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2. Genetic pain loss disorders

Author

Lischka, Annette, Lassuthova, Petra, Çakar, Arman, Record, Christopher J., Van Lent, Jonas, Baets, Jonathan, Dohrn, Maike F., Senderek, Jan, Lampert, Angelika, Bennett, David L., Wood, John N., Timmerman, Vincent, Hornemann, Thorsten, Auer-Grumbach, Michaela, Parman, Yesim, Hübner, Christian A., Elbracht, Miriam, Eggermann, Katja, Geoffrey Woods, C., Cox, James J., Reilly, Mary M., and Kurth, Ingo

Published
2022
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9. The genetic landscape of axonal neuropathies in the middle-aged and elderly: Focus on MME

Author

Senderek, Jan, Lassuthova, Petra, Kabzińska, Dagmara, Abreu, Lisa, Baets, Jonathan, Beetz, Christian, Braathen, Geir J., Brenner, David, Dalton, Joline, Dankwa, Lois, Deconinck, Tine, De Jonghe, Peter, Dräger, Bianca, Eggermann, Katja, Ellis, Melina, Fischer, Carina, Stojkovic, Tanya, Herrmann, David N., Horvath, Rita, Høyer, Helle, Iglseder, Stephan, Kennerson, Marina, Kinslechner, Katharina, Kohler, Jennefer N., Kurth, Ingo, Laing, Nigel G., Lamont, Phillipa J., N. Löscher, Wolfgang, Ludolph, Albert, Marques, Wilson, Jr, Nicholson, Garth, Ong, Royston, Petri, Susanne, Ravenscroft, Gianina, Rebelo, Adriana, Ricci, Giulia, Rudnik-Schöneborn, Sabine, Schirmacher, Anja, Schlotter-Weigel, Beate, Schoels, Ludger, Schüle, Rebecca, Synofzik, Matthis, Francou, Bruno, Strom, Tim M., Wagner, Johannes, Walk, David, Wanschitz, Julia, Weinmann, Daniela, Weishaupt, Jochen, Wiessner, Manuela, Windhager, Reinhard, Young, Peter, Züchner, Stephan, Toegel, Stefan, Seeman, Pavel, Kochański, Andrzej, and Auer-Grumbach, Michaela

Published
2020
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11. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author

Johannesen, Katrine Marie, Liu, Yuanyuan, Gjerulfsen, Catherine E., Koko, Mahmoud, Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina Duhring, Eltokhi, Ahmed, Rannap, Maert, Koch, Nils, Lauxmann, Stephan, Krueger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthova, Petra, Vlckova, Marketa, Lemke, Johannes, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell, Judith, Lund, Caroline, Klein, Karl Martin, Au, Py Billie, Rho, Jong, Ho, Alice, Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoi-Hansen, Christina, Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S., van der Zwaag, Bert, Harder, Aster, Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastien, Vaccarezza, Maria, Le, Ngoc Minh, Christensen, Jakob, Schmidt-Petersen, Mette, Gronborg, Sabine, Scherer, Stephen, Howe, Jennifer, Fazeli, Walid, Howell, Katherine, Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Benedicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vollo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caumes, Roseline, Roubertie, Agathe, Gelisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Koch-Hogrebe, Margarete, Perry, Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann, Mueller-Schlueter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destree, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddarth, Tan, Wen-Hann, Olson, Heather, Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark, Goldberg, Ethan M., Roser, Timo, Borggrafe, Ingo, Brunger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Lesca, Gaetan, Hedrich, Ulrike, Benda, Jan, Gardella, Elena, Lerche, Holger, and Moeller, Rikke Steensbjerre

Published
2021
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12. Loss of function mutations in HARS cause a spectrum of inherited peripheral neuropathies

Author

Safka Brozkova, Dana, Deconinck, Tine, Beth Griffin, Laurie, Ferbert, Andreas, Haberlova, Jana, Mazanec, Radim, Lassuthova, Petra, Roth, Christian, Pilunthanakul, Thanita, Rautenstrauss, Bernd, Janecke, Andreas R., Zavadakova, Petra, Chrast, Roman, Rivolta, Carlo, Zuchner, Stephan, Antonellis, Anthony, Beg, Asim A., De Jonghe, Peter, Senderek, Jan, Seeman, Pavel, and Baets, Jonathan

Published
2015
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13. The Cause of Hereditary Hearing Loss in GJB2 Heterozygotes—A Comprehensive Study of the GJB2/DFNB1 Region

Author

Safka Brozkova, Dana, primary, Uhrova Meszarosova, Anna, additional, Lassuthova, Petra, additional, Varga, Lukáš, additional, Staněk, David, additional, Borecká, Silvia, additional, Laštůvková, Jana, additional, Čejnová, Vlasta, additional, Rašková, Dagmar, additional, Lhota, Filip, additional, Gašperíková, Daniela, additional, and Seeman, Pavel, additional

Published
2021
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14. Prot2HG: a database of protein domains mapped to the human genome

Author

Stanek, David, Bis-Brewer, Dana M, Saghira, Cima, Danzi, Matt C, Seeman, Pavel, Lassuthova, Petra, and Zuchner, Stephan

