Abstract
Progressive myoclonus epilepsies (PMEs) are a group of rare, inherited disorders manifesting with action myoclonus, tonic-clonic seizures and ataxia. We sequenced the exomes of 84 unrelated individuals with PME of unknown cause and molecularly solved 26 cases (31%). Remarkably, a recurrent de novo mutation, c.959G>A (p.Arg320His), in KCNC1 was identified as a new major cause for PME. Eleven unrelated exome-sequenced (13%) and two affected individuals in a secondary cohort (7%) had this mutation. KCNC1 encodes KV3.1, a subunit of the KV3 voltage-gated potassium ion channels, which are major determinants of high-frequency neuronal firing. Functional analysis of the Arg320His mutant channel showed a dominant-negative loss-of-function effect. Ten cases had pathogenic mutations in known PME-associated genes (NEU1, NHLRC1, AFG3L2, EPM2A, CLN6 and SERPINI1). Identification of mutations in PRNP, SACS and TBC1D24 expand their phenotypic spectra to PME. These findings provide insights into the molecular genetic basis of PME and show the role of de novo mutations in this disease entity.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Accession codes
Accessions
Ensembl
NCBI Reference Sequence
Change history
09 December 2014
In the version of this article initially published online, the charge signs in the protein model in Figure 2b were incorrectly shifted upward and two charge signs were depicted as being above the protein domain. The error has been corrected for the print, PDF and HTML versions of this article.
References
Berkovic, S.F., Andermann, F., Carpenter, S. & Wolfe, L.S. Progressive myoclonus epilepsies: specific causes and diagnosis. N. Engl. J. Med. 315, 296–305 (1986).
Shahwan, A., Farrell, M. & Delanty, N. Progressive myoclonic epilepsies: a review of genetic and therapeutic aspects. Lancet Neurol. 4, 239–248 (2005).
Franceschetti, S. et al. Progressive myoclonic epilepsies: definitive and still undetermined causes. Neurology 82, 405–411 (2014).
Pennacchio, L.A. et al. Mutations in the gene encoding cystatin B in progressive myoclonus epilepsy (EPM1). Science 271, 1731–1734 (1996).
Berkovic, S.F. et al. Array-based gene discovery with three unrelated subjects shows SCARB2/LIMP-2 deficiency causes myoclonus epilepsy and glomerulosclerosis. Am. J. Hum. Genet. 82, 673–684 (2008).
Dibbens, L.M. et al. SCARB2 mutations in progressive myoclonus epilepsy (PME) without renal failure. Ann. Neurol. 66, 532–536 (2009).
Corbett, M.A. et al. A mutation in the Golgi Qb-SNARE gene GOSR2 causes progressive myoclonus epilepsy with early ataxia. Am. J. Hum. Genet. 88, 657–663 (2011).
Kollmann, K. et al. Cell biology and function of neuronal ceroid lipofuscinosis–related proteins. Biochim. Biophys. Acta 1832, 1866–1881 (2013).
Ramachandran, N., Girard, J.-M., Turnbull, J. & Minassian, B.A. The autosomal recessively inherited progressive myoclonus epilepsies and their genes. Epilepsia 50, 29–36 (2009).
Samocha, K.E. et al. A framework for the interpretation of de novo mutation in human disease. Nat. Genet. 46, 944–950 (2014).
Davis, R.L. et al. Association between conformational mutations in neuroserpin and onset and severity of dementia. Lancet 359, 2242–2247 (2002).
Hsiao, K. et al. Linkage of a prion protein missense variant to Gerstmann-Straussler syndrome. Nature 338, 342–345 (1989).
Baets, J. et al. Mutations in SACS cause atypical and late-onset forms of ARSACS. Neurology 75, 1181–1188 (2010).
Romano, A. et al. Comparative analysis and functional mapping of SACS mutations reveal novel insights into sacsin repeated architecture. Hum. Mutat. 34, 525–537 (2013).
Synofzik, M. et al. Autosomal recessive spastic ataxia of Charlevoix Saguenay (ARSACS): expanding the genetic, clinical and imaging spectrum. Orphanet J. Rare Dis. 8, 41 (2013).
Afawi, Z. et al. TBC1D24 mutation associated with focal epilepsy, cognitive impairment and a distinctive cerebro-cerebellar malformation. Epilepsy Res. 105, 240–244 (2013).
