndrome harboring a missense mutation in TRPV3. We conducted in silico analysis of TRPV3 to evaluate whether the p...
April 9, 2017: Journal of Dermatology
https://www.readbyqxmd.com/read/28389991/genotype-phenotype-correlation-in-18-egyptian-patients-with-glutaric-acidemia-type-i
#6
Ahmed Mosaeilhy, Magdy M Mohamed, George Priya Doss C, Heba S A El Abd, Radwa Gamal, Osama K Zaki, Hatem Zayed
Glutaric acidemia I (GAI) is an autosomal recessive metabolic disease caused by a deficiency of glutaryl-CoA dehydrogenase enzyme (GCDH). Patients with GAI are characterized by macrocephaly, acute encephalitis-like crises, dystonia and frontotemporal atrophy. In this study, we investigated 18 Egyptian patients that were diagnosed with GAI based on their clinical, neuroradiological, and biochemical profiles. Of the 18 patients, 16 had developmental delay and/or regression, dystonia was prominent in 75% of the cases, and three patients died...
April 7, 2017: Metabolic Brain Disease
https://www.readbyqxmd.com/read/28388287/in-silico-analysis-of-non-synonymous-single-nucleotide-polymorphisms-in-human-dazl-gene-associated-with-male-infertility
#7
Mili Nailwal, Jenabhai B Chauhan
In living systems the most frequent type of genetic mutation is the single nucleotide polymorphism (SNP). Non-synonymous SNPs (nsSNPs) or missense mutations arise in coding regions of a particular gene. nsSNPs result in a single amino acid substitution which may have effects on the structure and/or function of proteins. Spermatogenesis is a complex process where haploid spermatozoa are formed. The deleted in azoospermia like (DAZL) gene has a relationship with male infertility and dysfunction of DAZL may decrease the sperm count which leads to oligozoospermia or azoospermia...
April 7, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28386709/in-silico-analysis-of-five-missense-mutations-in-cyp1b1-gene-in-pakistani-families-affected-with-primary-congenital-glaucoma
#8
Sabika Firasat, Haiba Kaul, Usman Ali Ashfaq, Sobia Idrees
PURPOSE: The purpose of this study was to characterize the five missense mutations in CYP1B1 gene identified in Pakistani families affected with primary congenital glaucoma (PCG) using various bioinformatics and protein modeling tools. METHODS: We previously reported four novel missense mutations in CYP1B1 gene segregating in consanguineous Pakistani families. These mutations were identified by direct sequencing of all coding exons, the exon-intron boundaries and the 5' untranslated region of CYP1B1 using genomic DNA from affected and unaffected family members...
April 6, 2017: International Ophthalmology
https://www.readbyqxmd.com/read/28365451/genetic-analysis-and-literature-review-of-chinese-patients-with-familial-renal-glucosuria-identification-of-a-novel-slc5a2-mutation
#9
Xiaojing Wang, Miao Yu, Tong Wang, Huabing Zhang, Fan Ping, Qian Zhang, Jianping Xu, Kai Feng, Xinhua Xiao
BACKGROUND: Familial renal glucosuria (FRG) is an inherited renal tubular disorder characterized by persistent isolated glucosuria with normal blood glucose. SLC5A2 gene mutation was the causative of FRG. METHODS: Molecular genetic analysis of SLC5A2 gene by Sanger sequencing was conducted in two unrelated non-consanguineous Chinese families with isolated glucosuria. Extensive laboratory test and physical examination were performed. In silico algorithms were used to explore the potential effect of novel mutation on SGLT2 function...
March 29, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28296976/exome-wide-association-study-reveals-novel-susceptibility-genes-to-sporadic-dilated-cardiomyopathy
#10
Ulrike Esslinger, Sophie Garnier, Agathe Korniat, Carole Proust, Georgios Kararigas, Martina Müller-Nurasyid, Jean-Philippe Empana, Michael P Morley, Claire Perret, Klaus Stark, Alexander G Bick, Sanjay K Prasad, Jennifer Kriebel, Jin Li, Laurence Tiret, Konstantin Strauch, Declan P O'Regan, Kenneth B Marguiles, Jonathan G Seidman, Pierre Boutouyrie, Patrick Lacolley, Xavier Jouven, Christian Hengstenberg, Michel Komajda, Hakon Hakonarson, Richard Isnard, Eloisa Arbustini, Harald Grallert, Stuart A Cook, Christine E Seidman, Vera Regitz-Zagrosek, Thomas P Cappola, Philippe Charron, François Cambien, Eric Villard
AIMS: Dilated cardiomyopathy (DCM) is an important cause of heart failure with a strong familial component. We performed an exome-wide array-based association study (EWAS) to assess the contribution of missense variants to sporadic DCM. METHODS AND RESULTS: 116,855 single nucleotide variants (SNVs) were analyzed in 2796 DCM patients and 6877 control subjects from 6 populations of European ancestry. We confirmed two previously identified associations with SNVs in BAG3 and ZBTB17 and discovered six novel DCM-associated loci (Q-value<0...
