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Prediction of missense mutation

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https://www.readbyqxmd.com/read/29764441/case-report-identification-of-an-hnf1b-p-arg527gln-mutation-in-a-maltese-patient-with-atypical-early-onset-diabetes-and-diabetic-nephropathy
#1
Nikolai Paul Pace, Johann Craus, Alex Felice, Josanne Vassallo
BACKGROUND: The diagnosis of atypical non-autoimmune forms of diabetes mellitus, such as maturity onset diabetes of the young (MODY) presents several challenges, in view of the extensive clinical and genetic heterogeneity of the disease. In this report we describe a case of atypical non autoimmune diabetes associated with a damaging HNF1β mutation. This is distinguished by a number of uncharacteristic clinical features, including early-onset obesity, the absence of renal cysts and diabetic nephropathy...
May 15, 2018: BMC Endocrine Disorders
https://www.readbyqxmd.com/read/29760939/novel-tfap2a-mutation-in-a-japanese-family-with-branchio-oculo-facial-syndrome
#2
Taisuke Sato, Osamu Samura, Noriko Kato, Kosuke Taniguchi, Ken Takahashi, Yuki Ito, Hiroaki Aoki, Masahisa Kobayashi, Ohsuke Migita, Aikou Okamoto, Kenichiro Hata
Branchio-oculo-facial syndrome (BOFS) is a rare autosomal dominant disorder characterized by craniofacial, ocular, and ectodermal anomalies. BOFS is caused by mutation of the transcription factor AP2-alpha gene ( TFAP2A ). We performed detailed genetic analysis of a Japanese family with clinically suspected BOFS and identified a novel missense mutation resulting in a predicted amino-acid substitution in the highly conserved basic DNA-binding domain of TFAP2A (NM_003220.2:c.699A>C).
2018: Human Genome Variation
https://www.readbyqxmd.com/read/29757052/multimodal-characterization-of-a-novel-mutation-causing-vitamin-b6-responsive-gyrate-atrophy
#3
Xuan Cui, Ruben Jauregui, Karen Sophia Park, Stephen H Tsang
PURPOSE: Gyrate atrophy (GA) is a rare chorioretinal degeneration that results in the deterioration of night and peripheral vision, eventually leading to blindness. The disorder is caused by mutations in the gene encoding ornithine aminotransferase (OAT), causing increased levels of plasma ornithine. Treatment revolves around lowering plasma ornithine levels, with vitamin B6 supplementation being the preferred treatment. Nevertheless, most patients do not respond to this therapy. Here, we report a rare case of vitamin B6-responsive GA caused by a novel mutation in OAT and characterize the presentation with multimodal imaging...
May 14, 2018: Ophthalmic Genetics
https://www.readbyqxmd.com/read/29755658/combined-linkage-and-association-analysis-of-classical-hodgkin-lymphoma
#4
Alastair Lawrie, Shuo Han, Amit Sud, Fay Hosking, Timothee Cezard, David Turner, Caroline Clark, Graeme I Murray, Dominic J Culligan, Richard S Houlston, Mark A Vickers
The heritability of classical Hodgkin lymphoma (cHL) has yet to be fully deciphered. We report a family with five members diagnosed with nodular sclerosis cHL. Genetic analysis of the family provided evidence of linkage at chromosomes 2q35-37, 3p14-22 and 21q22, with logarithm of odds score >2. We excluded the possibility of common genetic variation influencing cHL risk at regions of linkage, by analysing GWAS data from 2,201 cHL cases and 12,460 controls. Whole exome sequencing of affected family members identified the shared missense mutations p...
April 17, 2018: Oncotarget
https://www.readbyqxmd.com/read/29755507/computational-protein-phenotype-characterization-of-il10ra-mutations-causative-to-early-onset-inflammatory-bowel-disease-ibd
#5
Fahad A Al-Abbasi, Kaleemuddin Mohammed, Saida Sadath, Babajan Banaganapalli, Khalidah Nasser, Noor A Shaik
The deleterious amino acid substitution mutations in IL-10 receptor alpha gene are most frequently reported in several autoimmune diseases including early onset-inflammatory bowel disease (IBD). Despite the important role of IL-10 RA in maintaining immune homeostasis, the specific structural and functional implications of these mutations on protein phenotype, stability, ligand binding and post translational characteristics is not well explored. Therefore, this study performed the multidimensional computational analysis of IL10RA missense variations causative to pediatric or early onset inflammatory bowel disease (<5 years of age)...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29742735/a-case-report-of-heterozygous-tinf2-gene-mutation-associated-with-pulmonary-fibrosis-in-a-patient-with-dyskeratosis-congenita
#6
Hongchun Du, Yubiao Guo, Di Ma, Kejing Tang, Decheng Cai, Yifeng Luo, Canmao Xie
RATIONALE: Dyskeratosis congenita (DC) is a rare inherited disease characterized by the classical mucocutaneous triad. Pulmonary fibrosis, bone marrow failure, and solid tumors are the main causes of mortality in DC. Pathogenic variants in TERT, TERC, and DKC1 have been identified in individuals with familial pulmonary fibrosis. Mutations in TINF2 gene have been reported to be associated with bone marrow failure in most cases. However, the relationship between TINF2 mutation and pulmonary fibrosis is not yet clear...