Campeau, P.M. et al. The genetic basis of DOORS syndrome: an exome-sequencing study. Lancet Neurol. 13, 44–58 (2014).
Corbett, M.A. et al. A focal epilepsy and intellectual disability syndrome is due to a mutation in TBC1D24. Am. J. Hum. Genet. 87, 371–375 (2010).
Falace, A. et al. TBC1D24, an ARF6-interacting protein, is mutated in familial infantile myoclonic epilepsy. Am. J. Hum. Genet. 87, 365–370 (2010).
Guven, A. & Tolun, A. TBC1D24 truncating mutation resulting in severe neurodegeneration. J. Med. Genet. 50, 199–202 (2013).
Harkin, L.A. et al. The spectrum of SCN1A-related infantile epileptic encephalopathies. Brain 130, 843–852 (2007).
Claes, L. et al. De novo mutations in the sodium-channel gene SCN1A cause severe myoclonic epilepsy of infancy. Am. J. Hum. Genet. 68, 1327–1332 (2001).
Ried, T. et al. Localization of a highly conserved human potassium channel gene (NGK2-KV4; KCNC1) to chromosome 11p15. Genomics 15, 405–411 (1993).
Waters, M.F. et al. Mutations in voltage-gated potassium channel KCNC3 cause degenerative and developmental central nervous system phenotypes. Nat. Genet. 38, 447–451 (2006).
Figueroa, K.P. et al. KCNC3: phenotype, mutations, channel biophysics—a study of 260 familial ataxia patients. Hum. Mutat. 31, 191–196 (2010).
Figueroa, K.P. et al. Frequency of KCNC3 DNA variants as causes of spinocerebellar ataxia 13 (SCA13). PLoS ONE 6, e17811 (2011).
Németh, A.H. et al. Next generation sequencing for molecular diagnosis of neurological disorders using ataxias as a model. Brain 136, 3106–3118 (2013).
Rudy, B. & McBain, C.J. Kv3 channels: voltage-gated K+ channels designed for high-frequency repetitive firing. Trends Neurosci. 24, 517–526 (2001).
Seoh, S.-A., Sigg, D., Papazian, D.M. & Bezanilla, F. Voltage-sensing residues in the S2 and S4 segments of the Shaker K+ channel. Neuron 16, 1159–1167 (1996).
Aggarwal, S.K. & MacKinnon, R. Contribution of the S4 segment to gating charge in the Shaker K+ channel. Neuron 16, 1169–1177 (1996).
Minassian, N.A., Lin, M.-C.A. & Papazian, D.M. Altered KV3.3 channel gating in early-onset spinocerebellar ataxia type 13. J. Physiol. (Lond.) 590, 1599–1614 (2012).
Moreau, A., Gosselin-Badaroudine, P. & Chahine, M. Biophysics, pathophysiology, and pharmacology of ion channel gating pores. Front. Pharmacol. 5, 53 (2014).
Starace, D.M. & Bezanilla, F. Histidine scanning mutagenesis of basic residues of the S4 segment of the Shaker K+ channel. J. Gen. Physiol. 117, 469–490 (2001).
Ho, C.S., Grange, R.W. & Joho, R.H. Pleiotropic effects of a disrupted K+ channel gene: reduced body weight, impaired motor skill and muscle contraction, but no seizures. Proc. Natl. Acad. Sci. USA 94, 1533–1538 (1997).
Joho, R.H., Ho, C.S. & Marks, G.A. Increased γ- and decreased δ-oscillations in a mouse deficient for a potassium channel expressed in fast-spiking interneurons. J. Neurophysiol. 82, 1855–1864 (1999).
Espinosa, F. et al. Alcohol hypersensitivity, increased locomotion, and spontaneous myoclonus in mice lacking the potassium channels KV3.1 and KV3.3. J. Neurosci. 21, 6657–6665 (2001).
Issa, F.A., Mazzochi, C., Mock, A.F. & Papazian, D.M. Spinocerebellar ataxia type 13 mutant potassium channel alters neuronal excitability and causes locomotor deficits in zebrafish. J. Neurosci. 31, 6831–6841 (2011).
Erisir, A., Lau, D., Rudy, B. & Leonard, C.S. Function of specific K+ channels in sustained high-frequency firing of fast-spiking neocortical interneurons. J. Neurophysiol. 82, 2476–2489 (1999).
Sabatini, B.L. & Regehr, W.G. Control of neurotransmitter release by presynaptic waveform at the granule cell to Purkinje cell synapse. J. Neurosci. 17, 3425–3435 (1997).
