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Missense variants & pathogenicity prediction

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https://www.readbyqxmd.com/read/28815929/aggregation-of-population-based-genetic-variation-over-protein-domain-homologues-and-its-potential-use-in-genetic-diagnostics
#1
Laurens Wiel, Hanka Venselaar, Joris A Veltman, Gerrit Vriend, Christian Gilissen
Whole exomes of patients with a genetic disorder are nowadays routinely sequenced but interpretation of the identified genetic variants remains a major challenge. The increased availability of population-based human genetic variation has given rise to measures of genetic tolerance that have been used, for example, to predict disease-causing genes in neurodevelopmental disorders. Here, we investigated whether combining variant information from homologous protein domains can improve variant interpretation. For this purpose, we developed a framework that maps population variation and known pathogenic mutations onto 2,750 "meta-domains"...
August 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/28813618/whole-exome-sequencing-identifies-novel-variants-for-tooth-agenesis
#2
N Dinckan, R Du, L E Petty, Z Coban-Akdemir, S N Jhangiani, I Paine, E H Baugh, A P Erdem, H Kayserili, H Doddapaneni, J Hu, D M Muzny, E Boerwinkle, R A Gibbs, J R Lupski, Z O Uyguner, J E Below, A Letra
Tooth agenesis is a common craniofacial abnormality in humans and represents failure to develop 1 or more permanent teeth. Tooth agenesis is complex, and variations in about a dozen genes have been reported as contributing to the etiology. Here, we combined whole-exome sequencing, array-based genotyping, and linkage analysis to identify putative pathogenic variants in candidate disease genes for tooth agenesis in 10 multiplex Turkish families. Novel homozygous and heterozygous variants in LRP6, DKK1, LAMA3, and COL17A1 genes, as well as known variants in WNT10A, were identified as likely pathogenic in isolated tooth agenesis...
August 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28807866/brca1-2-missense-mutations-and-the-value-of-in-silico-analyses
#3
Carolin E Sadowski, Daniela Kohlstedt, Cornelia Meisel, Katja Keller, Kerstin Becker, Luisa Mackenroth, Andreas Rump, Evelin Schröck, Pauline Wimberger, Karin Kast
INTRODUCTION: The clinical implications of genetic variants in BRCA1/2 in healthy and affected individuals are considerable. Variant interpretation, however, is especially challenging for missense variants. The majority of them are classified as variants of unknown clinical significance (VUS). Computational (in-silico) predictive programs are easy to access, but represent only one tool out of a wide range of complemental approaches to classify VUS. With this single-center study, we aimed to evaluate the impact of in-silico analyses in a spectrum of different BRCA1/2 missense variants...
August 11, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28805948/pathogenic-role-of-adgrg2-in-cbavd-patients-replicated-in-chinese-population
#4
B Yang, J Wang, W Zhang, H Pan, T Li, B Liu, H Li, B Wang
Congenital bilateral absence of the vas deferens (CBAVD) is an important cause of obstructive azoospermia and male infertility worldwide. Cystic fibrosis transmembrane conductance regulator (CFTR) mutations are the main pathogenic cause, although a proportion of cases are still unexplained. Recently, adhesion G protein-coupled receptor G2 (ADGRG2) gene, a novel pathogenic gene for CBAVD was identified. We did a single population replication study in Chinese CBAVD patients to replicate its role in CBAVD developing...
August 14, 2017: Andrology
https://www.readbyqxmd.com/read/28794409/annotating-pathogenic-non-coding-variants-in-genic-regions
#5
Sahar Gelfman, Quanli Wang, K Melodi McSweeney, Zhong Ren, Francesca La Carpia, Matt Halvorsen, Kelly Schoch, Fanni Ratzon, Erin L Heinzen, Michael J Boland, Slavé Petrovski, David B Goldstein
Identifying the underlying causes of disease requires accurate interpretation of genetic variants. Current methods ineffectively capture pathogenic non-coding variants in genic regions, resulting in overlooking synonymous and intronic variants when searching for disease risk. Here we present the Transcript-inferred Pathogenicity (TraP) score, which uses sequence context alterations to reliably identify non-coding variation that causes disease. High TraP scores single out extremely rare variants with lower minor allele frequencies than missense variants...
August 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28780519/analysis-of-genetic-and-clinical-characteristics-of-a-chinese-kallmann-syndrome-cohort-with-anos1-mutations
#6
Min Nie, Hongli Xu, Rongrong Chen, Jiangfeng Mao, Xi Wang, Shuyu Xiong, Junjie Zheng, Bingqing Yu, Mingxuan Cui, Wanlu Ma, Qibing Huang, Hongbing Zhang, Xueyan Wu
OBJECTIVE: To analyze ANOS1 gene mutations in a large Chinese Kallmann syndrome (KS) cohort and to characterize the clinical presentation of the disease in patients with ANOS1 mutations. PATIENTS AND METHODS: Chinese patients with KS, including 187 sporadic and 23 pedigree cases were recruited. Patients' ANOS1 gene sequences were analyzed by direct sequencing of PCR-amplified products. In silico analysis was used to assess functional relevance of newly identified missense mutations...