May 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29740699/de-novo-mutations-in-med13-a-component-of-the-mediator-complex-are-associated-with-a-novel-neurodevelopmental-disorder
#7
Lot Snijders Blok, Susan M Hiatt, Kevin M Bowling, Jeremy W Prokop, Krysta L Engel, J Nicholas Cochran, E Martina Bebin, Emilia K Bijlsma, Claudia A L Ruivenkamp, Paulien Terhal, Marleen E H Simon, Rosemarie Smith, Jane A Hurst, Heather McLaughlin, Richard Person, Amy Crunk, Michael F Wangler, Haley Streff, Joseph D Symonds, Sameer M Zuberi, Katherine S Elliott, Victoria R Sanders, Abigail Masunga, Robert J Hopkin, Holly A Dubbs, Xilma R Ortiz-Gonzalez, Rolph Pfundt, Han G Brunner, Simon E Fisher, Tjitske Kleefstra, Gregory M Cooper
Many genetic causes of developmental delay and/or intellectual disability (DD/ID) are extremely rare, and robust discovery of these requires both large-scale DNA sequencing and data sharing. Here we describe a GeneMatcher collaboration which led to a cohort of 13 affected individuals harboring protein-altering variants, 11 of which are de novo, in MED13; the only inherited variant was transmitted to an affected child from an affected mother. All patients had intellectual disability and/or developmental delays, including speech delays or disorders...
May 8, 2018: Human Genetics
https://www.readbyqxmd.com/read/29735971/functional-and-in-silico-assessment-of-gdf3-gene-variants-in-a-chinese-congenital-scoliosis-population
#8
Jia Chen, Xiaoxin Li, Yuchen Niu, Zhihong Wu, Guixing Qiu
BACKGROUND The present study aimed to evaluate the pathogenicity of 5 [i]GDF3[/i] gene variations using functional and [i]in silico[/i] assessment approaches in a Chinese congenital scoliosis population. MATERIAL AND METHODS We selected 13 patients carrying 5 variants from a congenital scoliosis cohort. The PCR products of samples were verified by Sanger sequencing. The data and sequence alignment were analyzed using Chromas and ClustalW. SIFT and PolyPhen-2 were used to predict the functional effects of each missense and amino acid substitutions...
May 8, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29733970/thyroxine-binding-globulin-deficiency-due-to-a-novel-serpina7-mutation-clinical-characterization-analysis-of-x-chromosome-inactivation-pattern-and-protein-structural-modeling
#9
Cristiane Jeyce Gomes Lima, Andressa Aby Faraj Linhares Maciel, Matheus de Oliveira Andrade, Vinicius Santos da Cunha, Juliana Forte Mazzeu, Lucas Bleicher, Francisco de Assis Rocha Neves, Adriana Lofrano-Porto
OBJECTIVE: Thyroxine-binding globulin (TBG) is the major human thyroid hormone transport protein, encoded by the SERPINA7 gene (Xq22.2). We aim to investigate the molecular basis of partial TBG deficiency (TBG-PD) in a female, by evaluating the X-chromosome inactivation pattern as well as the mutant protein structural modeling. DESIGN AND METHODS: Sequencing of the coding region of the SERPINA7 gene was performed in a female with a TBG-PD phenotype and her first-degree relatives...
May 4, 2018: Gene
https://www.readbyqxmd.com/read/29731845/analysis-of-human-muts-homolog-2-missense-mutations-in-patients-with-colorectal-cancer
#10
Xiaomei Zhang, Senqing Chen, Jun Yu, Yuanying Zhang, Min Lv, Ming Zhu
Germline mutations of DNA mismatch repair gene human MutS homolog 2 ( hMSH2 ) are associated with hereditary nonpolyposis colorectal cancer (HNPCC). A total of one-third of these mutations are missense mutations. Several hMSH2 missense mutations have been identified in patients in East Asia, although their function has not been evaluated. In the present study, the role of ten hMSH2 missense mutations in the pathogenesis of colorectal cancer was examined. The hMSH2/hMSH6 protein interaction system was established using yeast two-hybrid screening...