Subjects
Internet, Database Tool, Protein Domains, Genome, Human, Databases, Genetic, Computational Biology, Data Mining, Genetic Variation, Humans, Proteins, Molecular Sequence Annotation, Genomics, Data Curation
Abstract

Genetic variation occurring within conserved functional protein domains warrants special attention when examining DNA variation in the context of disease causation. Here we introduce a resource, freely available at www.prot2hg.com, that addresses the question of whether a particular variant falls onto an annotated protein domain and directly translates chromosomal coordinates onto protein residues. The tool can perform a multiple-site query in a simple way, and the whole dataset is available for download as well as incorporated into our own accessible pipeline. To create this resource, National Center for Biotechnology Information protein data were retrieved using the Entrez Programming Utilities. After processing all human protein domains, residue positions were reverse translated and mapped to the reference genome hg19 and stored in a MySQL database. In total, 760 487 protein domains from 42 371 protein models were mapped to hg19 coordinates and made publicly available for search or download (www.prot2hg.com). In addition, this annotation was implemented into the genomics research platform GENESIS in order to query nearly 8000 exomes and genomes of families with rare Mendelian disorders (tgp-foundation.org). When applied to patient genetic data, we found that rare (1%) variants. Similarly, variants described as pathogenic or likely pathogenic in ClinVar were more likely to be annotated onto a domain. In addition, we tested a dataset consisting of 60 causal variants in a cohort of patients with epileptic encephalopathy and found that 71% of them (43 variants) were propagated onto protein domains. In summary, we developed a resource that annotates variants in the coding part of the genome onto conserved protein domains in order to increase variant prioritization efficiency. Database URL: www.prot2hg.com

Published
2020

15. PURA syndrome : clinical delineation and genotype-phenotype study in 32 individuals with review of published literature

Author

Reijnders, Margot R. F., Janowski, Robert, Alvi, Mohsan, Self, Jay E., van Essen, Ton J., Vreeburg, Maaike, Rouhl, Rob P. W., Stevens, Servi J. C., Stegmann, Alexander P. A., Schieving, Jolanda, Pfundt, Rolph, van Dijk, Katinke, Smeets, Eric, Stumpel, Connie T. R. M., Bok, Levinus A., Cobben, Jan Maarten, Engelen, Marc, Mansour, Sahar, Whiteford, Margo, Chandler, Kate E., Douzgou, Sofia, Cooper, Nicola S., Tan, Ene-Choo, Foo, Roger, Lai, Angeline H. M., Rankin, Julia, Green, Andrew, Lönnqvist, Tuula, Isohanni, Pirjo, Williams, Shelley, Ruhoy, Ilene, Carvalho, Karen S., Dowling, James J., Lev, Dorit L., Sterbova, Katalin, Lassuthova, Petra, Neupauerova, Jana, Waugh, Jeff L., Keros, Sotirios, Clayton-Smith, Jill, Smithson, Sarah F., Brunner, Han G., van Hoeckel, Ceciel, Anderson, Mel, Clowes, Virginia E., Siu, Victoria Mok, Selber, Paulo, Leventer, Richard J., Nellaker, Christoffer, Niessing, Dierk, DDD Study, Clinicum, Children's Hospital, Lastenneurologian yksikkö, University of Helsinki, Research Programs Unit, Anu Wartiovaara / Principal Investigator, Research Programme for Molecular Neurology, and HUS Children and Adolescents

Subjects
ALPHA, GENES, REVEALS, 3112 Neurosciences, PATIENT, 5Q31.3 MICRODELETION SYNDROME, 3124 Neurology and psychiatry, POSTNATAL BRAIN-DEVELOPMENT
Abstract

Background De novo mutations in PURA have recently been described to cause PURA syndrome, a neurodevelopmental disorder characterised by severe intellectual disability (ID), epilepsy, feeding difficulties and neonatal hypotonia. Objectives T o delineate the clinical spectrum of PURA syndrome and study genotype-phenotype correlations. Methods Diagnostic or research-based exome or Sanger sequencing was performed in individuals with ID. We systematically collected clinical and mutation data on newly ascertained PURA syndrome individuals, evaluated data of previously reported individuals and performed a computational analysis of photographs. We classified mutations based on predicted effect using 3D in silico models of crystal structures of Drosophila-derived Pur-alpha homologues. Finally, we explored genotypephenotype correlations by analysis of both recurrent mutations as well as mutation classes. Results We report mutations in PURA (purine-rich element binding protein A) in 32 individuals, the largest cohort described so far. Evaluation of clinical data, including 22 previously published cases, revealed that all have moderate to severe ID and neonatal-onset symptoms, including hypotonia (96%), respiratory problems (57%), feeding difficulties (77%), exaggerated startle response (44%), hypersomnolence (66%) and hypothermia (35%). Epilepsy (54%) and gastrointestinal (69%), ophthalmological (51%) and endocrine problems (42%) were observed frequently. Computational analysis of facial photographs showed subtle facial dysmorphism. No strong genotype-phenotype correlation was identified by subgrouping mutations into functional classes. Conclusion We delineate the clinical spectrum of PURA syndrome with the identification of 32 additional individuals. The identification of one individual through targeted Sanger sequencing points towards the clinical recognisability of the syndrome. Genotype-phenotype analysis showed no significant correlation between mutation classes and disease severity.

