Single Missense Mutation in the Tyrosine Kinase Catalytic Domain Of
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Missense Mutations of MADH4: Characterization of the Mutational Hot Spot and Functional Consequences in Human Tumors
Vol. 10, 1597–1604, March 1, 2004 Clinical Cancer Research 1597 Featured Article Missense Mutations of MADH4: Characterization of the Mutational Hot Spot and Functional Consequences in Human Tumors Christine A. Iacobuzio-Donahue,1 Jason Song,5 Introduction Giovanni Parmiagiani,4 Charles J. Yeo,2,3 Human pancreatic ductal adenocarcinomas inactivate the Ralph H. Hruban,1,2 and Scott E. Kern2 tumor suppressor gene MADH4 (DPC4, SMAD4) with a high frequency (1). This inactivation occurs most commonly by Departments of 1Pathology, 2Oncology, 3Surgery, and 4Public Health, The Johns Hopkins Medical Institutions, Baltimore, Maryland, and homozygous deletion (HD), but some tumors may also inacti- 5Temple University School of Medicine, Philadelphia, Pennsylvania vate the gene by loss of heterozygosity (LOH) coupled with a mutation in the remaining allele. Inactivation by nonsense mu- tation may cause the loss of protein expression by enhanced Abstract proteosomal degradation (2, 3). Even when expressed as protein, Purpose and Experimental Design: The mutational spec- missense mutations may result in loss of a specific function of trum of MADH4 (DPC4/SMAD4) opens valuable insights the Madh4 protein such as DNA binding or Smad protein into the functions of this protein that confer its tumor- interactions (2–9). Thus, the location of these mutations can suppressive nature in human tumors. We present the provide clues to key structural features that mediate the tumor- MADH4 genetic status determined on a new set of pancre- suppressive function of MADH4. atic, biliary, and duodenal cancers with comparison to the Members of the Smad protein family, including Madh4, mutational data reported for various tumor types. -
Structural Effects of Point Mutations in Proteins Suvethigaa Shanthirabalan, Jacques Chomilier, Mathilde Carpentier
Structural effects of point mutations in proteins Suvethigaa Shanthirabalan, Jacques Chomilier, Mathilde Carpentier To cite this version: Suvethigaa Shanthirabalan, Jacques Chomilier, Mathilde Carpentier. Structural effects of point muta- tions in proteins. Proteins - Structure, Function and Bioinformatics, Wiley, 2018, 86 (8), pp.853-867. 10.1002/prot.25499. hal-01909365 HAL Id: hal-01909365 https://hal.sorbonne-universite.fr/hal-01909365 Submitted on 31 Oct 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Structural effects of point mutations in proteins Suvethigaa Shanthirabalan1, Jacques Chomilier2, Mathilde Carpentier1,2 1. Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France. 2. Sorbonne Université, CNRS, MNHN, IRD, IMPMC, BiBiP, Paris, France Corresponding author: [email protected] Mail: [email protected]; [email protected]; [email protected] Abstract A structural database of eleven families of chains differing by a single amino acid substitution has been built. Another structural dataset of 5 families with identical sequences has been used for comparison. The RMSD computed after a global superimposition of the mutated protein on each native one is smaller than the RMSD calculated among proteins of identical sequences. -
Bio 102 Practice Problems Genetic Code and Mutation
Bio 102 Practice Problems Genetic Code and Mutation Multiple choice: Unless otherwise directed, circle the one best answer: 1. Choose the one best answer: Beadle and Tatum mutagenized Neurospora to find strains that required arginine to live. Based on the classification of their mutants, they concluded that: A. one gene corresponds to one protein. B. DNA is the genetic material. C. "inborn errors of metabolism" were responsible for many diseases. D. DNA replication is semi-conservative. E. protein cannot be the genetic material. 