August 5, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28758091/identifying-the-kat6b-mutation-via-diagnostic-exome-sequencing-to-diagnose-say-barber-biesecker-young-simpson-syndrome-in-three-generations-of-a-family
#7
Yong Rok Kim, Jong Bum Park, Yung Jin Lee, Mi Jin Hong, Hyeong Tae Kim, Hyon J Kim
Diagnostic exome sequencing (DES) is a powerful tool to analyze the pathogenic variants leading to development delay (DD) and intellectual disability (ID). Recently, heterozygous de novo mutation of the histone acetyltransferase encoding gene KAT6B has been recognized as causing a syndrome with congenital anomalies and intellectual disability, namely Say-Barber-Biesecker-Young-Simpson (SBBYS) syndrome. Here we report a case of SBBYS syndrome in a third generation Korean family affected with a missense mutation in KAT6B, c...
June 2017: Annals of Rehabilitation Medicine
https://www.readbyqxmd.com/read/28678087/a-severe-case-of-congenital-thrombotic-thrombocytopenia-purpura-resulting-from-compound-heterozygosity-involving-a-novel-adamts13-pathogenic-variant
#8
Erin Conboy, Paige I Partain, Deepti Warad, Michelle L Kluge, Carola Arndt, Dong Chen, Vilmarie Rodriguez
We report a 9-year-old Chinese girl with congenital thrombotic thrombocytopenic purpura found to be a compound heterozygote for 2 pathogenic variants in the ADAMTS13 gene, including a novel variation. The girl suffered from recurrent, life-threatening episodes of thrombocytopenia and hemolysis, and laboratory testing showed ADAMST13 enzyme activity of <5%. Sequencing of the ADAMTS13 gene revealed a previously reported missense variant, c.1787C>T (p.Ala596Val), and a novel duplication defined as c.1007_1025dup19 (p...
July 3, 2017: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/28653649/functional-and-structural-characterisation-of-5-missense-mutations-of-the-phenylalanine-hydroxylase
#9
Martina Pecimonova, Emil Polak, Frantisek Csicsay, Kamila Reblova, Maja Stojiljkovic, Zdenko Levarski, Ludovit Skultety, Ludevit Kadasi, Andrea Soltysova
Phenylketonuria (PKU) and hyperphenylalaninemia (HPA) are a group of genetic disorders predominantly caused by mutations in the phenylalanine hydroxylase (PAH) gene. To date, more than 950 variants have been identified, however the pathogenic mechanism of many variants remains unknown. In this study, in silico prediction and in vitro prokaryotic and eukaryotic expression systems were used to functionally characterize five PAH missense variants (p.F233I, p.R270I, p.F331S, p.S350Y, and p.L358F) previously identified in Slovak and Czech patients...
June 27, 2017: General Physiology and Biophysics
https://www.readbyqxmd.com/read/28637664/expanded-repertoire-of-rasgrp2-variants-responsible-for-platelet-dysfunction-and-severe-bleeding
#10
Sarah K Westbury, Matthias Canault, Daniel Greene, Emilse Bermejo, Katharine Hanlon, Michele P Lambert, Carolyn M Millar, Paquita Nurden, Samya G Obaji, Shoshana Revel-Vilk, Chris Van Geet, Kate Downes, Sofia Papadia, Salih Tuna, Christopher Watt, Nihr BioResource-Rare Diseases Consortium, Kathleen Freson, Michael A Laffan, Willem H Ouwehand, Marie-Christine Alessi, Ernest Turro, Andrew D Mumford
Heritable platelet function disorders (PFDs) are genetically heterogeneous and poorly characterised. Pathogenic variants in RASGRP2, which encodes calcium and diacylglycerol-regulated guanine exchange factor I (CalDAG-GEFI), have been reported previously in three pedigrees with bleeding and reduced platelet aggregation responses. To better define the phenotype associated with pathogenic RASGRP2 variants, we compared high-throughput sequencing and phenotype data from 2,042 cases in pedigrees with unexplained bleeding or platelet disorders to data from 5,422 controls...
