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Missense variants & pathogenicity prediction

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https://www.readbyqxmd.com/read/27903293/personalized-medicine-approach-confirms-a-milder-case-of-abat-deficiency
#1
A Besse, A K Petersen, J V Hunter, V Appadurai, S R Lalani, P E Bonnen
ABAT deficiency (OMIM 613163) is a rare inborn error of metabolism caused by recessive variants in the gene 4-aminobutyric acid transaminase (ABAT), which is responsible for both the catalysis of GABA and maintenance of nucleoside pools in the mitochondria. To date, only a few patients have been reported worldwide. Their clinical presentation has been remarkably consistent with primary features of severe psychomotor retardation, encephalopathy, hypotonia, and infantile-onset refractory epilepsy. We report a new case of ABAT deficiency that marks an important departure from previous clinical findings...
December 1, 2016: Molecular Brain
https://www.readbyqxmd.com/read/27878139/compound-heterozygous-ldlr-variant-in-severely-affected-familial-hypercholesterolemia-patient
#2
Faisal A Al-Allaf, Abdullah Alashwal, Zainularifeen Abduljaleel, Mohiuddin M Taher, Abdellatif Bouazzaoui, Hala Abalkhail, Ahmad F Al-Allaf, Mohammad Athar
Familial hypercholesterolemia (FH) is most commonly caused by mutations in the LDL receptor (LDLR), which is responsible for hepatic clearance of LDL from the blood circulation. We described a severely affected FH proband and their first-degree blood relatives; the proband was resistant to statin therapy and was managed on an LDL apheresis program. In order to find the causative genetic variant in this family, direct exon sequencing of the LDLR, APOB and PCSK9 genes was performed. We identified a compound heterozygous mutation in the proband with missense p...
November 23, 2016: Acta Biochimica Polonica
https://www.readbyqxmd.com/read/27821657/the-ucl-low-density-lipoprotein-receptor-gene-variant-database-pathogenicity-update
#3
Sarah Leigh, Marta Futema, Ros Whittall, Alison Taylor-Beadling, Maggie Williams, Johan T den Dunnen, Steve E Humphries
BACKGROUND: Familial hypercholesterolaemia (OMIM 143890) is most frequently caused by variations in the low-density lipoprotein receptor (LDLR) gene. Predicting whether novel variants are pathogenic may not be straightforward, especially for missense and synonymous variants. In 2013, the Association of Clinical Genetic Scientists published guidelines for the classification of variants, with categories 1 and 2 representing clearly not or unlikely pathogenic, respectively, 3 representing variants of unknown significance (VUS), and 4 and 5 representing likely to be or clearly pathogenic, respectively...
November 7, 2016: Journal of Medical Genetics
https://www.readbyqxmd.com/read/27817865/mecr-mutations-cause-childhood-onset-dystonia-and-optic-atrophy-a-mitochondrial-fatty-acid-synthesis-disorder
#4
Gali Heimer, Juha M Kerätär, Lisa G Riley, Shanti Balasubramaniam, Eran Eyal, Laura P Pietikäinen, J Kalervo Hiltunen, Dina Marek-Yagel, Jeffrey Hamada, Allison Gregory, Caleb Rogers, Penelope Hogarth, Martha A Nance, Nechama Shalva, Alvit Veber, Michal Tzadok, Andreea Nissenkorn, Davide Tonduti, Florence Renaldo, Ichraf Kraoua, Celeste Panteghini, Lorella Valletta, Barbara Garavaglia, Mark J Cowley, Velimir Gayevskiy, Tony Roscioli, Jonathon M Silberstein, Chen Hoffmann, Annick Raas-Rothschild, Valeria Tiranti, Yair Anikster, John Christodoulou, Alexander J Kastaniotis, Bruria Ben-Zeev, Susan J Hayflick
Mitochondrial fatty acid synthesis (mtFAS) is an evolutionarily conserved pathway essential for the function of the respiratory chain and several mitochondrial enzyme complexes. We report here a unique neurometabolic human disorder caused by defective mtFAS. Seven individuals from five unrelated families presented with childhood-onset dystonia, optic atrophy, and basal ganglia signal abnormalities on MRI. All affected individuals were found to harbor recessive mutations in MECR encoding the mitochondrial trans-2-enoyl-coenzyme A-reductase involved in human mtFAS...