2. Choose the one best answer. Which one of the following is NOT part of the definition of a gene? A. A physical unit of heredity B. Encodes a protein C. Segement of a chromosome D. Responsible for an inherited characteristic E. May be linked to other genes 3. A mutation converts an AGA codon to a TGA codon (in DNA). This mutation is a: A. Termination mutation B. Missense mutation C. Frameshift mutation D. Nonsense mutation E. Non-coding mutation 4. Beadle and Tatum performed a series of complex experiments that led to the idea that one gene encodes one enzyme. Which one of the following statements does not describe their experiments? A. They deduced the metabolic pathway for the synthesis of an amino acid. B. Many different auxotrophic mutants of Neurospora were isolated. C. Cells unable to make arginine cannot survive on minimal media. D. Some mutant cells could survive on minimal media if they were provided with citrulline or ornithine. E. Homogentisic acid accumulates and is excreted in the urine of diseased individuals. 5. -
Large Accumulation of Mrna and DNA Point Modi¢Cations in a Plant
FEBS Letters 472 (2000) 14^16 FEBS 23560 View metadata, citation and similar papers at core.ac.uk brought to you by CORE Large accumulation of mRNA and DNA point modi¢cationsprovided in by a Elsevier plant - Publisher Connector senescent tissue Maria Plaa;*, Anna Jofre¨a, Maria Martellb, Marisa Molinasa, Jordi Go¨mezb aLaboratori del Suro, Universitat de Girona, Campus Montilivi sn, E-17071 Girona, Spain bLiver Unit, Department of Medicine, Universitat Auto©noma de Barcelona, Hospital General Universitari Vall d'Hebron, E-08035 Barcelona, Spain Received 26 January 2000 Edited by Takashi Gojobori We investigated the frequency of cDNA modi¢cation in Abstract Although nucleic acids are the paradigm of genetic information conservation, they are inherently unstable molecules cork (phellem) compared to a normally growing young tissue that suffer intrinsic and environmental damage. Oxidative stress (root tip) using cork-oak (Quercus suber) as a model system. has been related to senescence and aging and, recently, it has For this purpose, we analyzed a population of Qs_hsp17 been shown that mutations accumulate at high frequency in mRNA sequences (reverse transcription PCR products form mitochondrial DNA with age. We investigated RNA and DNA position 32^401, AC AJ000691) in cork and in root tip tissue modifications in cork, a senescent plant tissue under high [6]. Cork (phellem) is an external layer of protective tissue, endogenous oxidative stress conditions. When compared to consisting of several layers of cells that deposit large amounts normally growing young tissue, cork revealed an unexpected of suberin and undergo programmed cell death. Due to phen- high frequency of point modifications in both cDNA (Pn = oxy radicals generated during suberin synthesis [7,8], cork 1/1784) and nuclear DNA (Pn = 1/1520). -
Point Mutations Underlying NF1 and NF2 and Increased Risk of Malignancy
Central Annals of Otolaryngology and Rhinology Mini Review *Corresponding author Andrea L.O. Hebb, MSc, PhD, RN, Maritime Lateral Skull Base Clinic, Otolaryngology, Neurosurgery and the Point Mutations Underlying NF1 Stereotactic Radiotherapy Group QEII Health Science Centre, Halifax, Canada; Email: [email protected] and NF2 and Increased Risk of Submitted: 12 February 2020 Accepted: 25 February 2020 Published: 27 February 2020 Malignancy ISSN: 2379-948X Copyright 1 2 3,4 3,4 Myles Davidson , Haupt TS , Morris DP , Shoman NM , © 2020 Davidson M, et al. 2,4 1,2,4 Walling SA , and Hebb ALO * OPEN ACCESS 1Department of Psychology, Saint Mary’s University, Canada 2Division of Neurosurgery, Dalhousie University, Canada Keywords 3 Division of Otolaryngology, Dalhousie University, Canada • Neurofibromatosis 4 Maritime Lateral Skull Base Clinic, Otolaryngology, Neurosurgery and the Stereotactic • Missense mutation Radiotherapy Group QEII Health Science Centre, Canada • Frameshift mutation • Nonsense mutation Abstract • KRAS gene • Colorectal cancer Neurofibromatosis Type-1 and Neurofibromatosis Type-2 are autosomal dominant • Acoustic neuroma tumor suppressor disorders that result from inherited or spontaneous mutations in • Vestibular schwannoma their respective genes. Neurofibromatosis Type-1 has been attributed to a non-sense • Meningioma mutation in chromosome 17 and Neurofibromatosis Type-2 a point mutation in its gene on chromosome 22. The following discussion briefly reviews point and frameshift mutations and explores the relationship between point mutations and development of malignancies in patients with Neurofibromatosis Type-1 and Neurofibromatosis Type-2. INTRODUCTION producing phenylalanine hydroxylase, the majority of which are missense mutations [4]. A point mutation is the change of one base for another in the DNA sequence. -