Published
2018

16. Mutations in ATP1A1 Cause Dominant Charcot-Marie-Tooth Type 2

Author

Lassuthova, Petra, primary, Rebelo, Adriana P., additional, Ravenscroft, Gianina, additional, Lamont, Phillipa J., additional, Davis, Mark R., additional, Manganelli, Fiore, additional, Feely, Shawna M., additional, Bacon, Chelsea, additional, Brožková, Dana Šafka, additional, Haberlova, Jana, additional, Mazanec, Radim, additional, Tao, Feifei, additional, Saghira, Cima, additional, Abreu, Lisa, additional, Courel, Steve, additional, Powell, Eric, additional, Buglo, Elena, additional, Bis, Dana M., additional, Baxter, Megan F., additional, Ong, Royston W., additional, Marns, Lorna, additional, Lee, Yi-Chung, additional, Bai, Yunhong, additional, Isom, Daniel G., additional, Barro-Soria, René, additional, Chung, Ki W., additional, Scherer, Steven S., additional, Larsson, H. Peter, additional, Laing, Nigel G., additional, Choi, Byung-Ok, additional, Seeman, Pavel, additional, Shy, Michael E., additional, Santoro, Lucio, additional, and Zuchner, Stephan, additional

Published
2018
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17. Loss of function mutations in HARS cause a spectrum of inherited peripheral neuropathies

Author

Safka Brozkova, Dana, Deconinck, Tine, Beth Griffin, Laurie, Ferbert, Andreas, Haberlova, Jana, Mazanec, Radim, Lassuthova, Petra, Roth, Christian, Pilunthanakul, Thanita, Rautenstrauss, Bernd, Janecke, Andreas R., Zavadakova, Petra, Chrast, Roman, Rivolta, Carlo, Zuchner, Stephan, Antonellis, Anthony, Beg, Asim A., De Jonghe, Peter, Senderek, Jan, Seeman, Pavel, Baets, Jonathan, Safka Brozkova, Dana, Deconinck, Tine, Beth Griffin, Laurie, Ferbert, Andreas, Haberlova, Jana, Mazanec, Radim, Lassuthova, Petra, Roth, Christian, Pilunthanakul, Thanita, Rautenstrauss, Bernd, Janecke, Andreas R., Zavadakova, Petra, Chrast, Roman, Rivolta, Carlo, Zuchner, Stephan, Antonellis, Anthony, Beg, Asim A., De Jonghe, Peter, Senderek, Jan, Seeman, Pavel, and Baets, Jonathan

Abstract

Using linkage analysis and whole-exome sequencing, Safka Brozkova et al. reveal missense mutations in the histidyl-tRNA synthetase gene in 23 patients from four families with axonal and demyelinating neuropathies of varying severity. The mutations cause loss of function in yeast complementation assays and neurotoxicity in a C. elegans model

Published
2017

18. PURA syndrome: clinical delineation and genotype-phenotype study in 32 individuals with review of published literature

Author

Reijnders, Margot R F, primary, Janowski, Robert, additional, Alvi, Mohsan, additional, Self, Jay E, additional, van Essen, Ton J, additional, Vreeburg, Maaike, additional, Rouhl, Rob P W, additional, Stevens, Servi J C, additional, Stegmann, Alexander P A, additional, Schieving, Jolanda, additional, Pfundt, Rolph, additional, van Dijk, Katinke, additional, Smeets, Eric, additional, Stumpel, Connie T R M, additional, Bok, Levinus A, additional, Cobben, Jan Maarten, additional, Engelen, Marc, additional, Mansour, Sahar, additional, Whiteford, Margo, additional, Chandler, Kate E, additional, Douzgou, Sofia, additional, Cooper, Nicola S, additional, Tan, Ene-Choo, additional, Foo, Roger, additional, Lai, Angeline H M, additional, Rankin, Julia, additional, Green, Andrew, additional, Lönnqvist, Tuula, additional, Isohanni, Pirjo, additional, Williams, Shelley, additional, Ruhoy, Ilene, additional, Carvalho, Karen S, additional, Dowling, James J, additional, Lev, Dorit L, additional, Sterbova, Katalin, additional, Lassuthova, Petra, additional, Neupauerová, Jana, additional, Waugh, Jeff L, additional, Keros, Sotirios, additional, Clayton-Smith, Jill, additional, Smithson, Sarah F, additional, Brunner, Han G, additional, van Hoeckel, Ceciel, additional, Anderson, Mel, additional, Clowes, Virginia E, additional, Siu, Victoria Mok, additional, DDD study, The, additional, Selber, Paulo, additional, Leventer, Richard J, additional, Nellaker, Christoffer, additional, Niessing, Dierk, additional, Hunt, David, additional, and Baralle, Diana, additional

Published
2017
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19. Loss of function mutations inHARScause a spectrum of inherited peripheral neuropathies