December 1, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27804176/comparison-of-bioinformatics-prediction-molecular-modeling-and-functional-analyses-of-foxc1-mutations-in-patients-with-axenfeld-rieger-syndrome
#5
Morteza Seifi, Tim Footz, Sherry A M Taylor, Michael A Walter
Mutations in the forkhead box C1 gene (FOXC1) cause Axenfeld-Rieger syndrome (ARS). Here, we investigated the effect of four ARS missense variants on FOXC1 structure and function, and examined the predictive value of four in silico programs for all 31 FOXC1 missense variants identified to date. Molecular modeling of the FOXC1 forkhead domain predicts that c.402G> A (p.C135Y) alters FOXC1's structure. In contrast, c.378A> G (p.H128R) and c.481A> G (p.M161V) are not predicted to change FOXC1's structure...
November 2, 2016: Human Mutation
https://www.readbyqxmd.com/read/27783279/frequency-of-pathogenic-germline-mutation-in-chek2-palb2-mre11-and-rad50-in-patients-at-high-risk-for-hereditary-breast-cancer
#6
Haeyoung Kim, Dae-Yeon Cho, Doo Ho Choi, Mijin Oh, Inkyung Shin, Won Park, Seung Jae Huh, Seok Jin Nam, Jeong Eon Lee, Seok Won Kim
PURPOSE: This study was performed to evaluate the frequency of mutations in CHEK2, PALB2, MRE11, and RAD50 among Korean patients at high risk for hereditary breast cancer. METHODS: A total of 235 Korean patients with hereditary breast cancer who tested negative for BRCA1/2 mutation were enrolled to this study. Entire coding regions of CHEK2, PALB2, MRE11, and RAD50 were analyzed using massively parallel sequencing (MPS). Sequence variants detected by MPS were confirmed by Sanger sequencing...
October 25, 2016: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/27708576/a-novel-ccm2-gene-mutation-associated-with-familial-cerebral-cavernous-malformation
#7
Wen-Qing Huang, Cong-Xia Lu, Ya Zhang, Ke-Hui Yi, Liang-Liang Cai, Ming-Li Li, Han Wang, Qing Lin, Chi-Meng Tzeng
Background: Cerebral cavernous malformations (CCMs) are common vascular malformations that predominantly arise in the central nervous system and are mainly characterized by enlarged vascular cavities without intervening brain parenchyma. Familial CCMs (FCCMs) is inherited in an autosomal dominant pattern with incomplete penetrance and variable symptoms. Methods: Mutations of three pathogenic genes, CCM1, CCM2, and CCM3, were investigated by direct DNA sequencing in a Chinese family with multiple CCM lesions...
2016: Frontiers in Aging Neuroscience
https://www.readbyqxmd.com/read/27703146/improving-the-in-silico-assessment-of-pathogenicity-for-compensated-variants
#8
Luisa Azevedo, Matthew Mort, Antonio C Costa, Raquel M Silva, Dulce Quelhas, Antonio Amorim, David N Cooper
Understanding the functional sequelae of amino-acid replacements is of fundamental importance in medical genetics. Perhaps, the most intuitive way to assess the potential pathogenicity of a given human missense variant is by measuring the degree of evolutionary conservation of the substituted amino-acid residue, a feature that generally serves as a good proxy metric for the functional/structural importance of that residue. However, the presence of putatively compensated variants as the wild-type alleles in orthologous proteins of other mammalian species not only challenges this classical view of amino-acid essentiality but also precludes the accurate evaluation of the functional impact of this type of missense variant using currently available bioinformatic prediction tools...
October 5, 2016: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/27681385/de-novo-missense-variants-in-ppp1cb-are-associated-with-intellectual-disability-and-congenital-heart-disease
#9
Lijiang Ma, Yavuz Bayram, Heather M McLaughlin, Megan T Cho, Alyson Krokosky, Clesson E Turner, Kristin Lindstrom, Caleb P Bupp, Katey Mayberry, Weiyi Mu, Joann Bodurtha, Veronique Weinstein, Neda Zadeh, Wendy Alcaraz, Zöe Powis, Yunru Shao, Daryl A Scott, Andrea M Lewis, Janson J White, Shalani N Jhangiani, Elif Yilmaz Gulec, Seema R Lalani, James R Lupski, Kyle Retterer, Rhonda E Schnur, Ingrid M Wentzensen, Sherri Bale, Wendy K Chung
Intellectual disabilities are genetically heterogeneous and can be associated with congenital anomalies. Using whole-exome sequencing (WES), we identified five different de novo missense variants in the protein phosphatase-1 catalytic subunit beta (PPP1CB) gene in eight unrelated individuals who share an overlapping phenotype of dysmorphic features, macrocephaly, developmental delay or intellectual disability (ID), congenital heart disease, short stature, and skeletal and connective tissue abnormalities. Protein phosphatase-1 (PP1) is a serine/threonine-specific protein phosphatase involved in the dephosphorylation of a variety of proteins...