Methods for Detection of Point Mutations: Performance and Quality
Clinical Chemistry 43:7 1114–1128 (1997) Review Methods for detection of point mutations: performance and quality assessment Downloaded from https://academic.oup.com/clinchem/article/43/7/1114/5640834 by guest on 29 September 2021 Peter Nollau and Christoph Wagener*, on behalf of the IFCC Scientific Division, Committee on Molecular Biology Techniques We give an overview of current methods for the detec- 10) What kind of quality assessment can be achieved? tion of point mutations as well as small insertions and Here, different methods for the detection of point muta- deletions in clinical diagnostics. For each method, the tions and small deletions or insertions will be discussed following characteristics are specified: (a) principle, (b) on the basis of the above criteria (for simplification, we major modifications, (c) maximum fragment size that shall refer to point mutations only in the text, though in can be analyzed, (d) ratio and type of mutations that can general, small deletions or insertions are detected equally be detected, (e) minimum ratio of mutant to wild-type well by the methods described). In general, PCR is either alleles at which mutations can be detected, and (f) used for the generation of DNA fragments, or is part of detection methods. Special attention is paid to the the detection method. Screening methods for unknown possibilities of quality assessment and the potential for mutations as well as methods for the detection of known standardization and automation. mutations are included. Though DNA sequencing tech- niques will not be covered, we stress that DNA sequenc- INDEXING TERMS: alleles • electrophoresis • gene insertions ing is considered the gold standard and remains the • gene deletions • polymerase chain reaction definitive procedure for the detection of mutations so far. -
Nonsense and Missense Mutations in Hemophilia A: Estimate of the Relative Mutation Rate at CG Dinucleotides Hagop Youssoufian,* Stylianos E
Am. J. Hum. Genet. 42:718-725, 1988 Nonsense and Missense Mutations in Hemophilia A: Estimate of the Relative Mutation Rate at CG Dinucleotides Hagop Youssoufian,* Stylianos E. Antonarakis,* William Bell,t Anne M. Griffin,4 and Haig H. Kazazian, Jr.* *Genetics Unit, Department of Pediatrics, and tDivision of Hematology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore; and tDivision of Hematology, Department of Medicine, University of North Carolina School of Medicine, Chapel Hill Summary Hemophilia A is an X-linked disease of coagulation caused by deficiency of factor VIII. Using cloned cDNA and synthetic oligonucleotide probes, we have now screened 240 patients and found CG-to-TG transitions in an exon in nine. We have previously reported four of these patients; and here we report the remaining five, all of whom were severely affected. In one patient a TaqI site was lost in exon 23, and in the other four it was lost in exon 24. The novel exon 23 mutation is a CG-to-TG substitution at the codon for amino acid residue 2166, producing a nonsense codon in place of the normal codon for arginine. Simi- larly, the exon 24 mutations are also generated by CG-to-TG transitions, either on the sense strand produc- ing nonsense mutations or on the antisense strand producing missense mutations (Arg to Gln) at position 2228. The novel missense mutations are the first such mutations observed in association with severe hemo- philia A. These results provide further evidence that recurrent mutations are not uncommon in hemophilia A, and they also allow us to estimate that the extent of hypermutability of CG dinucleotides is 10-20 times greater than the average mutation rate for hemophilia A. -
The Genomics Era: the Future of Genetics in Medicine - Glossary
