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Prediction of missense mutation

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https://www.readbyqxmd.com/read/28444906/carbamoyl-phosphate-synthetase-1-deficiency-diagnosed-by-whole-exome-sequencing
#1
Guoqing Zhang, Yulin Chen, Huiqun Ju, Fei Bei, Jing Li, Jian Wang, Jianhua Sun, Jun Bu
BACKGROUND: Carbamoyl Phosphate Synthetase 1 deficiency (CPS1D) is a rare autosomal recessive inborn metabolic disease characterized mainly by hyperammonemia. The fatal nature of CPS1D and its similar symptoms with other urea cycle disorders (UCDs) make its diagnosis difficult, and the molecular diagnosis is hindered due to the large size of the causative gene CPS1. Therefore, the objective of the present study was to investigate the clinical applicability of exome sequencing in molecular diagnosis of CPS1D in Chinese population...
April 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28442722/mutational-screening-of-slc39a5-leprel1-and-lrpap1-in-a-cohort-of-187-high-myopia-patients
#2
Chun-Yun Feng, Xiao-Qiong Huang, Xue-Wen Cheng, Rong-Han Wu, Fan Lu, Zi-Bing Jin
High myopia (HM) is a leading cause of mid-way blindness with a high heritability in East Asia. Although only a few disease genes have been reported, a small proportion of patients could be identified with genetic predispositions. In order to expand the mutation spectrum of the causative genes in Chinese adult population, we investigated three genes, SLC39A5, LEPREL1 and LRPAP1, in a cohort of 187 independent Chinese patients with high myopia. Sanger sequencing was used to find possible pathogenic mutations, which were further screened in normal controls...
April 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28442542/missense-mutations-in-the-wd40-domain-of-ahi1-cause-non-syndromic-retinitis-pigmentosa
#3
Thanh-Minh T Nguyen, Sarah Hull, Ronald Roepman, L Ingeborgh van den Born, Machteld M Oud, Erik de Vrieze, Lisette Hetterschijt, Stef J F Letteboer, Sylvia E C van Beersum, Ellen A Blokland, Helger G Yntema, Frans P M Cremers, Paul A van der Zwaag, Gavin Arno, Erwin van Wijk, Andrew R Webster, Lonneke Haer-Wigman
BACKGROUND: Recent findings suggesting that Abelson helper integration site 1 (AHI1) is involved in non-syndromic retinal disease have been debated, as the functional significance of identified missense variants was uncertain. We assessed whether AHI1 variants cause non-syndromic retinitis pigmentosa (RP). METHODS: Exome sequencing was performed in three probands with RP. The effects of the identified missense variants in AHI1 were predicted by three-dimensional structure homology modelling...
April 25, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28434495/dysfunction-of-the-cerebral-glucose-transporter-slc45a1-in-individuals-with-intellectual-disability-and-epilepsy
#4
Myriam Srour, Noriaki Shimokawa, Fadi F Hamdan, Christina Nassif, Chantal Poulin, Lihadh Al Gazali, Jill A Rosenfeld, Noriyuki Koibuchi, Guy A Rouleau, Aisha Al Shamsi, Jacques L Michaud
Glucose transport across the blood brain barrier and into neural cells is critical for normal cerebral physiologic function. Dysfunction of the cerebral glucose transporter GLUT1 (encoded by SLC2A1) is known to result in epilepsy, intellectual disability (ID), and movement disorder. Using whole-exome sequencing, we identified rare homozygous missense variants (c.526C>T [p.Arg176Trp] and c.629C>T [p.Ala210Val]) in SLC45A1, encoding another cerebral glucose transporter, in two consanguineous multiplex families with moderate to severe ID, epilepsy, and variable neuropsychiatric features...