Author

Safka Brozkova, Dana, primary, Deconinck, Tine, additional, Beth Griffin, Laurie, additional, Ferbert, Andreas, additional, Haberlova, Jana, additional, Mazanec, Radim, additional, Lassuthova, Petra, additional, Roth, Christian, additional, Pilunthanakul, Thanita, additional, Rautenstrauss, Bernd, additional, Janecke, Andreas R., additional, Zavadakova, Petra, additional, Chrast, Roman, additional, Rivolta, Carlo, additional, Zuchner, Stephan, additional, Antonellis, Anthony, additional, Beg, Asim A., additional, De Jonghe, Peter, additional, Senderek, Jan, additional, Seeman, Pavel, additional, and Baets, Jonathan, additional

Published
2015
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22. PURA syndrome: clinical delineation and genotype-phenotype study in 32 individuals with review of published literature

Author

Reijnders, Margot R F, Janowski, Robert, Alvi, Mohsan, Self, Jay E, van Essen, Ton J, Vreeburg, Maaike, Rouhl, Rob P W, Stevens, Servi J C, Stegmann, Alexander P A, Schieving, Jolanda, Pfundt, Rolph, van Dijk, Katinke, Smeets, Eric, Stumpel, Connie T R M, Bok, Levinus A, Cobben, Jan Maarten, Engelen, Marc, Mansour, Sahar, Whiteford, Margo, Chandler, Kate E, Douzgou, Sofia, Cooper, Nicola S, Tan, Ene-Choo, Foo, Roger, Lai, Angeline H M, Rankin, Julia, Green, Andrew, Lonnqvist, Tuula, Isohanni, Pirjo, Williams, Shelley, Ruhoy, Ilene, Carvalho, Karen S, Dowling, James J, Lev, Dorit L, Sterbova, Katalin, Lassuthova, Petra, Neupauerová, Jana, Waugh, Jeff L, Keros, Sotirios, Clayton-Smith, Jill, Smithson, Sarah F, Brunner, Han G, van Hoeckel, Ceciel, Anderson, Mel, Clowes, Virginia E, Siu, Victoria Mok, DDD study, The, Selber, Paulo, Leventer, Richard J, Nellaker, Christoffer, Niessing, Dierk, Hunt, David, and Baralle, Diana

Abstract

BackgroundDe novo mutations in PURAhave recently been described to cause PURA syndrome, a neurodevelopmental disorder characterised by severe intellectual disability (ID), epilepsy, feeding difficulties and neonatal hypotonia.ObjectivesTo delineate the clinical spectrum of PURA syndrome and study genotype-phenotype correlations.MethodsDiagnostic or research-based exome or Sanger sequencing was performed in individuals with ID. We systematically collected clinical and mutation data on newly ascertained PURA syndrome individuals, evaluated data of previously reported individuals and performed a computational analysis of photographs. We classified mutations based on predicted effect using 3D in silico models of crystal structures of Drosophila-derived Pur-alpha homologues. Finally, we explored genotype-phenotype correlations by analysis of both recurrent mutations as well as mutation classes.ResultsWe report mutations in PURA(purine-rich element binding protein A) in 32 individuals, the largest cohort described so far. Evaluation of clinical data, including 22 previously published cases, revealed that all have moderate to severe ID and neonatal-onset symptoms, including hypotonia (96%), respiratory problems (57%), feeding difficulties (77%), exaggerated startle response (44%), hypersomnolence (66%) and hypothermia (35%). Epilepsy (54%) and gastrointestinal (69%), ophthalmological (51%) and endocrine problems (42%) were observed frequently. Computational analysis of facial photographs showed subtle facial dysmorphism. No strong genotype-phenotype correlation was identified by subgrouping mutations into functional classes.ConclusionWe delineate the clinical spectrum of PURA syndrome with the identification of 32 additional individuals. The identification of one individual through targeted Sanger sequencing points towards the clinical recognisability of the syndrome. Genotype-phenotype analysis showed no significant correlation between mutation classes and disease severity.

Published
2018
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23. Loss of function mutations in HARS cause a spectrum of inherited peripheral neuropathies.

Author

Brozkova, Dana Safka, Deconinck, Tine, Griffin, Laurie Beth, Ferbert, Andreas, Haberlova, Jana, Mazanec, Radim, Lassuthova, Petra, Roth, Christian, Pilunthanakul, Thanita, Rautenstrauss, Bernd, Janecke, Andreas R., Zavadakova, Petra, Chrast, Roman, Rivolta, Carlo, Zuchner, Stephan, Antonellis, Anthony, Beg, Asim A., De Jonghe, Peter, Senderek, Jan, and Seeman, Pavel