The Genomics Era: the Future of Genetics in Medicine - Glossary The glossary below provides a list of key terms used throughout the course. You do not need to read them all now; we’ll be linking back to the main glossary step wherever these terms appear, so you may refer back to this list if you are unsure of the terminology being used. Term Definition The process of matching reads back to their original Alignment position in the reference genome. An allele is one of a number of alternative forms of the same gene or genetic locus. We inherit one copy Allele of our genetic code from our mother and one copy of our genetic code from our father. Each copy is known as an allele. Microarray based genomic comparative hybridisation. This is a technique used to detect chromosome imbalances by comparing patient and control DNA and comparing differences between the two sets. It is Array CGH a useful technique for detecting small chromosome deletions and duplications which would not have been detected with more traditional karyotyping techniques. A unit of DNA. There are four bases which form the Base cross links (or rungs) of the DNA double helix: adenine (A), thymine (T), guanine (G) and cytosine (C). Capture see Target enrichment. The process by which a cell becomes specialized in Cell differentiation order to perform a specific function. Centromere The point at which the sister chromatids are joined. #1 FutureLearn A structure located in the nucleus all living cells, comprised of DNA bound around proteins called histones. The normal number of chromosomes in each Chromosome human cell nucleus is 46 and is composed of 22 pairs of autosomes and a pair of sex chromosomes which determine gender: males have an X and a Y chromosome whilst females have two X chromosomes. -
Teacher Materials (PDF)
The Making of the Fittest: LESSON The Birth and Death of Genes TEACHER MATERIALS THE MOLECULAR EVOLUTION OF GENE BIRTH AND DEATH OVERVIEW This advanced lesson describes how mutation is a key element in both the birth and death of genes. Students proceed through a series of presentation slides that include background information, examples, and embedded video, and animation links. Questions challenge students to synthesize information and apply what they learn regarding how genes are gained and lost through evolutionary time. KEY CONCEPTS AND LEARNING OBJECTIVES • Mutations are changes in an organism’s DNA. They occur at random. • Whether or not a mutation has an effect on an organism’s traits depends on the type of mutation and its location. • Mutations can result in both the appearance of new genes and the loss of existing genes. • One way that a new gene can arise is when a gene is duplicated and one copy (or both copies) of the gene accumulates mutations, which change the function of the gene. • One way that a gene can be lost is when one or more mutations accumulate that destroy its function. Students will be able to • analyze gene sequences and transcribe DNA into messenger RNA (mRNA); • translate mRNA into a sequence of amino acids by using a genetic code chart; and • compare wild-type and mutated DNA sequences to determine the type of mutation present. CURRICULUM CONNECTIONS Curriculum Standards NGSS (April 2013) HS-LS1-1, HS-LS3-1, HS-LS3-2, HS-LS4-2, HS-LS4-4, HS-LS4-5 HS.LS1.A, HS.LS3.A, HS.LS3.B, HS.LS4.B, HS.LS4.C Common Core -
Genetics of Sma
CURE SMA CARE SERIES BOOKLET A SOURCE OF INFORMATION AND SUPPORT FOR INDIVIDUALS LIVING WITH SPINAL MUSCULAR ATROPHY AND THEIR FAMILIES. GENETICS OF SMA 1 SMA AND GENETICS Spinal muscular atrophy (SMA) is often referred to by several terms, including “genetic disease,” ‘’autosomal recessive genetic disorder,” “motor-neuron disease,” or ‘’neuromuscular disease.” SMA is a genetic disease. “Genetic” means it is relating to the genes and is inherited. Genes are responsible for our traits and unique characteristics. In SMA, there is a mutation in a gene responsible for the survival motor neuron (SMN) protein, a protein that is critical to the function of the nerves that control normal muscle movements. SMA is an autosomal recessive genetic disorder. “Autosomal recessive” refers to how the disease is inherited, or passed down, from the parents to the child. In SMA, the individual who is affected by SMA inherits two copies of a non-working gene—one copy from each parent. SMA is a motor-neuron disease. “Motor-neuron” refers to the type of nerve cell that sends messages to and from muscles responsible for movement and control of the head, neck, chest, abdomen, legs, and limbs. In SMA, the motor-neurons in the spinal cord do not have enough SMN protein. As a result, these motor-neurons do not function normally and may die, resulting in muscle weakness and atrophy (shrinkage). SMA is a neuromuscular disease. A “neuromuscular disease” affects the neuromuscular system. This can include problems with the nerves that control muscles, the muscles, and the communication between the nerves and the muscles. -