April 18, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28425625/a-missense-mutation-in-damage-specific-dna-binding-protein-2-is-a-genetic-risk-factor-for-limbal-squamous-cell-carcinoma-in-horses
#5
Rebecca R Bellone, Jiayin Liu, Jessica L Petersen, Maura Mack, Moriel Singer-Berk, Cord Drögemüller, Julia Malvick, Barbara Wallner, Gottfried Brem, M Cecilia Penedo, Mary Lassaline
Squamous cell carcinoma (SCC) is the most common cancer of the equine eye, frequently originating at the limbus, with the potential to invade the cornea, cause visual impairment, and result in loss of the eye. Several breeds of horses have a high occurrence of limbal SCC implicating a genetic basis for limbal SCC predisposition. Pedigree analysis in the Haflinger breed supports a simple recessive mode of inheritance and a genome wide association study (N=23) identified a 1.5 Mb locus on ECA12 significantly associated with limbal SCC (Pcorrected = 0...
April 20, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28423512/kinase-analysis-of-penile-squamous-cell-carcinoma-on-multiple-platforms-to-identify-potential-therapeutic-targets
#6
Eddy S Yang, Christopher D Willey, Amitkumar Mehta, Michael R Crowley, David K Crossman, Dongquan Chen, Joshua C Anderson, Gurudatta Naik, Deborah L Della Manna, Tiffiny S Cooper, Guru Sonpavde
Penile squamous cell carcinoma (PSCC) is an orphan malignancy with poorly understood biology and suboptimal systemic therapy. Given that kinases may be drivers and readily actionable, we performed comprehensive multiplatform analysis of kinases in PSCC tumor and normal tissue. Fresh frozen tumors were collected from 11 patients with PSCC. After macrodissection to demarcate tumor from normal tissue, the samples underwent multiplatform analysis of kinases. Next Generation Sequencing (NGS) of 517 kinase genes was performed using Agilent Kinome capture and run on the Illumina MiSeq at PE150bp...
March 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422960/predicting-the-impact-of-lynch-syndrome-causing-missense-mutations-from-structural-calculations
#7
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/28419241/central-hypothyroidism-due-to-a-trhr-mutation-causing-impaired-ligand-affinity-and-transactivation-of-gq
#8
Marta García, Jesús González de Buitrago, Mireia Jiménez-Rosés, Leonardo Pardo, Patricia M Hinkle, José C Moreno
Context: Central congenital hypothyroidism (CCH) is an underdiagnosed disorder characterized by deficient production and bioactivity of TSH leading to low thyroid hormone synthesis. TRH receptor (TRHR) defects are rare recessive disorders usually associated with incidentally identified CCH and short stature in childhood. Objectives: Clinical and genetic characterization of a consanguineous family of Roma origin with central hypothyroidism and identification of underlying molecular mechanisms...
April 17, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28413019/germline-mutations-in-cdh23-encoding-cadherin-related-23-are-associated-with-both-familial-and-sporadic-pituitary-adenomas
#9
Qilin Zhang, Cheng Peng, Jianping Song, Yichao Zhang, Jianhua Chen, Zhijian Song, Xuefei Shou, Zengyi Ma, Hong Peng, Xuemin Jian, Wenqiang He, Zhao Ye, Zhiqiang Li, Yongfei Wang, Hongying Ye, Zhaoyun Zhang, Ming Shen, Feng Tang, Hong Chen, Zhifeng Shi, Chunjui Chen, Zhengyuan Chen, Yue Shen, Ye Wang, Shaoyong Lu, Jian Zhang, Yiming Li, Shiqi Li, Ying Mao, Liangfu Zhou, Hai Yan, Yongyong Shi, Chuanxin Huang, Yao Zhao
Pituitary adenoma (PA) is one of the most common intracranial neoplasms. Several genetic predisposing factors for PA have been identified, but they account for a small portion of cases. In this study, we sought to identify the PA genetic risk factors by focusing on causative mutations for PAs. Among the 4 affected and 17 asymptomatic members from one family with familial PA, whole-exome sequencing identified cosegregation of the PA phenotype with the heterozygous missense mutation c.4136G>T (p.Arg1379Leu) in cadherin-related 23 (CDH23)...
