1. Evaluation of Presumably Disease Causing SCN1A Variants in a Cohort of Common Epilepsy Syndromes
- Author
-
Lal, D., Reinthaler, E. M., Dejanovic, B., May, P., Thiele, H., Lehesjoki, A. . E., Schwarz, G., Riesch, E., Ikram, M. A., Van Duijn, C. M., Uitterlinden, A. G., Hofman, A., Steinböck, H., Gruber sedlmayr, U., Neophytou, B., Zara, F., Hahn, A., Gormley, P., Becker, F., Weber, Y. G., Cilio, M. R., Kunz, W. S., Krause, R., Zimprich, F., Lemke, J. R., Nürnberg, P., Sander, T., Lerche, H., Neubauer, B. A., Palotie, A., Ruppert, A. K., Suls, A., Siren, A., Koeleman, B., Haberlandt, E., Ronen, G. M., Caglayan, H., Hjalgrim, H., Muhle, H., Schulz, H., Helbig, I., Altmüller, J., Geldner, J., Schubert, J., Jabbari, K., Everett, K., Feucht, M., Balestri, M., Nothnagel, M., Striano, Pasquale, Møller, R. S., Nabbout, R., Balling, R., Baulac, S., Bianchi, A., La Neve, A., Minetti, Carlo, Giuseppe, C., Neuroscience Center, Research Programs Unit, Anna-Elina Lehesjoki / Principal Investigator, Research Programme for Molecular Neurology, Institute for Molecular Medicine Finland, Aarno Palotie / Principal Investigator, Genomics of Neurological and Neuropsychiatric Disorders, Epidemiology, Neurology, Radiology & Nuclear Medicine, Internal Medicine, Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group) [research center], and Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) [research center]
- Subjects
0301 basic medicine ,Male ,Genetics and Molecular Biology (all) ,FEBRILE SEIZURES PLUS ,Disease ,Pathogenesis ,Bioinformatics ,Pathology and Laboratory Medicine ,Biochemistry ,Epilepsy ,Database and Informatics Methods ,0302 clinical medicine ,Risk Factors ,Medicine and Health Sciences ,Medicine ,SCN1A ,Myoclonic Seizures ,NEURONAL SODIUM-CHANNEL ,MUTATION ,Multidisciplinary ,SEVERE MYOCLONIC EPILEPSY ,Research Support, Non-U.S. Gov't ,Medicine (all) ,Syndrome ,Clinical Trial ,3. Good health ,PREVALENCE ,Multicenter Study ,Neurology ,Cohort ,Female ,Genetics & genetic processes [F10] [Life sciences] ,Génétique & processus génétiques [F10] [Sciences du vivant] ,Sequence Analysis ,DRAVET SYNDROME ,Research Article ,Science ,Mutation, Missense ,Amino Acid Substitution ,Case-Control Studies ,Humans ,NAV1.1 Voltage-Gated Sodium Channel ,Agricultural and Biological Sciences (all) ,Biochemistry, Genetics and Molecular Biology (all) ,GENERALIZED EPILEPSY ,Sequence Databases ,Research and Analysis Methods ,ITALIAN PATIENTS ,03 medical and health sciences ,Dravet syndrome ,Journal Article ,Genetics ,HEMIPLEGIC MIGRAINE ,Tonic-Clonic Seizures ,Generalized epilepsy ,Molecular Biology Techniques ,Sequencing Techniques ,Molecular Biology ,business.industry ,Case-control study ,3112 Neurosciences ,Biology and Life Sciences ,Human Genetics ,Epileptic Seizures ,medicine.disease ,GENE ,Human genetics ,030104 developmental biology ,Biological Databases ,Epilepsy syndromes ,Mutation Databases ,Genetics of Disease ,3111 Biomedicine ,Missense ,business ,030217 neurology & neurosurgery - Abstract
A. Palotie on työryhmän jäsen. Objective The SCN1A gene, coding for the voltage-gated Na+ channel alpha subunit NaV1.1, is the clinically most relevant epilepsy gene. With the advent of high-throughput next-generation sequencing, clinical laboratories are generating an ever-increasing catalogue of SCN1A variants. Variants are more likely to be classified as pathogenic if they have already been identified previously in a patient with epilepsy. Here, we critically re-evaluate the pathogenicity of this class of variants in a cohort of patients with common epilepsy syndromes and subsequently ask whether a significant fraction of benign variants have been misclassified as pathogenic. Methods We screened a discovery cohort of 448 patients with a broad range of common genetic epilepsies and 734 controls for previously reported SCN1A mutations that were assumed to be disease causing. We re-evaluated the evidence for pathogenicity of the identified variants using in silico predictions, segregation, original reports, available functional data and assessment of allele frequencies in healthy individuals as well as in a follow up cohort of 777 patients. Results and Interpretation We identified 8 known missense mutations, previously reported as pathogenic, in a total of 17 unrelated epilepsy patients (17/448; 3.80%). Our re-evaluation indicates that 7 out of these 8 variants (p.R27T; p.R28C; p.R542Q; p.R604H; p.T1250M; p.E1308D; p.R1928G; NP_001159435.1) are not pathogenic. Only the p. T1174S mutation may be considered as a genetic risk factor for epilepsy of small effect size based on the enrichment in patients (P = 6.60 x 10(-4); OR = 0.32, fishers exact test), previous functional studies but incomplete penetrance. Thus, incorporation of previous studies in genetic counseling of SCN1A sequencing results is challenging and may produce incorrect conclusions.
- Published
- 2016
- Full Text
- View/download PDF