A Novel Missense Mutation in HSF4 Causes Autosomal-Dominant
Eye (2018) 32, 806–812 © 2018 Macmillan Publishers Limited, part of Springer Nature. All rights reserved 0950-222X/18 www.nature.com/eye 1,5 1,2,5 3,4 LABORATORY STUDY A novel missense V Berry , N Pontikos , A Moore , ACW Ionides3, V Plagnol2, ME Cheetham1 mutation in HSF4 and M Michaelides1,3 causes autosomal- dominant congenital lamellar cataract in a British family Abstract manifestations and is a predominant feature in 4200 genetic disorders. Congenital cataract may Purpose Inherited cataract, opacification of the lens, is the most common worldwide be familial and display considerable genotypic 4 cause of blindness in children. We aimed to and phenotypic heterogeneity. Inheritance is identify the genetic cause of isolated most commonly autosomal dominant (AD), 1 Department of Genetics, autosomal-dominant lamellar cataract in a usually with complete penetrance but with UCL Institute of five-generation British family. highly variable expressivity. The phenotypic Ophthalmology, London, fi UK Methods Whole exome sequencing (WES) classi cation of the cataract depends on the was performed on two affected individuals of position and type of the lens opacity such as: 2UCL Genetics Institute, the family and further validated by direct anterior polar, posterior polar, nuclear, lamellar, University College London, sequencing in family members. coralliform, blue-dot (cerulean), cortical, London UK Results A novel missense mutation pulverulent, polymorphic, complete cataract, 4 and posterior nuclear cataract.5,6 Significant 3 fi NM_001040667.2:c.190A G;p.K64E was Moor elds Eye Hospital, fi London, UK identi ed in the DNA-binding-domain of progress has been made in identifying the heat-shock transcription factor 4 (HSF4) and molecular genetic basis of human cataract. -
Niemann-Pick Disease: a Frequent Missense Mutation in the Acid
Proc. Natl. Acad. Sci. USA Vol. 88, pp. 3748-3752, May 1991 Genetics Niemann-Pick disease: A frequent missense mutation in the acid sphingomyelinase gene of Ashkenazi Jewish type A and B patients (lysosomal hydrolase/sphingomyelin/lysosomal storage disease/polymerase chain reaction/heterozygote detection) ORNA LEVRAN, ROBERT J. DESNICK, AND EDWARD H. SCHUCHMAN* Division of Medical and Molecular Genetics, Mount Sinai School of Medicine, New York, NY 10029 Communicated by Donald S. Fredrickson, November 26, 1990 ABSTRACT Although the A and B subtypes of Niemana- sence of neurologic manifestations, and survival into adult- Pick disease (NPD) both result from the deficient activity of ad hood. The nature of the biochemical and molecular defects sphingomyelinase (ASM; sphingomyelin cholinephosphohydro- that underlie the remarkable clinical heterogeneity in the A lase, EC 3.1.4.12) and the lysosomal aumaon of sphingo- and B subtypes remains unknown. Although patients with myelin, they have remarkably distinct phenotypes. Type A dis- both subtypes have residual ASM activity (~1 to 10% of ease s afatal neurodegenerative disorderofinfancy, whereas tpe normal), biochemical analyses cannot reliably distinguish the B disease has no neurologic miestations and is characterized two phenotypes. Moreover, the clinical course of type B primarily by reticuloendothelial involvement and survival into NPD is highly variable, and it is not presently possible to adulthood. Both disorders are more frequent among individuals correlate disease severity with the level of residual ASM of Ashkenai Jewis ancestry than in the general population. The activity. recent isolation and characterization of cDNA and genomic Types A and B NPD occur at least 10 times more frequently sequences encoding ASM has facilitated investigation of the among individuals of Ashkenazi Jewish ancestry than in the molecular lesions causing the NPD subtypes.