Irie, T., Matsuzaki, Y., Sekino, Y. & Hirai, H. KV3.3 channels harbouring a mutation of spinocerebellar ataxia type 13 alter excitability and induce cell death in cultured cerebellar Purkinje cells. J. Physiol. (Lond.) 592, 229–247 (2014).
Gan, L. & Kaczmarek, L.K. When, where, and how much? Expression of the KV3.1 potassium channel in high-frequency firing neurons. J. Neurobiol. 37, 69–79 (1998).
GTEx Consortium. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 45, 580–585 (2013).
Wulff, H., Castle, N.A. & Pardo, L.A. Voltage-gated potassium channels as therapeutic targets. Nat. Rev. Drug Discov. 8, 982–1001 (2009).
Kälviäinen, R. et al. Clinical picture of EPM1-Unverricht-Lundborg disease. Epilepsia 49, 549–556 (2008).
Lehtinen, M.K. et al. Cystatin B deficiency sensitizes neurons to oxidative stress in progressive myoclonus epilepsy, EPM1. J. Neurosci. 29, 5910–5915 (2009).
Okuneva, O. et al. Abnormal microglial activation in the Cstb−/− mouse, a model for progressive myoclonus epilepsy, EPM1. Glia. 10.1002/glia.22760 (18 October 2014)
Buzzi, A. et al. Loss of cortical GABA terminals in Unverricht-Lundborg disease. Neurobiol. Dis. 47, 216–224 (2012).
Joensuu, T. et al. Gene expression alterations in the cerebellum and granule neurons of Cstb−/− mouse are associated with early synaptic changes and inflammation. PLoS ONE 9, e89321 (2014).
Kong, A. et al. Rate of de novo mutations and the importance of father's age to disease risk. Nature 488, 471–475 (2012).
Brooks, N.L., Corey, M.J. & Schwalbe, R.A. Characterization of N-glycosylation consensus sequences in the KV3.1 channel. FEBS J. 273, 3287–3300 (2006).
Hall, M.K., Cartwright, T.A., Fleming, C.M. & Schwalbe, R.A. Importance of glycosylation on function of a potassium channel in neuroblastoma cells. PLoS ONE 6, e19317 (2011).
Bonten, E., van der Spoel, A., Fornerod, M., Grosveld, G. & d'Azzo, A. Characterization of human lysosomal neuraminidase defines the molecular basis of the metabolic storage disorder sialidosis. Genes Dev. 10, 3156–3169 (1996).
Lukong, K.E. et al. Characterization of the sialidase molecular defects in sialidosis patients suggests the structural organization of the lysosomal multienzyme complex. Hum. Mol. Genet. 9, 1075–1085 (2000).
Canafoglia, L. et al. Expanding sialidosis spectrum by genome-wide screening: NEU1 mutations in adult-onset myoclonus. Neurology 82, 2003–2006 (2014).
Chan, E.M. et al. Mutations in NHLRC1 cause progressive myoclonus epilepsy. Nat. Genet. 35, 125–127 (2003).
Leutenegger, A.-L. et al. Estimation of the inbreeding coefficient through use of genomic data. Am. J. Hum. Genet. 73, 516–523 (2003).
Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
DePristo, M.A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
McLaren, W. et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069–2070 (2010).
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).
Kent, W.J. et al. The Human Genome Browser at UCSC. Genome Res. 12, 996–1006 (2002).
Kircher, M. et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet. 46, 310–315 (2014).
Adzhubei, I.A. et al. A method and server for predicting damaging missense mutations. Nat. Methods 7, 248–249 (2010).
Kumar, P., Henikoff, S. & Ng, P.C. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat. Protoc. 4, 1073–1081 (2009).
Schwarz, J.M., Rodelsperger, C., Schuelke, M. & Seelow, D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat. Methods 7, 575–576 (2010).
Liu, X., Jian, X. & Boerwinkle, E. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum. Mutat. 34, E2393–E2402 (2013).
1000 Genomes Project Consortium. An integrated map of genetic variation from 1,092 human genomes. Nature 491, 56–65 (2012).
Browning, B.L. & Browning, S.R. Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics 194, 459–471 (2013).
Robinson, J.T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
Hamosh, A., Scott, A.F., Amberger, J.S., Bocchini, C.A. & McKusick, V.A. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 33, D514–D517 (2005).
