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In silico analysis missense mutation

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https://www.readbyqxmd.com/read/28532645/identification-of-a-novel-psen1-mutation-leu232pro-in-a-korean-patient-with-early-onset-alzheimer-s-disease-and-a-family-history-of-dementia
#1
Jiyun Park, Seong Soo A An, Vo Van Giau, Kyuhwan Shim, Young Chul Youn, Eva Bagyinszky, SangYun Kim
In the present study, a novel mutation in exon 7 of presenilin 1 (Leu232Pro) was discovered in a Korean patient with early-onset Alzheimer's disease, who represented memory decline at 37 years of age, followed by impairment in spatial activity and concentrations and personality changes. Imaging analyses with magnetic resonance scan showed diffuse atrophy in the frontoparietal regions. Targeted next generation sequencing and Sanger sequencing identified a heterozygous T to C transition at position 695 (c.695T>C) of in presenilin 1 gene (PSEN1), resulting in a novel missense mutation at codon 232 from leucine to proline (L232P)...
April 26, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/28503092/management-of-gene-variants-of-unknown-significance-analysis-method-and-risk-assessment-of-the-vhl-mutation-p-p81s-c-241c-t
#2
REVIEW
Daniela Alosi, Marie Luise Bisgaard, Sophie Nowak Hemmingsen, Lotte Nylandsted Krogh, Hanne Birte Mikkelsen, Marie Louise Mølgaard Binderup
BACKGROUND: Evaluation of the pathogenicity of a gene variant of unknown significance (VUS) is crucial for molecular diagnosis and genetic counseling, but can be challenging. This is especially so in phenotypically variable diseases, such as von Hippel-Lindau disease (vHL). vHL is caused by germline mutations in the VHL gene, which predispose to the development of multiple tumors such as central nervous system hemangioblastomas and renal cell carcinoma (RCC). OBJECTIVE: We propose a method for the evaluation of VUS pathogenicity through our experience with the VHL missense mutation c...
February 2017: Current Genomics
https://www.readbyqxmd.com/read/28493373/the-novel-%C3%AE-b-crystallin-cryab-mutation-p-d109g-causes-restrictive-cardiomyopathy
#3
Andreas Brodehl, Anna Gaertner-Rommel, Bärbel Klauke, Simon Andre Grewe, Ilona Schirmer, Andreas Peterschröder, Lothar Faber, Matthias Vorgerd, Jan Gummert, Dario Anselmetti, Uwe Schulz, Lech Paluszkiewicz, Hendrik Milting
Restrictive cardiomyopathy (RCM) is a rare heart disease characterized by diastolic dysfunction and atrial enlargement. The genetic etiology of RCM is not completely known. We identified by a next-generation sequencing panel the novel CRYAB missense mutation c.326A>G, p.D109G in a small family with RCM in combination with skeletal myopathy with an early onset of the disease. CRYAB encodes αB-Crystallin, a member of the small heat shock protein family, which is highly expressed in cardiac and skeletal muscle...
May 11, 2017: Human Mutation
https://www.readbyqxmd.com/read/28461402/stearoyl-acyl-carrier-protein-desaturase-mutations-uncover-an-impact-of-stearic-acid-in-leaf-and-nodule-structure
#4
Naoufal Lakhssassi, Vincent Colantonio, Nicholas David Flowers, Zhou Zhou, Jason Scott Henry, Shiming Liu, Khalid Meksem
Stearoyl-acyl carrier protein desaturase (SACPD-C) has been reported to control the accumulation of seed stearic acid; however, no study has previously reported its involvement in leaf stearic acid content and impact on leaf structure and morphology. A subset of an EMS mutagenized population of soybean c.v. 'Forrest' was screened to identify mutants within the GmSACPD-C gene. Using a forward genetics approach, one nonsense and four missense Gmsacpd-c mutants were identified to have high levels of seed, nodule, and leaf stearic acid content...
May 1, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28449065/a-homozygous-missense-mutation-in-eral1-encoding-a-mitochondrial-rrna-chaperone-causes-perrault-syndrome
#5
Iliana A Chatzispyrou, Marielle Alders, Sergio Guerrero-Castillo, Ruben Zapata Perez, Martin A Haagmans, Laurent Mouchiroud, Janet Koster, Rob Ofman, Frank Baas, Hans R Waterham, Johannes N Spelbrink, Johan Auwerx, Marcel M Mannens, Riekelt H Houtkooper, Astrid S Plomp
Perrault syndrome (PS) is a rare recessive disorder characterized by ovarian dysgenesis and sensorineural deafness. It is clinically and genetically heterogeneous, and previously mutations have been described in different genes, mostly related to mitochondrial proteostasis. We diagnosed three unrelated females with PS and set out to identify the underlying genetic cause using exome sequencing. We excluded mutations in the known PS genes, but identified a single homozygous mutation in the ERAL1 gene (c.707A>T; p...
April 25, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28422960/predicting-the-impact-of-lynch-syndrome-causing-missense-mutations-from-structural-calculations
#6
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 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28410400/inherited-variants-in-genes-somatically-mutated-in-thyroid-cancer
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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