December 2016: Human Genetics
https://www.readbyqxmd.com/read/27667161/next-generation-sequencing-of-hereditary-hemochromatosis-related-genes-novel-likely-pathogenic-variants-found-in-the-portuguese-population
#10
Ricardo Faria, Bruno Silva, Catarina Silva, Pedro Loureiro, Ana Queiroz, Sofia Fraga, Jorge Esteves, Diana Mendes, Rita Fleming, Luís Vieira, João Gonçalves, Paula Faustino
Hereditary hemochromatosis (HH) is an autosomal recessive disorder characterized by excessive iron absorption resulting in pathologically increased body iron stores. It is typically associated with common HFE gene mutation (p.Cys282Tyr and p.His63Asp). However, in Southern European populations up to one third of HH patients do not carry the risk genotypes. This study aimed to explore the use of next-generation sequencing (NGS) technology to analyse a panel of iron metabolism-related genes (HFE, TFR2, HJV, HAMP, SLC40A1, and FTL) in 87 non-classic HH Portuguese patients...
October 2016: Blood Cells, Molecules & Diseases
https://www.readbyqxmd.com/read/27666373/revel-an-ensemble-method-for-predicting-the-pathogenicity-of-rare-missense-variants
#11
Nilah M Ioannidis, Joseph H Rothstein, Vikas Pejaver, Sumit Middha, Shannon K McDonnell, Saurabh Baheti, Anthony Musolf, Qing Li, Emily Holzinger, Danielle Karyadi, Lisa A Cannon-Albright, Craig C Teerlink, Janet L Stanford, William B Isaacs, Jianfeng Xu, Kathleen A Cooney, Ethan M Lange, Johanna Schleutker, John D Carpten, Isaac J Powell, Olivier Cussenot, Geraldine Cancel-Tassin, Graham G Giles, Robert J MacInnis, Christiane Maier, Chih-Lin Hsieh, Fredrik Wiklund, William J Catalona, William D Foulkes, Diptasri Mandal, Rosalind A Eeles, Zsofia Kote-Jarai, Carlos D Bustamante, Daniel J Schaid, Trevor Hastie, Elaine A Ostrander, Joan E Bailey-Wilson, Predrag Radivojac, Stephen N Thibodeau, Alice S Whittemore, Weiva Sieh
The vast majority of coding variants are rare, and assessment of the contribution of rare variants to complex traits is hampered by low statistical power and limited functional data. Improved methods for predicting the pathogenicity of rare coding variants are needed to facilitate the discovery of disease variants from exome sequencing studies. We developed REVEL (rare exome variant ensemble learner), an ensemble method for predicting the pathogenicity of missense variants on the basis of individual tools: MutPred, FATHMM, VEST, PolyPhen, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP, SiPhy, phyloP, and phastCons...
October 6, 2016: American Journal of Human Genetics
https://www.readbyqxmd.com/read/27627812/x-linked-and-autosomal-recessive-alport-syndrome-pathogenic-variant-features-and-further-genotype-phenotype-correlations
#12
Judith Savige, Helen Storey, Hae Il Cheong, Hee Gyung Kang, Eujin Park, Pascale Hilbert, Anton Persikov, Carmen Torres-Fernandez, Elisabet Ars, Roser Torra, Jens Michael Hertz, Mads Thomassen, Lev Shagam, Dongmao Wang, Yanyan Wang, Frances Flinter, Mato Nagel
Alport syndrome results from mutations in the COL4A5 (X-linked) or COL4A3/COL4A4 (recessive) genes. This study examined 754 previously- unpublished variants in these genes from individuals referred for genetic testing in 12 accredited diagnostic laboratories worldwide, in addition to all published COL4A5, COL4A3 and COL4A4 variants in the LOVD databases. It also determined genotype-phenotype correlations for variants where clinical data were available. Individuals were referred for genetic testing where Alport syndrome was suspected clinically or on biopsy (renal failure, hearing loss, retinopathy, lamellated glomerular basement membrane), variant pathogenicity was assessed using currently-accepted criteria, and variants were examined for gene location, and age at renal failure onset...
