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Missense variants & pathogenicity prediction

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https://www.readbyqxmd.com/read/28637664/expanded-repertoire-of-rasgrp2-variants-responsible-for-platelet-dysfunction-and-severe-bleeding
#1
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
#2
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...
June 21, 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
#3
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
#4
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
#5
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
#6
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 2(nd) for SUMO-ligase and 3(rd) for NAGLU, according to the CAGI independent assessors...
May 24, 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
#7
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
#8
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
#9
Laura C Hernández-Ramírez, Ryhem Gam, Nuria Valdés, Maya Lodish, Nathan Pankratz, Aurélio Balsalobre, Yves Gauthier, Fabio R Faucz, Giampaolo Trivellin, Prashant Chittiboina, John Lane, Denise M Kay, Aggeliki Dimopoulou, Stephane Gaillard, Mario Neou, Jerome 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...
May 22, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28525652/determination-of-scn1a-genetic-variants-in-mexican-patients-with-refractory-epilepsy-and-dravet-syndrome
#10
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
#11
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...
May 18, 2017: Movement Disorders: Official Journal of the Movement Disorder Society
https://www.readbyqxmd.com/read/28518218/comparison-and-optimization-of-in-silico-algorithms-for-predicting-the-pathogenicity-of-sodium-channel-variants-in-epilepsy
#12
Katherine D Holland, Thomas M Bouley, Paul S Horn
OBJECTIVE: Variants in neuronal voltage-gated sodium channel α-subunits genes SCN1A, SCN2A, and SCN8A are common in early onset epileptic encephalopathies and other autosomal dominant childhood epilepsy syndromes. However, in clinical practice, missense variants are often classified as variants of uncertain significance when missense variants are identified but heritability cannot be determined. Genetic testing reports often include results of computational tests to estimate pathogenicity and the frequency of that variant in population-based databases...
May 18, 2017: Epilepsia
https://www.readbyqxmd.com/read/28508593/missense-variant-pathogenicity-predictors-generalize-well-across-a-range-of-function-specific-prediction-challenges
#13
Vikas Pejaver, Sean D Mooney, Predrag Radivojac
The steady advances in machine learning and accumulation of biomedical data have contributed to the development of numerous computational models that assess the impact of missense variants. Different methods, however, operationalize impact differently. Two common tasks in this context are the prediction of the pathogenicity of variants and the prediction of their effects on a protein's function. These are related but distinct problems, and it is unclear whether methods developed for one are optimized for the other...
May 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/28494185/functional-analysis-of-rare-variants-in-mismatch-repair-proteins-augments-results-from-computation-based-predictive-methods
#14
Sanjeevani Arora, Peter J Huwe, Rahmat Sikder, Manali Shah, Amanda J Browne, Randy Lesh, Emmanuelle Nicolas, Sanat Deshpande, Michael J Hall, Roland L Dunbrack, Erica A Golemis
The cancer-predisposing Lynch Syndrome (LS) arises from germline mutations in DNA mismatch repair (MMR) genes, predominantly MLH1, MSH2, MSH6,and PMS2. A major challenge for clinical diagnosis of LS is the frequent identification of variants of uncertain significance (VUS) in these genes, as it is often difficult to determine variant pathogenicity, particularly for missense variants. Generic programs such as SIFT and PolyPhen-2, and MMR gene-specific programs such as PON-MMR and MAPP-MMR, are often used to predict deleterious or neutral effects of VUS in MMR genes...
May 11, 2017: Cancer Biology & Therapy
https://www.readbyqxmd.com/read/28487885/novel-de-novo-variant-in-ebf3-is-likely-to-impact-dna-binding-in-a-patient-with-a-neurodevelopmental-disorder-and-expanded-phenotypes-patient-report-in-silico-functional-assessment-and-review-of-published-cases
#15
Patrick R Blackburn, Sarah S Barnett, Michael T Zimmermann, Margot A Cousin, Charu Kaiwar, Filippo Pinto E Vairo, Zhiyv Niu, Matthew J Ferber, Raul A Urrutia, Duygu Selcen, Eric W Klee, Pavel N Pichurin
Pathogenic variants in EBF3 were recently described in three back-to-back publications in association with a novel neurodevelopmental disorder characterized by intellectual disability, speech delay, ataxia, and facial dysmorphisms. In this report, we describe an additional patient carrying a de novo missense variant in EBF3 (c.487C>T, p.(Arg163Trp)) that falls within a conserved residue in the zinc knuckle motif of the DNA binding domain. Without a solved structure of the DNA binding domain, we generated a homology-based atomic model and performed molecular dynamics simulations for EBF3, which predicted decreased DNA affinity for p...
May 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28482824/novel-missense-mutation-in-the-bzip-transcription-factor-maf-associated-with-congenital-cataract-developmental-delay-seizures-and-hearing-loss-aym%C3%A3-gripp-syndrome
#16
Shari Javadiyan, Jamie E Craig, Shiwani Sharma, Karen M Lower, Theresa Casey, Eric Haan, Emmanuelle Souzeau, Kathryn P Burdon
BACKGROUND: Cataract is a major cause of severe visual impairment in childhood. The purpose of this study was to determine the genetic cause of syndromic congenital cataract in an Australian mother and son. METHOD: Fifty-one genes associated with congenital cataract were sequenced in the proband using a custom Ampliseq library on the Ion Torrent Personal Genome Machine (PGM). Reads were aligned against the human genome (hg19) and variants were annotated. Variants were prioritised for validation by Sanger sequencing if they were novel, rare or previously reported to be associated with paediatric cataract and were predicted to be protein changing...
May 8, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28462455/a-novel-mertk-mutation-causing-retinitis-pigmentosa
#17
Hasenin Al-Khersan, Kaanan P Shah, Segun C Jung, Alex Rodriguez, Ravi K Madduri, Michael A Grassi
PURPOSE: Retinitis pigmentosa (RP) is a genetically heterogeneous inherited retinal dystrophy. To date, over 80 genes have been implicated in RP. However, the disease demonstrates significant locus and allelic heterogeneity not entirely captured by current testing platforms. The purpose of the present study was to characterize the underlying mutation in a patient with RP without a molecular diagnosis after initial genetic testing. METHODS: Whole-exome sequencing of the affected proband was performed...
May 1, 2017: Graefe's Archive for Clinical and Experimental Ophthalmology
https://www.readbyqxmd.com/read/28422960/predicting-the-impact-of-lynch-syndrome-causing-missense-mutations-from-structural-calculations
#18
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/28403410/assessing-the-pathogenicity-of-ryr1-variants-in-malignant-hyperthermia
#19
A Merritt, P Booms, M-A Shaw, D M Miller, C Daly, J G Bilmen, K M Stowell, P D Allen, D S Steele, P M Hopkins
Background: . Missense variants in the ryanodine receptor 1 gene ( RYR1 ) are associated with malignant hyperthermia but only a minority of these have met the criteria for use in predictive DNA diagnosis. We examined the utility of a simplified method of segregation analysis and a functional assay for determining the pathogenicity of recurrent RYR1 variants associated with malignant hyperthermia. Methods: . We identified previously uncharacterised RYR1 variants found in four or more malignant hyperthermia families and conducted simplified segregation analyses...
April 1, 2017: British Journal of Anaesthesia
https://www.readbyqxmd.com/read/28394649/adamtsl4-assessment-in-ectopia-lentis-reveals-a-recurrent-founder-mutation-in-polynesians
#20
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
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