May 2018: Oncology Letters
https://www.readbyqxmd.com/read/29728705/pathogenic-variants-in-e3-ubiquitin-ligase-rlim-rnf12-lead-to-a-syndromic-x-linked-intellectual-disability-and-behavior-disorder
#11
Suzanna G M Frints, Aysegul Ozanturk, Germán Rodríguez Criado, Ute Grasshoff, Bas de Hoon, Michael Field, Sylvie Manouvrier-Hanu, Scott E Hickey, Molka Kammoun, Karen W Gripp, Claudia Bauer, Christopher Schroeder, Annick Toutain, Theresa Mihalic Mosher, Benjamin J Kelly, Peter White, Andreas Dufke, Eveline Rentmeester, Sungjin Moon, Daniel C Koboldt, Kees E P van Roozendaal, Hao Hu, Stefan A Haas, Hans-Hilger Ropers, Lucinda Murray, Eric Haan, Marie Shaw, Renee Carroll, Kathryn Friend, Jan Liebelt, Lynne Hobson, Marjan De Rademaeker, Joep Geraedts, Jean-Pierre Fryns, Joris Vermeesch, Martine Raynaud, Olaf Riess, Joost Gribnau, Nicholas Katsanis, Koen Devriendt, Peter Bauer, Jozef Gecz, Christelle Golzio, Cristina Gontan, Vera M Kalscheuer
RLIM, also known as RNF12, is an X-linked E3 ubiquitin ligase acting as a negative regulator of LIM-domain containing transcription factors and participates in X-chromosome inactivation (XCI) in mice. We report the genetic and clinical findings of 84 individuals from nine unrelated families, eight of whom who have pathogenic variants in RLIM (RING finger LIM domain-interacting protein). A total of 40 affected males have X-linked intellectual disability (XLID) and variable behavioral anomalies with or without congenital malformations...
May 4, 2018: Molecular Psychiatry
https://www.readbyqxmd.com/read/29726057/mutations-and-common-variants-in-the-human-arginase-1-arg1-gene-impact-on-patients-diagnostic-and-protein-structure-considerations
#12
Carmen Diez-Fernandez, Véronique Rüfenacht, Corinne Gemperle, Ralph Fingerhut, Johannes Häberle
The urea cycle disorder argininemia is caused by a defective arginase 1 (ARG1) enzyme resulting from mutations in the ARG1 gene. Patients generally develop hyperargininemia, spastic paraparesis, progressive neurological and intellectual impairment and persistent growth retardation. Interestingly, in contrast to other urea cycle disorders, hyperammonemia is rare. We report here 66 mutations (12 of which are novel), including 30 missense mutations, 7 nonsense, 10 splicing, 15 deletions, two duplications, one small insertion and one translation initiation codon mutation...
May 3, 2018: Human Mutation
https://www.readbyqxmd.com/read/29724887/four-novel-mutations-in-the-alpl-gene-in-chinese-patients-with-odonto-childhood-and-adult-hypophosphatasia
#13
Lijun Xu, Qianqian Pang, Yan Jiang, Ou Wang, Mei Li, Xiaoping Xing, Weibo Xia
Background and purpose: Hypophosphatasiais (HPP) is a rare inherited disorder characterized by defective bone and/or dental mineralization, and decreased serum alkaline phosphatase activity. ALPL , the only gene related with HPP, encodes tissue non-specific alkaline phosphatase (TNSALP). Few studies were carried out in ALPL gene mutations in the Chinese population with HPP. The purpose of this study is to elucidate the clinical and genetic characteristics of HPP in 5 unrelated Chinese families and 2 sporadic patients...
May 3, 2018: Bioscience Reports
https://www.readbyqxmd.com/read/29723276/entprise-x-predicting-disease-associated-frameshift-and-nonsense-mutations
#14
Hongyi Zhou, Mu Gao, Jeffrey Skolnick
To exploit the plethora of information provided by Next Generation Sequencing, the identification of the genetic mutations responsible for disease in general or cancer in particular, among the thousands of neutral germline or somatic variations is a crucial task. Genome-wide association studies for the detection of disease-associated genes or cancer drivers can only identify common variations or driver genes in a cohort of patients. Thus, they cannot discover unique disease-associated mutations or cancer driver genes on a personal basis...
2018: PloS One
https://www.readbyqxmd.com/read/29704291/a-missense-mutation-in-ebf2-was-segregated-with-imperforate-anus-in-a-family-across-three-generations
#15
Shinn Young Kim, Hyun-Sun Ko, Namshin Kim, Seon-Hee Yim, Seung-Hyun Jung, Jiwoong Kim, Myung-Duk Lee, Yeun-Jun Chung
The etiology of imperforate anus, a major phenotype of anorectal malformation (ARM), is still unknown and not a single gene has been reported to be associated with it. We studied a Korean family with six affected members with imperforate anus across three generations by whole exome sequencing and identified a missense mutation in the EBF2 gene (c.215C > T; p.Ala72Val). This mutation is completely segregated with the disease phenotype in the family and is evolutionarily highly conserved among diverse vertebrates...