Abstract

Inherited peripheral neuropathies are a genetically heterogeneous group of disorders characterized by distal muscle weakness and sensory loss. Mutations in genes encoding aminoacyl-tRNA synthetases have been implicated in peripheral neuropathies, suggesting that these tRNA charging enzymes are uniquely important for the peripheral nerve. Recently, a mutation in histidyl-tRNA synthetase (HARS) was identified in a single patient with a late-onset, sensory-predominant peripheral neuropathy; however, the genetic evidence was lacking, making the significance of the finding unclear. Here, we present clinical, genetic, and functional data that implicate HARS mutations in inherited peripheral neuropathies. The associated phenotypic spectrum is broad and encompasses axonal and demyelinating motor and sensory neuropathies, including four young patients presenting with pure motor axonal neuropathy. Genome-wide linkage studies in combination with whole-exome and conventional sequencing revealed four distinct and previously unreported heterozygous HARS mutations segregating with autosomal dominant peripheral neuropathy in four unrelated families (p.Thr132Ile, p.Pro134His, p.Asp175Glu and p.Asp364Tyr). All mutations cause a loss of function in yeast complementation assays, and p.Asp364Tyr is dominantly neurotoxic in a Caenorhabditis elegans model. This study demonstrates the role of HARS mutations in peripheral neuropathy and expands the genetic and clinical spectrum of aminoacyl-tRNA synthetase-related human disease. [ABSTRACT FROM AUTHOR]

Published
2015
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24. The Cause of Hereditary Hearing Loss in GJB2 Heterozygotes—A Comprehensive Study of the GJB2 /DFNB1 Region.

Author

Safka Brozkova, Dana, Uhrova Meszarosova, Anna, Lassuthova, Petra, Varga, Lukáš, Staněk, David, Borecká, Silvia, Laštůvková, Jana, Čejnová, Vlasta, Rašková, Dagmar, Lhota, Filip, Gašperíková, Daniela, Seeman, Pavel, and Fischer, Judith

Subjects
HEARING disorders, GENETIC carriers, MOLECULAR probes, PERIODONTAL probe
Abstract

Hearing loss is a genetically heterogeneous sensory defect, and the frequent causes are biallelic pathogenic variants in the GJB2 gene. However, patients carrying only one heterozygous pathogenic (monoallelic) GJB2 variant represent a long-lasting diagnostic problem. Interestingly, previous results showed that individuals with a heterozygous pathogenic GJB2 variant are two times more prevalent among those with hearing loss compared to normal-hearing individuals. This excess among patients led us to hypothesize that there could be another pathogenic variant in the GJB2 region/DFNB1 locus. A hitherto undiscovered variant could, in part, explain the cause of hearing loss in patients and would mean reclassifying them as patients with GJB2 biallelic pathogenic variants. In order to detect an unknown causal variant, we examined 28 patients using NGS with probes that continuously cover the 0.4 Mb in the DFNB1 region. An additional 49 patients were examined by WES to uncover only carriers. We did not reveal a second pathogenic variant in the DFNB1 region. However, in 19% of the WES-examined patients, the cause of hearing loss was found to be in genes other than the GJB2. We present evidence to show that a substantial number of patients are carriers of the GJB2 pathogenic variant, albeit only by chance. [ABSTRACT FROM AUTHOR]

Published
2021
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25. Genotype-phenotype correlations in SCN8A-related disorders reveal prognostic and therapeutic implications

Author

Johannesen, Katrine M., Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E., Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krueger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthova, Petra, Vlckova, Marketa, Lemke, Johannes R., Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Au, P. Y. Billie, Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S., Braakman, Hilde M. H., van der Zwaag, Bert, Harder, Aster V. E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Christensen, Jakob, Gronborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Benedicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vollo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gelisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Muller-Schluter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destree, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brunger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O., Lesca, Gaetan, Hedrich, Ulrike B. S., Benda, Jan, Gardella, Elena, Lerche, Holger, Moller, Rikke S., Johannesen, Katrine M., Liu, Yuanyuan, Koko, Mahmoud, Gjerulfsen, Cathrine E., Sonnenberg, Lukas, Schubert, Julian, Fenger, Christina D., Eltokhi, Ahmed, Rannap, Maert, Koch, Nils A., Lauxmann, Stephan, Krueger, Johanna, Kegele, Josua, Canafoglia, Laura, Franceschetti, Silvana, Mayer, Thomas, Rebstock, Johannes, Zacher, Pia, Ruf, Susanne, Alber, Michael, Sterbova, Katalin, Lassuthova, Petra, Vlckova, Marketa, Lemke, Johannes R., Platzer, Konrad, Krey, Ilona, Heine, Constanze, Wieczorek, Dagmar, Kroell-Seger, Judith, Lund, Caroline, Klein, Karl Martin, Au, P. Y. Billie, Rho, Jong M., Ho, Alice W., Masnada, Silvia, Veggiotti, Pierangelo, Giordano, Lucio, Accorsi, Patrizia, Hoei-Hansen, Christina E., Striano, Pasquale, Zara, Federico, Verhelst, Helene, Verhoeven, Judith S., Braakman, Hilde M. H., van der Zwaag, Bert, Harder, Aster V. E., Brilstra, Eva, Pendziwiat, Manuela, Lebon, Sebastian, Vaccarezza, Maria, Christensen, Jakob, Gronborg, Sabine, Scherer, Stephen W., Howe, Jennifer, Fazeli, Walid, Howell, Katherine B., Leventer, Richard, Stutterd, Chloe, Walsh, Sonja, Gerard, Marion, Gerard, Benedicte, Matricardi, Sara, Bonardi, Claudia M., Sartori, Stefano, Berger, Andrea, Hoffman-Zacharska, Dorota, Mastrangelo, Massimo, Darra, Francesca, Vollo, Arve, Motazacker, M. Mahdi, Lakeman, Phillis, Nizon, Mathilde, Betzler, Cornelia, Altuzarra, Cecilia, Caume, Roseline, Roubertie, Agathe, Gelisse, Philippe, Marini, Carla, Guerrini, Renzo, Bilan, Frederic, Tibussek, Daniel, Koch-Hogrebe, Margarete, Perry, M. Scott, Ichikawa, Shoji, Dadali, Elena, Sharkov, Artem, Mishina, Irina, Abramov, Mikhail, Kanivets, Ilya, Korostelev, Sergey, Kutsev, Sergey, Wain, Karen E., Eisenhauer, Nancy, Wagner, Monisa, Savatt, Juliann M., Muller-Schluter, Karen, Bassan, Haim, Borovikov, Artem, Nassogne, Marie-Cecile, Destree, Anne, Schoonjans, An-Sofie, Meuwissen, Marije, Buzatu, Marga, Jansen, Anna, Scalais, Emmanuel, Srivastava, Siddharth, Tan, Wen-Hann, Olson, Heather E., Loddenkemper, Tobias, Poduri, Annapurna, Helbig, Katherine L., Helbig, Ingo, Fitzgerald, Mark P., Goldberg, Ethan M., Roser, Timo, Borggraefe, Ingo, Brunger, Tobias, May, Patrick, Lal, Dennis, Lederer, Damien, Rubboli, Guido, Heyne, Henrike O., Lesca, Gaetan, Hedrich, Ulrike B. S., Benda, Jan, Gardella, Elena, Lerche, Holger, and Moller, Rikke S.