Lemke, J.R. et al. Targeted next generation sequencing as a diagnostic tool in epileptic disorders. Epilepsia 53, 1387–1398 (2012).
Petrovski, S., Wang, Q., Heinzen, E.L., Allen, A.S. & Goldstein, D.B. Genic intolerance to functional variation and the interpretation of personal genomes. PLoS Genet. 9, e1003709 (2013).
Fuentes Fajardo, K.V. et al. Detecting false-positive signals in exome sequencing. Hum. Mutat. 33, 609–613 (2012).
UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 42, D191–D198 (2014).
Shoffner, J.M. et al. Myoclonic epilepsy and ragged-red fiber disease (MERRF) is associated with a mitochondrial DNA tRNALys mutation. Cell 61, 931–937 (1990).
Ye, J. et al. Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics 13, 134 (2012).
Gu, Y., Barry, J., McDougel, R., Terman, D. & Gu, C. Alternative splicing regulates KV3.1 polarized targeting to adjust maximal spiking frequency. J. Biol. Chem. 287, 1755–1769 (2012).
Acknowledgements
We thank the patients and family members who contributed samples for the purpose of this study. We also thank the following for patient referrals: K. Joost, K. Carvalho, C. Marques Lourenco, P. Cossette, A. Covanis, A. Parmeggiani, P. Van Bogaert, S. Mole, A. Sierra Marcos, M. Carreno and S.S. Rich. We thank P. Hakala, E. Hämäläinen, B. Johns, R. Schulz, J. Damiano, H. Löffler and N. Jezutkovic for sample logistics and technical assistance in the laboratory, C. Scott and J. Durham (Wellcome Trust Sanger Institute) for exome sequence processing, P. Gormley, B. Winsvold and P. Palta for assistance in exome data analysis, and A. Farooq Bazai for support. CSC–IT Center for Science, Ltd., is acknowledged for the allocation of computational resources.
This study was supported by the Folkhälsan Research Foundation (A.-E.L.), Academy of Finland grant 141549 (A.-E.L.), Wellcome Trust grants 089062 and 098051 (A.P.), European Commission Framework Programme 7 (FP7) project 201413 ENGAGE (A.P.), project 242167 SynSys (A.P.), Health-2010 projects 261433 BioSHare (A.P.) and project 261123 gEUVADIS (A.P.), Academy of Finland grants 251704 and 263401 (A.P.), the Sigrid Juselius Foundation (A.P.), US NIH grant RFA-HL-12-007 (A.P.), the Emil Aaltonen Foundation (M.M.), Epilepsiatutkimussäätiö (M.M.), University of Helsinki Funds (M.M.), the Doctoral Programme in Biomedicine (M.M.), National Health and Medical Research Council (NHMRC) of Australia program grant 628952 (S.F.B., L.M.D. and I.E.S.), NHMRC Career Development Fellowship 1032603 (L.M.D.), NHMRC Early Career Fellowship 1016715 (S.E.H.), the German Network for Rare Diseases of the Federal Ministry of Education and Research (BMBF), IonNeurONet 01GM1105A (S. Maljevic and H.L.), the EuroEPINOMICS program of the European Science Foundation, German Research Foundation (DFG) grant Le1030/11-1 (H.L. and S. Maljevic), NHMRC program grant 400121 (S.P.) and NMHRC fellowship 1005050 (S.P.). The Florey Institute of Neuroscience and Mental Health (S.P.) is supported by government infrastructure funds from the state of Victoria.
Author information
Authors and Affiliations
Contributions
Study design and management: S.F.B., L.M.D., A.P. and A.-E.L. Coordination of the collection of study subjects and clinical data: S.F.B., K.L.O., M.A.B. and A.-E.L. Subject ascertainment and phenotyping: S.F.B., K.L.O., L.C., S.F., R.M., E.A., F.A., A.G., P.T., L.L., I.E.S., C.C., A.F., E.F., J.A., A.A., B.B., E.S., M.T., P.R., M.D.K., C.O., D.M.A., B.A.E., A.C., M.L., E.L., V.S., J.M., M.P., A.J.E., B.K., M.D., R.S.M., R.S., Z.A. and B.B.-Z. Analysis of the exome sequencing data: M.M. and S. Markkinen. Sanger sequencing, sequence data analysis and mosaicism analysis: M.M., M.A.B., T.J., S.E.H. and M.S.H. Interpretation of genetic data: M.M., S.F.B., L.M.D., A.P. and A.-E.L. Evaluation of the mutation rate in KCNC1: K.E.S. and M.J.D. Functional analysis and interpretation: S. Maljevic, S.P. and H.L. Manuscript writing: M.M., S.F.B., L.M.D., K.L.O., S. Maljevic, H.L., A.P. and A.-E.L. All authors critically revised the manuscript.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
Integrated supplementary information
Supplementary Figure 1 Visualization of sequence reads at the c.959G>A mutation site in KCNC1.