June 21, 2017: Blood
https://www.readbyqxmd.com/read/28635953/rare-rnf213-variants-in-the-c-terminal-region-encompassing-the-ring-finger-domain-are-associated-with-moyamoya-angiopathy-in-caucasians
#11
Stéphanie Guey, Markus Kraemer, Dominique Hervé, Thomas Ludwig, Manoëlle Kossorotoff, Françoise Bergametti, Jan Claudius Schwitalla, Simone Choi, Lucile Broseus, Isabelle Callebaut, Emmanuelle Genin, Elisabeth Tournier-Lasserve
Moyamoya angiopathy (MMA) is a cerebral angiopathy affecting the terminal part of internal carotid arteries. Its prevalence is 10 times higher in Japan and Korea than in Europe. In East Asian countries, moyamoya is strongly associated to the R4810K variant in the RNF213 gene that encodes for a protein containing a RING-finger and two AAA+ domains. This variant has never been detected in Caucasian MMA patients, but several rare RNF213 variants have been reported in Caucasian cases. Using a collapsing test based on exome data from 68 European MMA probands and 573 ethnically matched controls, we showed a significant association between rare missense RNF213 variants and MMA in European patients (odds ratio (OR)=2...
August 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28611552/a-novel-mutation-in-pitx2-in-a-patient-with-axenfeld-rieger-syndrome
#12
Susan J Hassed, Shibo Li, Weihong Xu, Ashley C Taylor
Axenfeld-Rieger syndrome is a rare autosomal dominant condition. Anomalies include anterior segment dysgenesis of the eye, dental anomalies, maxillary hypoplasia, periumbilical anomalies, and congenital heart defects. We report a patient with Peters anomaly, dysmorphic features, congenital heart defect, umbilical hernia, short stature, and developmental delay. Diagnostic sequencing of 23 genes known to be causally related to the condition was performed on the patient, parents, and maternal grandparents. A variant of uncertain significance in PITX2 was identified...
March 2017: Molecular Syndromology
https://www.readbyqxmd.com/read/28576516/a-novel-missense-mutation-in-the-slc26a4-gene-causes-nonsyndromic-hearing-loss-and-enlarged-vestibular-aqueduct
#13
Xiaoguang He, Qi Peng, Siping Li, Pengyuan Zhu, Chunqiu Wu, Chunbao Rao, Jiang Chang, Mingyu Xie, Baimao Zhong, Xiaomei Lu
OBJECTIVES: We aimed to investigate the genetic causes of hearing loss in a Chinese proband with nonsyndromic hearing loss and enlarged vestibular aqueduct syndrome. METHODS: We conducted clinical and genetic evaluations in a deaf proband and his normal-hearing parents. Multiplex PCR technology combined with Ion Torrent™ next-generation sequencing technology was used to detect the pathogenic mutations. As a control, a group of 1500 previously studied healthy newborns from the same ethnic background were subjected to deafness gene screening using the same method as in our previous study...
April 2017: International Journal of Pediatric Otorhinolaryngology
https://www.readbyqxmd.com/read/28546994/sdha-related-tumorigenesis-a-new-case-series-and-literature-review-for-variant-interpretation-and-pathogenicity
#14
Ruth T Casey, David B Ascher, Eleanor Rattenberry, Louise Izatt, Katrina A Andrews, Helen L Simpson, Benjamen Challis, Soo-Mi Park, Venkata R Bulusu, Fiona Lalloo, Douglas E V Pires, Hannah West, Graeme R Clark, Philip S Smith, James Whitworth, Thomas G Papathomas, Phillipe Taniere, Rosina Savisaar, Laurence D Hurst, Emma R Woodward, Eamonn R Maher
PURPOSE: To evaluate the role of germline SDHA mutation analysis by (1) comprehensive literature review, (2) description of novel germline SDHA mutations and (3) in silico structural prediction analysis of missense substitutions in SDHA. PATIENTS AND METHODS: A systematic literature review and a retrospective review of the molecular and clinical features of patients identified with putative germline variants in UK molecular genetic laboratories was performed. To evaluate the molecular consequences of SDHA missense variants, a novel model of the SDHA/B/C/D complex was generated and the structural effects of missense substitutions identified in the literature, our UK novel cohort and a further 32 "control missense variants" were predicted by the mCSM computational platform...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28544272/ensemble-variant-interpretation-methods-to-predict-enzyme-activity-and-assign-pathogenicity-in-the-cagi4-naglu-human-n-acetyl-glucosaminidase-and-ube2i-human-sumo-ligase-challenges
#15
Yizhou Yin, Kunal Kundu, Lipika R Pal, John Moult
CAGI (Critical Assessment of Genome Interpretation) conducts community experiments to determine the state of the art in relating genotype to phenotype. Here, we report results obtained using newly developed ensemble methods to address two CAGI4 challenges: enzyme activity for population missense variants found in NAGLU (Human N-acetyl-glucosaminidase) and random missense mutations in Human UBE2I (Human SUMO E2 ligase), assayed in a high-throughput competitive yeast complementation procedure. The ensemble methods are effective, ranked second for SUMO-ligase and third for NAGLU, according to the CAGI independent assessors...