2016: PloS One
https://www.readbyqxmd.com/read/27616605/assessing-the-general-population-frequency-of-rare-coding-variants-in-the-ext1-and-ext2-genes-previously-implicated-in-hereditary-multiple-exostoses
#13
Diana L Cousminer, Alexandre Arkader, Benjamin F Voight, Maurizio Pacifici, Struan F A Grant
Hereditary multiple exostoses (HME) is a rare childhood-onset skeletal disease linked to mutations in exostosin glycosyltransferase 1 (EXT1) or 2 (EXT2). Patients are heterozygous for either an EXT1 or EXT2 mutation, and it is widely assumed that exostosis formation and associated defects, such as growth retardation and skeletal deformities, require loss-of-heterozygosity or a second hit in affected cells. However, the relevance and phenotypic impact of many presumed pathogenic EXT variants remain uncertain...
November 2016: Bone
https://www.readbyqxmd.com/read/27602407/kcnq2-encephalopathy-features-mutational-hot-spots-and-ezogabine-treatment-of-11-patients
#14
John J Millichap, Kristen L Park, Tammy Tsuchida, Bruria Ben-Zeev, Lionel Carmant, Robert Flamini, Nishtha Joshi, Paul M Levisohn, Eric Marsh, Srishti Nangia, Vinodh Narayanan, Xilma R Ortiz-Gonzalez, Marc C Patterson, Phillip L Pearl, Brenda Porter, Keri Ramsey, Emily L McGinnis, Maurizio Taglialatela, Molly Tracy, Baouyen Tran, Charu Venkatesan, Sarah Weckhuysen, Edward C Cooper
OBJECTIVE: To advance the understanding of KCNQ2 encephalopathy genotype-phenotype relationships and to begin to assess the potential of selective KCNQ channel openers as targeted treatments. METHODS: We retrospectively studied 23 patients with KCNQ2 encephalopathy, including 11 treated with ezogabine (EZO). We analyzed the genotype-phenotype relationships in these and 70 previously described patients. RESULTS: The mean seizure onset age was 1...
October 2016: Neurology. Genetics
https://www.readbyqxmd.com/read/27596133/clinical-characterization-and-mutation-spectrum-of-german-patients-with-familial-hypercholesterolemia
#15
Thomas Grenkowitz, Ursula Kassner, Marion Wühle-Demuth, Bastian Salewsky, Adrian Rosada, Tomasz Zemojtel, Werner Hopfenmüller, Berend Isermann, Katrin Borucki, Franz Heigl, Ulrich Laufs, Stephan Wagner, Marcus E Kleber, Priska Binner, Winfried März, Elisabeth Steinhagen-Thiessen, Ilja Demuth
BACKGROUND AND AIMS: Autosomal-dominant familial hypercholesterolemia (FH) is characterized by elevated plasma levels of low-density lipoprotein cholesterol (LDL-C) and a dramatically increased risk to develop cardiovascular disease (CVD). Mutations in three major genes have been associated with FH: the LDL receptor gene (LDLR), the apolipoprotein B gene (APOB), and the proprotein convertase subtilisin/kexin 9 gene (PCSK9). Here we investigated the frequency and the spectrum of FH causing mutations in Germany...
October 2016: Atherosclerosis
https://www.readbyqxmd.com/read/27557340/the-prevalence-clinical-and-molecular-characteristics-of-congenital-hypothyroidism-caused-by-duox2-mutations-a-population-based-cohort-study-in-guangzhou
#16
M Tan, Y Huang, X Jiang, P Li, C Tang, X Jia, Q Chen, W Chen, H Sheng, Y Feng, D Wu, L Liu
Thyroid dyshormonogenesis (DH) has recently been reported to be more frequently associated with mutations in the dual oxidase 2 (DUOX2) gene. The present study was aimed to investigate the prevalence, clinical, and molecular characteristics of congenital hypothyroidism (CH) caused by DUOX2 mutations in Guangzhou. A population-based cohort of 156 patients with CH was recruited based on neonatal screening among 433 578 newborns born in Guangzhou from 2011 to 2012. Genetic analysis of DUOX2 was performed in 96 patients with suspected thyroid dyshormonogenesis (SDH) by PCR-amplified direct sequencing...