Abstract

We report detailed functional analyses and genotype-phenotype correlations in 392 individuals carrying disease-causing variants in SCN8A, encoding the voltage-gated Na+ channel Na(v)1.6, with the aim of describing clinical phenotypes related to functional effects. Six different clinical subgroups were identified: Group 1, benign familial infantile epilepsy (n = 15, normal cognition, treatable seizures); Group 2, intermediate epilepsy (n = 33, mild intellectual disability, partially pharmaco-responsive); Group 3, developmental and epileptic encephalopathy (n = 177, severe intellectual disability, majority pharmaco-resistant); Group 4, generalized epilepsy (n = 20, mild to moderate intellectual disability, frequently with absence seizures); Group 5, unclassifiable epilepsy (n = 127); and Group 6, neurodevelopmental disorder without epilepsy (n = 20, mild to moderate intellectual disability). Those in Groups 1-3 presented with focal or multifocal seizures (median age of onset: 4 months) and focal epileptiform discharges, whereas the onset of seizures in patients with generalized epilepsy was later (median: 42 months) with generalized epileptiform discharges. We performed functional studies expressing missense variants in ND7/23 neuroblastoma cells and primary neuronal cultures using recombinant tetrodotoxin-insensitive human Na(v)1.6 channels and whole-cell patch-clamping. Two variants causing developmental and epileptic encephalopathy showed a strong gain-of-function (hyperpolarizing shift of steady-state activation, strongly increased neuronal firing rate) and one variant causing benign familial infantile epilepsy or intermediate epilepsy showed a mild gain-of-function (defective fast inactivation, less increased firing). In contrast, all three variants causing generalized epilepsy induced a loss-of-function (reduced current amplitudes, depolarizing shift of steady-state activation, reduced neuronal firing). Functional effects were known for 170 individuals. All 136

26. Loss of function mutations in HARS cause a spectrum of inherited peripheral neuropathies

Author

Safka Brozkova, Dana, Deconinck, Tine, Beth Griffin, Laurie, Ferbert, Andreas, Haberlova, Jana, Mazanec, Radim, Lassuthova, Petra, Roth, Christian, Pilunthanakul, Thanita, Rautenstrauss, Bernd, Janecke, Andreas R., Zavadakova, Petra, Chrast, Roman, Rivolta, Carlo, Zuchner, Stephan, Antonellis, Anthony, Beg, Asim A., De Jonghe, Peter, Senderek, Jan, Seeman, Pavel, Baets, Jonathan, Safka Brozkova, Dana, Deconinck, Tine, Beth Griffin, Laurie, Ferbert, Andreas, Haberlova, Jana, Mazanec, Radim, Lassuthova, Petra, Roth, Christian, Pilunthanakul, Thanita, Rautenstrauss, Bernd, Janecke, Andreas R., Zavadakova, Petra, Chrast, Roman, Rivolta, Carlo, Zuchner, Stephan, Antonellis, Anthony, Beg, Asim A., De Jonghe, Peter, Senderek, Jan, Seeman, Pavel, and Baets, Jonathan

Abstract

Using linkage analysis and whole-exome sequencing, Safka Brozkova et al. reveal missense mutations in the histidyl-tRNA synthetase gene in 23 patients from four families with axonal and demyelinating neuropathies of varying severity. The mutations cause loss of function in yeast complementation assays and neurotoxicity in a C. elegans model