The mutation is between the vertical dashed lines. Snapshots were taken using the Integrative Genomics Viewer1.
Supplementary Figure 2 Sanger sequencing chromatograms of one of the case-parent trios with the de novo c.959G>A mutation in KCNC1.
The mutation is indicated by an arrow. Chromatograms for the other Sanger-sequenced trios with the KCNC1 mutation are similar.
Supplementary Figure 3 Segregation of pathogenic or probably pathogenic mutations in known PME, epilepsy or neurodegenerative disease genes.
Subject IDs for the exome-sequenced cases are presented. n.d., not determined.
Supplementary Figure 4 Multiple-sequence alignments at sites with novel pathogenic missense mutations in the known PME genes.
The novel mutations in (a) NEU1, (b) NHLRC1, (c) EPM2A, (d) CLN6 and (e) AFG3L2 identified in this study are presented above the alignments. Previously reported disease-associated missense mutations obtained from the literature are shown below the alignments. Gene homologs and amino acid sequences were obtained from NCBI HomoloGene. Alignments were performed using ClustalX2. Asterisks, colons and periods indicate positions with fully conserved, strongly similar and weakly similar residues, respectively. ClustalX default coloring was used to group amino acids with similar properties. The domain structure of AFG3L2 (ref. 3) is also presented (bottom in e). Mutation references are as follows. NEU1: R294S4; A298V5,6; R305C7; and P316S8. NHLRC1: L279P9 and E280K10. EPM2A: T187A11; A188G12; T194I13,14; and E210K9. CLN6: L169P15 and Y172del16. AFG3L2: Y616C17; N432T, S674H, E691K, A694E and R702Q3; T654I, M666R, M666T, M666V, G671R and G671E18; Y689H19; and E700K20.
Supplementary Figure 5 Multiple-sequence alignments at sites with probably pathogenic missense mutations in SACS and TBC1D24.
The mutations identified in (a) SACS and (b) TBC1D24 in this study are presented above the alignments. Previously reported disease-associated missense mutations obtained from the literature are presented below the alignments. Gene homologs and amino acid sequences were obtained and alignments were performed as described in Supplementary Figure 4. The domain structure of TBC1D24 (ref. 21) is presented in b. Mutation references are as follows. SACS: T458I22,23; R474C22; C991R and P2798Q24; and V995F23. TBC1D24: Q20E, R40C, R40L, G110C, R242C and L333F25; D70Y and R293P21; D147H and A515V26; F229C27; and F251L28.
Supplementary information
Combined Supplementary PDF
Supplementary Figures 1–5 and Supplementary Note. (PDF 1766 kb)
Supplementary Tables 1–8
Supplementary Tables 1–8. (XLSX 135 kb)
Source data
Rights and permissions
About this article
Cite this article
Muona, M., Berkovic, S., Dibbens, L. et al. A recurrent de novo mutation in KCNC1 causes progressive myoclonus epilepsy. Nat Genet 47, 39–46 (2015). https://doi.org/10.1038/ng.3144
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/ng.3144
This article is cited by
-
Single-cell RNA sequencing in donor and end-stage heart failure patients identifies NLRP3 as a therapeutic target for arrhythmogenic right ventricular cardiomyopathy
BMC Medicine (2024)
-
Investigation of a novel TBC1D24 variation causing autosomal dominant non-syndromic hearing loss
Scientific Reports (2024)
-
Overexpression of KCNN4 channels in principal neurons produces an anti-seizure effect without reducing their coding ability
Gene Therapy (2024)
-
Whole-Exome Sequencing Analysis of Idiopathic Hypogonadotropic Hypogonadism: Comparison of Varicocele and Nonobstructive Azoospermia
Reproductive Sciences (2024)
-
A Heterozygous Phospholamban Variant (p.R14del) Leads to Left Ventricular Involvement and Heart Failure Phenotypes in Arrhythmogenic Right Ventricular Cardiomyopathy
Phenomics (2024)