September 2016: Hormone and Metabolic Research, Hormon- und Stoffwechselforschung, Hormones et Métabolisme
https://www.readbyqxmd.com/read/27553520/analysis-of-large-scale-whole-exome-sequencing-data-to-determine-the-prevalence-of-genetically-distinct-forms-of-neuronal-ceroid-lipofuscinosis
#17
David E Sleat, Erika Gedvilaite, Yeting Zhang, Peter Lobel, Jinchuan Xing
The neuronal ceroid lipofuscinoses (NCLs) are a group of fatal, mostly recessive neurodegenerative lysosomal storage diseases. While clinically similar, they are genetically distinct and result from mutations in at least twelve different genes. Estimates of NCL incidence range from 0.6 to 14 per 100,000 live births but vary widely between populations and are influenced by whether patients are classified based upon clinical or genetic criteria. We investigated mutations in twelve NCL genes in ~61,000 individuals represented in the Exome Aggregation Consortium (ExAC) whole exome sequencing database...
November 30, 2016: Gene
https://www.readbyqxmd.com/read/27550844/de-novo-and-inherited-mutations-in-the-x-linked-gene-clcn4-are-associated-with-syndromic-intellectual-disability-and-behavior-and-seizure-disorders-in-males-and-females
#18
E E Palmer, T Stuhlmann, S Weinert, E Haan, H Van Esch, M Holvoet, J Boyle, M Leffler, M Raynaud, C Moraine, H van Bokhoven, T Kleefstra, K Kahrizi, H Najmabadi, H-H Ropers, M R Delgado, D Sirsi, S Golla, A Sommer, M P Pietryga, W K Chung, J Wynn, L Rohena, E Bernardo, D Hamlin, B M Faux, D K Grange, L Manwaring, J Tolmie, S Joss, J M Cobben, F A M Duijkers, J M Goehringer, T D Challman, F Hennig, U Fischer, A Grimme, V Suckow, L Musante, J Nicholl, M Shaw, S P Lodh, Z Niu, J A Rosenfeld, P Stankiewicz, T J Jentsch, J Gecz, M Field, V M Kalscheuer
Variants in CLCN4, which encodes the chloride/hydrogen ion exchanger CIC-4 prominently expressed in brain, were recently described to cause X-linked intellectual disability and epilepsy. We present detailed phenotypic information on 52 individuals from 16 families with CLCN4-related disorder: 5 affected females and 2 affected males with a de novo variant in CLCN4 (6 individuals previously unreported) and 27 affected males, 3 affected females and 15 asymptomatic female carriers from 9 families with inherited CLCN4 variants (4 families previously unreported)...
August 23, 2016: Molecular Psychiatry
https://www.readbyqxmd.com/read/27544631/three-novel-mutations-and-genetic-epidemiology-analysis-of-the-gap-junction-beta-1-gjb1-gene-among-hungarian-charcot-marie-tooth-disease-patients
#19
Gyorgy Mate Milley, Edina Timea Varga, Zoltan Grosz, Benjamin Bereznai, Zsuzsanna Aranyi, Judit Boczan, Peter Dioszeghy, Bernadette Kálmán, Aniko Gal, Maria Judit Molnar
Pathogenic variants of the gap junction beta 1 (GJB1) gene are responsible for the Charcot-Marie-Tooth neuropathy X type 1 (CMTX1). In this study, we report the mutation frequency of GJB1 in 210 Hungarian CMT patients and the phenotype comparison between male and female CMTX1 patients. Altogether, 13 missense substitutions were found in the GJB1 gene. Among them, 10 have been previously described as pathogenic variants (p.Arg15Trp, p.Val63Ile, p.Leu89Val, p.Ala96Gly, p.Arg107Trp, p.Arg142Gln, p.Arg164Trp, p...
October 2016: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/27544226/reevaluation-of-rint1-as-a-breast-cancer-predisposition-gene
#20
Na Li, Ella R Thompson, Simone M Rowley, Simone McInerny, Lisa Devereux, David Goode, LifePool Investigators, Michelle W Wong-Brown, Rodney J Scott, Alison H Trainer, Kylie L Gorringe, Paul A James, Ian G Campbell
Rad50 interactor 1 (RINT1) has recently been reported as an intermediate-penetrance (odds ratio 3.24) breast cancer susceptibility gene, as well as a risk factor for Lynch syndrome. The coding regions and exon-intron boundaries of RINT1 were sequenced in 2024 familial breast cancer cases previously tested negative for BRCA1, BRCA2, and PALB2 mutations and 1886 population-matched cancer-free controls using HaloPlex Targeted Enrichment Assays. Only one RINT1 protein-truncating variant was detected in a control...
September 2016: Breast Cancer Research and Treatment
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