September 2017: Human Mutation
https://www.readbyqxmd.com/read/28542722/a-homozygous-potentially-pathogenic-variant-in-the-paxbp1-gene-in-a-large-family-with-global-developmental-delay-and-myopathic-hypotonia
#16
Essa Alharby, Alia M Albalawi, Abdul Nasir, Sabri A Alhijji, Amer Mahmood, Khushnooda Ramzan, Firoz Abdusamad, Abdulkarim Aljohani, Osama Abdelsalam, Amr Eldardear, Sulman Basit
PAX binding protein 1 (PAXBP1) is an adaptor protein linking the transcription factor PAX3 and PAX7 to the histone methylation machinery. PAXBP1 is a nuclear protein and its high expression is known in brain cerebellar hemisphere and cerebellum. Moreover, it is also found in abundance in muscle precursor cells that are involved in myogenesis and skeletal muscles formation. Whole genome SNP genotyping and exome sequencing in a family with distinct syndrome of global developmental delay and hypotonia mapped the disease locus to the chromosome 21q22...
May 19, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28535199/genotype-phenotype-correlation-in-patients-with-isovaleric-acidemia-comparative-structural-modelling-and-computational-analysis-of-novel-variants
#17
Osama K Zaki, George Priya Doss C, Salsabil A Ali, Ghadeer G Murad, Shaima A Elashi, Maryam Sa Ebnou, D Thirumal Kumar, Ola Khalifa, Radwa Gamal, Heba S A El Abd, Bilal N Nasr, Hatem Zayed
Isovaleric acidemia (IVA) is an autosomal recessive inborn error of leucine metabolism. It is caused by a deficiency in the mitochondrial isovaleryl-CoA dehydrogenase (IVD) enzyme. In this study, we investigated eight patients with IVA. The patients diagnoses were confirmed by urinary organic acid analysis and the blood C5-Carnitine value. A molecular genetic analysis of the IVD gene revealed nine different variants: five were missense variants (c.1193G>A; p. R398Q, c.1207T>A; p. Y403N, c.872C>T; p...
May 23, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28533356/loss-of-function-mutations-in-the-cables1-gene-are-a-novel-cause-of-cushing-s-disease
#18
Laura C Hernández-Ramírez, Ryhem Gam, Nuria Valdés, Maya B Lodish, Nathan Pankratz, Aurelio Balsalobre, Yves Gauthier, Fabio R Faucz, Giampaolo Trivellin, Prashant Chittiboina, John Lane, Denise M Kay, Aggeliki Dimopoulos, Stephan Gaillard, Mario Neou, Jérôme Bertherat, Guillaume Assié, Chiara Villa, James L Mills, Jacques Drouin, Constantine A Stratakis
The CABLES1 cell cycle regulator participates in the adrenal-pituitary negative feedback, and its expression is reduced in corticotropinomas, pituitary tumors with a largely unexplained genetic basis. We investigated the presence of CABLES1 mutations/copy number variations (CNVs) and their associated clinical, histopathological and molecular features in patients with Cushing's disease (CD). Samples from 146 pediatric (118 germline DNA only/28 germline and tumor DNA) and 35 adult (tumor DNA) CD patients were screened for CABLES1 mutations...
August 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28525652/determination-of-scn1a-genetic-variants-in-mexican-patients-with-refractory-epilepsy-and-dravet-syndrome
#19
R E Jiménez-Arredondo, A J L Brambila-Tapia, F M Mercado-Silva, M T Magaña-Torres, L E Figuera
Mutations in the SCN1A gene can result in syndromes associated with epilepsy, including the Dravet syndrome (DS). However, the prevalence of such mutations in these diseases varies widely between different studies, and has not been examined in Mexican patients with epilepsy. Therefore, the objective of this study was to determine the frequency of SCN1A mutations (in the exon 26) in a cohort of Mexican patients with DS and refractory epilepsy (RE). We recruited 24 Mexican patients (14 males and 10 females), of which 15 were diagnosed with RE and 9 were diagnosed with DS...
May 18, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28520167/kmt2b-rare-missense-variants-in-generalized-dystonia
#20
Michael Zech, Robert Jech, Petra Havránková, Anna Fečíková, Riccardo Berutti, Dušan Urgošík, David Kemlink, Tim M Strom, Jan Roth, Evžen Růžička, Juliane Winkelmann
BACKGROUND: Recently a novel syndrome of childhood-onset generalized dystonia originating from mutations in lysine-specific methyltransferase 2B (KMT2B) has been reported. METHODS: We sequenced the exomes of 4 generalized dystonia-affected probands recruited from a Prague movement disorders center (Czech Republic). Bioinformatics analyses were conducted to select candidate causal variants in described dystonia-mutated genes. After cosegregation testing, checklists from the American College of Medical Genetics and Genomics were adopted to judge variant pathogenicity...
July 2017: Movement Disorders: Official Journal of the Movement Disorder Society
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