27. Mutations in ATP1A1 Cause Dominant Charcot-Marie-Tooth Type 2

Author

Dana Šafka Brožková, Rene Barro-Soria, H. Peter Larsson, Petra Laššuthová, Shawna M. E. Feely, Pavel Seeman, Eric Powell, Yi-Chung Lee, Elena Buglo, Daniel G. Isom, Cima Saghira, Feifei Tao, Royston Ong, Yunhong Bai, Steven S. Scherer, Lorna Marns, Chelsea Bacon, Gianina Ravenscroft, Megan F. Baxter, Lisa Abreu, Stephan Züchner, Jana Haberlová, Phillipa J. Lamont, Adriana P. Rebelo, Fiore Manganelli, Mark R. Davis, Lucio Santoro, Steve Courel, Ki Wha Chung, Dana M. Bis, Radim Mazanec, Michael E. Shy, Byung Ok Choi, Nigel G. Laing, Lassuthova, Petra, Rebelo, Adriana P., Ravenscroft, Gianina, Lamont, Phillipa J., Davis, Mark R., Manganelli, Fiore, Feely, Shawna M., Bacon, Chelsea, Brožková, Dana Šafka, Haberlova, Jana, Mazanec, Radim, Tao, Feifei, Saghira, Cima, Abreu, Lisa, Courel, Steve, Powell, Eric, Buglo, Elena, Bis, Dana M., Baxter, Megan F., Ong, Royston W., Marns, Lorna, Lee, Yi-Chung, Bai, Yunhong, Isom, Daniel G., Barro-Soria, René, Chung, Ki W., Scherer, Steven S., Larsson, H. Peter, Laing, Nigel G., Choi, Byung-Ok, Seeman, Pavel, Shy, Michael E., Santoro, Lucio, and Zuchner, Stephan

Subjects
Adult, Male, 0301 basic medicine, Charcot-Marie-Tooth, axonal neuropathy, Protein subunit, Mutant, Xenopus, Biology, Young Adult, 03 medical and health sciences, 0302 clinical medicine, Genetic, Charcot-Marie-Tooth Disease, Report, Genetics, Humans, Missense mutation, Family, Amino Acid Sequence, Na+,K+ATPase, Na+/K+-ATPase, Child, Gene, Genetics (clinical), Aged, Genes, Dominant, Aged, 80 and over, CMT, genetic matchmaking, ATP1A1, Middle Aged, biology.organism_classification, Molecular biology, Axolemma, Pedigree, 030104 developmental biology, Mutation, Female, Mendelian disease, Sodium-Potassium-Exchanging ATPase, 030217 neurology & neurosurgery, Immunostaining
Abstract

Although mutations in more than 90 genes are known to cause CMT, the underlying genetic cause of CMT remains unknown in more than 50% of affected individuals. The discovery of additional genes that harbor CMT2-causing mutations increasingly depends on sharing sequence data on a global level. In this way—by combining data from seven countries on four continents—we were able to define mutations in ATP1A1, which encodes the alpha1 subunit of the Na+,K+-ATPase, as a cause of autosomal-dominant CMT2. Seven missense changes were identified that segregated within individual pedigrees: c.143T>G (p.Leu48Arg), c.1775T>C (p.Ile592Thr), c.1789G>A (p.Ala597Thr), c.1801_1802delinsTT (p.Asp601Phe), c.1798C>G (p.Pro600Ala), c.1798C>A (p.Pro600Thr), and c.2432A>C (p.Asp811Ala). Immunostaining peripheral nerve axons localized ATP1A1 to the axolemma of myelinated sensory and motor axons and to Schmidt-Lanterman incisures of myelin sheaths. Two-electrode voltage clamp measurements on Xenopus oocytes demonstrated significant reduction in Na+ current activity in some, but not all, ouabain-insensitive ATP1A1 mutants, suggesting a loss-of-function defect of the Na+,K+ pump. Five mutants fall into a remarkably narrow motif within the helical linker region that couples the nucleotide-binding and phosphorylation domains. These findings identify a CMT pathway and a potential target for therapy development in degenerative diseases of peripheral nerve axons.

Published
2018
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28. Scientific Business Abstracts.