April 8, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28410400/inherited-variants-in-genes-somatically-mutated-in-thyroid-cancer
#10
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
#11
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/28403827/a-novel-mutation-in-homeobox-dna-binding-domain-of-hoxc13-gene-underlies-pure-hair-and-nail-ectodermal-dysplasia-ectd9-in-a-pakistani-family
#12
Anwar Kamal Khan, Noor Muhammad, Abdul Aziz, Sher Alam Khan, Khadim Shah, Abdul Nasir, Muzammil Ahmad Khan, Saadullah Khan
BACKGROUND: Pure hair and nail ectodermal dysplasia (PHNED) is a congenital disorder of hair abnormalities and nail dysplasia. Both autosomal recessive and dominant inheritance fashion of PHNED occurs. In literature, to date, five different forms of PHNED have been reported at molecular level, having three genes known and two loci with no gene yet. METHODS: In this study, a four generations consanguineous family of Pakistani origin with autosomal recessive PHNED was investigated...
April 12, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28394649/adamtsl4-assessment-in-ectopia-lentis-reveals-a-recurrent-founder-mutation-in-polynesians
#13
Katherine A van Bysterveldt, Rasha Al Taie, Will Ikink, Verity F Oliver, Andrea L Vincent
BACKGROUND: To clinically characterize a cohort of patients with ectopia lentis (EL), or Marfanoid features in whom a definite genetic diagnosis of Marfan syndrome (MFS) had been excluded (atypical MFS), and to evaluate the contribution of mutations in ADAMTSL4 (OMIM * 610113), and P3H2 (LEPREL1; OMIM * 610341) to disease in this population. MATERIALS AND METHODS: Subjects underwent comprehensive ophthalmic examination, including keratometry. Mutational analysis of ADAMTSL4 and P3H2 was undertaken using PCR, high resolution melting analysis, and sequencing...
April 10, 2017: Ophthalmic Genetics
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
#14
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/28390392/emerging-role-of-mutations-in-epigenetic-regulators-including-mll2-derived-from-the-cancer-genome-atlas-for-cervical-cancer
#15
Xia Li
BACKGROUND: Cervical cancer is the second most common cause of cancer deaths in women worldwide. The aim of this study is to exploit novel pathogenic genes in cervical carcinogenesis. METHOD: The somatic mutations from 194 patients with cervical cancer were obtained from the Cancer Genome Atlas (TCGA) publically accessible exome-sequencing database. We investigated mutated gene enrichment in the 12 cancer core pathways and predicted possible post-translational modifications...
April 8, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28389991/genotype-phenotype-correlation-in-18-egyptian-patients-with-glutaric-acidemia-type-i
#16
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/28389643/characterization-of-atp7a-missense-mutants-suggests-a-correlation-between-intracellular-trafficking-and-severity-of-menkes-disease
#17
Tina Skjørringe, Per Amstrup Pedersen, Sidsel Salling Thorborg, Poul Nissen, Pontus Gourdon, Lisbeth Birk Møller
Menkes disease (MD) is caused by mutations in ATP7A, encoding a copper-transporting P-type ATPase which exhibits copper-dependent trafficking. ATP7A is found in the Trans-Golgi Network (TGN) at low copper concentrations, and in the post-Golgi compartments and the plasma membrane at higher concentrations. Here we have analyzed the effect of 36 ATP7A missense mutations identified in phenotypically different MD patients. Nine mutations identified in patients with severe MD, virtually eliminated ATP7A synthesis, in most cases due to aberrant RNA splicing...
April 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28389567/large-scale-analysis-of-variation-in-the-insulin-like-growth-factor-family-in-humans-reveals-rare-disease-links-and-common-polymorphisms
#18
Peter Rotwein
The insulin-like growth factors IGF1 and IGF2 are closely related proteins that are essential for normal growth and development in humans and other species and play critical roles in many physiological and patho-physiological processes. IGF actions are mediated by trans-membrane receptors and modulated by IGF binding proteins. The importance of IGF actions in human physiology is strengthened by the rarity of inactivating mutations in their genes, and by the devastating impact caused by such mutations on normal development and somatic growth...
April 7, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28388287/in-silico-analysis-of-non-synonymous-single-nucleotide-polymorphisms-in-human-dazl-gene-associated-with-male-infertility
#19
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
#20
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
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