April 28, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29703613/noonan-syndrome-severe-phenotype-and-ptpn11-mutations
#16
Pilar Carrasco Salas, Gertrudis Gómez-Molina, Páxedes Carreto-Alba, Reyes Granell-Escobar, Ignacio Vázquez-Rico, Antonio León-Justel
INTRODUCTION AND OBJECTIVE: Noonan syndrome (NS) is a genetic disorder characterized by a wide range of distinctive features and health problems. It caused in 50% of cases by missense mutations in PTPN11 gene. It has been postulated that it is possible to predict the disease course based into the impact of mutations on the protein. PATIENTS AND METHODS: We report two cases of severe NS phenotype including hydrops fetalis. PTPN11 gene was studied in germinal cells of both patients by sequencing...
April 24, 2018: Medicina Clínica
https://www.readbyqxmd.com/read/29702980/chrne-compound-heterozygous-mutations-in-congenital-myasthenic-syndrome-a-case-report
#17
Kunfang Yang, Hongyi Cheng, Fang Yuan, Linyi Meng, Rongrong Yin, Yuanfeng Zhang, Simei Wang, Chunmei Wang, Yanfen Lu, Jiaming Xi, Qin Lu, Yucai Chen
RATIONALE: Congenital myasthenic syndrome (CMSs) are a group of rare genetic disorders of the neurological junction, which can result in structural or functional weakness. Here, we characterized a case of CMS in order to clarify the diagnosis and expand the understanding of it. The molecular diagnosis had implications for choice of treatment and genetic counseling. PATIENT CONCERNS: A 3-year-old male patient with CMS had ptosis and limb weakness for 2 months after birth...
April 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29701718/structure-function-mutational-analysis-and-prediction-of-the-potential-impact-of-high-risk-non-synonymous-single-nucleotide-polymorphism-on-poliovirus-2a-protease-stability-using-comprehensive-informatics-approaches
#18
Amna Younus, Saba Munawar, Muhammad Faraz Bhatti, Aqsa Ikram, Faryal Mehwish Awan, Ishrat Jabeen, Nasar Virk, Hussnain Ahmed Janjua, Muhammad Arshad
Polio viral proteinase 2A performs several essential functions in genome replication. Its inhibition prevents viral replication, thus making it an excellent substrate for drug development. In this study, the three-dimensional structure of 2A protease was determined and optimized by homology modelling. To predict the molecular basis of the interaction of small molecular agonists, docking simulations were performed on a structurally diverse dataset of poliovirus 2A protease (PV2Apr &deg;) inhibitors. Docking results were employed to identify high risk missense mutations that are highly damaging to the structure, as well as the function, of the protease...
April 26, 2018: Genes
https://www.readbyqxmd.com/read/29696773/complex-phenotype-of-dyskeratosis-congenita-and-mood-dysregulation-with-novel-homozygous-rtel1-and-tph1-variants
#19
Rachel A Ungar, Neelam Giri, Maryland Pao, Payal P Khincha, Weiyin Zhou, Blanche P Alter, Sharon A Savage
Dyskeratosis congenita (DC) is an inherited bone marrow failure syndrome caused by germline mutations in telomere biology genes. Patients have extremely short telomeres for their age and a complex phenotype including oral leukoplakia, abnormal skin pigmentation, and dysplastic nails in addition to bone marrow failure, pulmonary fibrosis, stenosis of the esophagus, lacrimal ducts and urethra, developmental anomalies, and high risk of cancer. We evaluated a patient with features of DC, mood dysregulation, diabetes, and lack of pubertal development...
April 25, 2018: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29692759/report-of-a-novel-shox-missense-variant-in-a-boy-with-short-stature-and-his-mother-with-leri-weill-dyschondrosteosis
#20
Laura Lucchetti, Paolo Prontera, Amedea Mencarelli, Ester Sallicandro, Annalisa Mencarelli, Marta Cofini, Alberto Leonardi, Gabriela Stangoni, Laura Penta, Susanna Esposito
Heterozygous mutations in the SHOX gene or in the upstream and downstream enhancer elements are associated with 2-22% of cases of idiopathic short stature (OMIM #300582) and with 60% of cases of Leri-Weill dyschondrosteosis (OMIM #127300) with which female subjects are generally more severely affected. Approximately 80-90% of SHOX pathogenic variants are deletions or duplications, and the remaining 10-20% are point mutations that primarily give rise to missense variants. The clinical interpretation of novel variants, particularly missense variants, can be challenging and can remain of uncertain significance...
2018: Frontiers in Endocrinology
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