Author

Cooles F, Vidal-Pedrola G, Naamane N, Pratt A, Barron-Millar B, Anderson A, Hilkens C, Casement J, Bondet V, Duffy D, Zhang F, Shukla R, Isaacs J, Little M, Payne M, Coupe N, Fairfax B, Taylor CA, Mackay S, Milotay G, Bos S, Hunter B, Mcdonald D, Merces G, Sheldon G, Pradère P, Majo J, Pulle J, Vanstapel A, Vanaudenaerde BM, Vos R, Filby AJ, Fisher AJ, Collier J, Lambton J, Suomi F, Prigent M, Guissart C, Erskine D, Rozanska A, Mccorvie T, Trimouille A, Imam A, Hobson E, Mccullagh H, Frengen E, Misceo D, Bjerre A, Smeland M, Klingenberg C, Alkuraya F, Mcfarland R, Alston C, Yue W, Legouis R, Koenig M, Lako M, Mcwilliams T, Oláhová M, Taylor R, Newman W, Harkness R, McDermott J, Metcalfe K, Khan N, Macken W, Pitceathly R, Record C, Maroofian R, Sabir A, Santra S, Urquhart J, Demain L, Byers H, Beaman G, Yue W, Taylor R, Durmusalioglu E, Atik T, Isik E, Cogulu O, Reunert J, Marquardt T, Ryba L, Buchert-Lo R, Haack T, Lassuthova P, Polavarapu K, Lochmuller H, Horvath R, Jamieson P, Reilly M, O'Keefe R, Boggan R, Ng YS, Franklin I, Alston C, Blakely E, Büchner B, Bugiardini E, Colclough K, Feeney C, Hanna M, Hattersley A, Klopstock T, Kornblum C, Mancuso M, Patel K, Pitceathly R, Pizzamiglio C, Prokisch H, Schäfer J, Schaefer A, Shepherd M, Thaele A, Thomas R, Turnbull D, Gorman G, Woodward C, McFarland R, Taylor R, Cordell H, Pickett S, Tsilifis C, Pearce M, Gennery A, Daly A, Darlay R, Zatorska M, Worthington S, Anstee Q, Cordell H, Reeves H, Nizami S, Mauricio-Muir J, McCain M, Singh R, Wordsworth J, Kadharusman M, Watson R, Masson S, McPherson S, Burt A, Tiniakos D, Littler P, Nsengimana J, Zhang S, Mann D, Jamieson D, Leslie J, Shukla R, Wilson C, Betts J, Croall I, Hoggard N, Bennett J, Naamane N, Hollingsworth KG, Pratt AG, Egail M, Feeney C, Di Leo V, Taylor RW, Dodds R, Anderson AE, Sayer AA, Isaacs JD, McCracken C, Condurache DG, Szabo L, Elghazaly H, Walter F, Meade A, Chakraverty R, Harvey N, Manisty C, Petersen S, Neubauer S, Raisi-Estabragh Z, Allen L, Taylor P, Carlsson A, Hagopian W, Hedlund E, Hill A, Jones A, Ludvigsson J, Onengut-Gumuscu S, Redondo M, Rich S, Gillespie K, Dayan C, Oram R, Resteu A, Wonders K, Schattenberg J, Straub B, Ekstedt M, Berzigotti A, Geier A, Francque S, Driessen A, Boursier J, Yki-Jarvinen H, Arola J, Aithal G, Holleboom A, Verheij J, Yunis C, Trylesinski A, Papatheodoridis G, Petta S, Romero-Gomez M, Bugianesi E, Paradis V, Ratziu V, Tiniakos D, Anstee Q, Burton J, Ciminata G, Geue C, Quinn T, Glover E, Morais M, Reynolds G, Denby L, Ali S, Lennon R, Sheerin N, Yang F, Zounemat-Kermani N, Dixey P, Adcock IM, Bloom CI, Chung KF, Govaere O, Hasoon M, Alexander L, Cockell S, Tiniakos D, Ekstedt M, Schattenberg JM, Boursier J, Bugianesi E, Ratziu V, Daly AK, and Anstee QM

Published
2024
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29. Prot2HG: a database of protein domains mapped to the human genome.

Author

Stanek D, Bis-Brewer DM, Saghira C, Danzi MC, Seeman P, Lassuthova P, and Zuchner S

Subjects
Data Curation methods, Data Mining methods, Humans, Internet, Molecular Sequence Annotation methods, Proteins chemistry, Proteins genetics, Proteins metabolism, Computational Biology methods, Databases, Genetic, Genetic Variation, Genome, Human genetics, Genomics methods, Protein Domains genetics
Abstract

Genetic variation occurring within conserved functional protein domains warrants special attention when examining DNA variation in the context of disease causation. Here we introduce a resource, freely available at www.prot2hg.com, that addresses the question of whether a particular variant falls onto an annotated protein domain and directly translates chromosomal coordinates onto protein residues. The tool can perform a multiple-site query in a simple way, and the whole dataset is available for download as well as incorporated into our own accessible pipeline. To create this resource, National Center for Biotechnology Information protein data were retrieved using the Entrez Programming Utilities. After processing all human protein domains, residue positions were reverse translated and mapped to the reference genome hg19 and stored in a MySQL database. In total, 760 487 protein domains from 42 371 protein models were mapped to hg19 coordinates and made publicly available for search or download (www.prot2hg.com). In addition, this annotation was implemented into the genomics research platform GENESIS in order to query nearly 8000 exomes and genomes of families with rare Mendelian disorders (tgp-foundation.org). When applied to patient genetic data, we found that rare (<1%) variants in the Genome Aggregation Database were significantly more annotated onto a protein domain in comparison to common (>1%) variants. Similarly, variants described as pathogenic or likely pathogenic in ClinVar were more likely to be annotated onto a domain. In addition, we tested a dataset consisting of 60 causal variants in a cohort of patients with epileptic encephalopathy and found that 71% of them (43 variants) were propagated onto protein domains. In summary, we developed a resource that annotates variants in the coding part of the genome onto conserved protein domains in order to increase variant prioritization efficiency., Database URL: www.prot2hg.com., (© The Author(s) 2020. Published by Oxford University Press.)

Published
2020
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