2017: PloS One
https://www.readbyqxmd.com/read/28274275/whole-exome-sequencing-coupled-with-unbiased-functional-analysis-reveals-new-hirschsprung-disease-genes
#11
Hongsheng Gui, Duco Schriemer, William W Cheng, Rajendra K Chauhan, Guillermo Antiňolo, Courtney Berrios, Marta Bleda, Alice S Brooks, Rutger W W Brouwer, Alan J Burns, Stacey S Cherny, Joaquin Dopazo, Bart J L Eggen, Paola Griseri, Binta Jalloh, Thuy-Linh Le, Vincent C H Lui, Berta Luzón-Toro, Ivana Matera, Elly S W Ngan, Anna Pelet, Macarena Ruiz-Ferrer, Pak C Sham, Iain T Shepherd, Man-Ting So, Yunia Sribudiani, Clara S M Tang, Mirjam C G N van den Hout, Herma C van der Linde, Tjakko J van Ham, Wilfred F J van IJcken, Joke B G M Verheij, Jeanne Amiel, Salud Borrego, Isabella Ceccherini, Aravinda Chakravarti, Stanislas Lyonnet, Paul K H Tam, Maria-Mercè Garcia-Barceló, Robert M W Hofstra
BACKGROUND: Hirschsprung disease (HSCR), which is congenital obstruction of the bowel, results from a failure of enteric nervous system (ENS) progenitors to migrate, proliferate, differentiate, or survive within the distal intestine. Previous studies that have searched for genes underlying HSCR have focused on ENS-related pathways and genes not fitting the current knowledge have thus often been ignored. We identify and validate novel HSCR genes using whole exome sequencing (WES), burden tests, in silico prediction, unbiased in vivo analyses of the mutated genes in zebrafish, and expression analyses in zebrafish, mouse, and human...
March 8, 2017: Genome Biology
https://www.readbyqxmd.com/read/28107443/identification-of-the-pla2g6-c-1579g-a-missense-mutation-in-papillon-dog-neuroaxonal-dystrophy-using-whole-exome-sequencing-analysis
#12
Masaya Tsuboi, Manabu Watanabe, Kazumi Nibe, Natsuko Yoshimi, Akihisa Kato, Masahiro Sakaguchi, Osamu Yamato, Miyuu Tanaka, Mitsuru Kuwamura, Kazuya Kushida, Takashi Ishikura, Tomoyuki Harada, James Kenn Chambers, Sumio Sugano, Kazuyuki Uchida, Hiroyuki Nakayama
Whole exome sequencing (WES) has become a common tool for identifying genetic causes of human inherited disorders, and it has also recently been applied to canine genome research. We conducted WES analysis of neuroaxonal dystrophy (NAD), a neurodegenerative disease that sporadically occurs worldwide in Papillon dogs. The disease is considered an autosomal recessive monogenic disease, which is histopathologically characterized by severe axonal swelling, known as "spheroids," throughout the nervous system. By sequencing all eleven DNA samples from one NAD-affected Papillon dog and her parents, two unrelated NAD-affected Papillon dogs, and six unaffected control Papillon dogs, we identified 10 candidate mutations...
2017: PloS One
https://www.readbyqxmd.com/read/28101780/update-of-the-spectrum-of-mucopolysaccharidoses-type-iii-in-tunisia-identification-of-three-novel-mutations-and-in-silico-structural-analysis-of-the-missense-mutations
#13
Souad Ouesleti, Maria Francisca Coutinho, Isaura Ribeiro, Abdehedi Miled, Dalila Saidane Mosbahi, Sandra Alves
BACKGROUND: Mucopolysaccharidoses type III (MPS III) are a group of autosomal recessive lysosomal storage diseases, caused by mutations in genes that code for enzymes involved in the lysosomal degradation of heparan sulphate: heparan sulfate sulfamidase (SGSH), α-N-acetylglucosaminidase (NAGLU), heparan sulfate acetyl-CoA: α-glucosaminide N-acetyltransferase (HGSNAT), and N-acetylglucosamine-6-sulfatase (GNS). METHODS: In this study, we have performed the molecular analysis of the SGSH, NAGLU and HGSNAT genes in 10 patients from 6 different MPS III Tunisian families...
January 19, 2017: World Journal of Pediatrics: WJP
https://www.readbyqxmd.com/read/28096187/gprasp2-a-novel-causative-gene-mutated-in-an-x-linked-recessive-syndromic-hearing-loss
#14
Guangqian Xing, Jun Yao, Chunyu Liu, Qinjun Wei, Xuli Qian, Lingxin Wu, Yajie Lu, Xin Cao
BACKGROUND: A substantial amount of nuclear genes have been identified to be implicated in genetic hearing loss, while X-linked hearing loss is genetically heterogeneous and relatively infrequent. OBJECTIVE: To identify the causative gene mutation in a five-generation Chinese family with an X-linked recessive syndromic hearing loss (SHL). METHODS: Targeted X-chromosome exome sequencing was conducted, and cosegregation analysis was performed in the members of the affected family...
January 17, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28089752/three-novel-mutations-of-arg1-identified-in-chinese-patients-with-argininemia-detected-by-newborn-screening
#15
Ting Zhang, Jianbin Yang, Xiaoshan Yin, Ping Yu, Robert Mooney, Xinwen Huang, Ming Qi
Argininemia is a rare autosomal recessive genetic disorder caused by deficiency of arginase Ι, resulting from mutations in the ARG1 gene. Few genetic studies of ARG1 mutations in Chinese patients have been reported. In this study, two argininemia patients were initially diagnosed by tandem mass spectrometry in newborn screening. Mutation analysis of the ARG1 gene was performed by direct sequencing. Three novel mutations were identified and in silico methods were used to predict the impact of these mutations on the activity of enzyme...
March 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
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
#16
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
#17
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
#18
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
#19
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
#20
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
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