Author: Jensen, Anders A ; Perrin, Laurence ; Borovikov, Artem ; Levrat, Virginie ; Fenger, Christina D ; Levy, Jonathan ; Leeuwen, Lisette ; Fahlke, Christoph ; Bayat, Allan ; Lesca, Gaetan ; Kovermann, Peter ; Sharkov, Artem ; Møller, Rikke S

BACKGROUNDExcitatory amino acid transporter 2 (EAAT2) is the predominant glutamate transporter and a key mediator of excitatory neurotransmission in the human brain. Here we present a cohort of 18 individuals harbouring 13 different SLC1A2 variants, who all present with neurodevelopmental impairment with variable symptoms and disease severities, and we delineate the impact of these variants on EAAT2 function.METHODSThe consequences of nine novel missense SLC1A2 variants for expression, transport and anion channel properties of EAAT2 expressed in mammalian cells were characterized by confocal microscopy, enzyme-linked immunosorbent and [³H]-D-aspartate uptake assays, and electrophysiological recordings.FINDINGSTen of the 13 SLC1A2 variants mediated significant changes to EAAT2 expression and/or function. These molecular phenotypes were classified into three categories: overall loss-of-function (F249Sfs∗17, A432D, A439V, c.1421+1G>C), mild gain-of-anion-channel function (I276S, G360A), and mixed loss-of-transport/gain-of-anion-channel function (G82R, L85R, L85P, P289R). In contrast, L37P, H542R and I546T did not mediate significant changes to EAAT2 expression or function. Although specific clinical outcomes in individuals carrying variants within each category varied somewhat, the three categories overall translated into distinct clinical phenotypes in terms of phenotypic traits and severity.INTERPRETATIONThe observed associations between functional effects and clinical phenotypes produced by these variants offer valuable insights for future predictions of progression and severity of SLC1A2-associated neurodevelopmental disorders. Furthermore, these associations between variant-induced changes in EAAT2 function and phenotypic traits could assist in tailoring personalized treatments of these disorders.FUNDINGThis work was funded by the German Ministry of Education and Research and by the Lundbeck Foundation.

23 Apr 2024·S.S. Korsakov Journal of Neurology and Psychiatry

A case of rare hereditary Siddiqi syndrome with novel neuropsychiatric signs

Article

Author: Chausova, P.A. ; Lotnik, E.E. ; Rudenskaya, G.E. ; Shchagina, O.A. ; Bostanova, F.M. ; Medvedeva, A.S.

A fifth world case of autosomal recessive Siddiqi syndrome (SIDDIS) related to FITM2 gene is presented. In a consanguineous Lezgin (a Dagestan ethnicity) family, there were two affected brothers aged 28 yrs (proband, personally examined) and 32 yrs. Whole-exome sequencing followed by familial Sanger sequencing detected a novel FITM2 missence variant c.452A>G, p.Asp151Gly homozygous in both patients and heterozygous in parents and unaffected brother. SIDDIS typical features in the patients were physical and motor delay with neuropsychiatric regress, loss of speech and walking, early-onset progressive sensorineural deafness, cognitive deficiency, skin lesion. However, there was no dystonia, which is a characteristic SIDDIS feature, while at least the proband had spastic paraparesis not described in SIDDIS earlier. Another distinction was mental state: behavioral disorders in both patients, positive symptoms in the proband and severe cognitive impairment in the brother. The case expands our understanding of the clinical and molecular-genetic spectrum of SIDDIS.

04 Apr 2024·Brain

Deciphering the impact of coding and non-coding SCN1A gene variants on RNA splicing

Article

Author: Skoblov, Mikhail ; Sharova, Margarita ; Filatova, Alexandra ; Sparber, Peter ; Pyankov, Denis ; Davydenko, Ksenia

AbstractVariants that disrupt normal pre-mRNA splicing are increasingly being recognized as a major cause of monogenic disorders. The SCN1A gene, a key epilepsy gene that is linked to various epilepsy phenotypes, is no exception. Approximately 10% of all reported variants in the SCN1A gene are designated as splicing variants, with many located outside of the canonical donor and acceptor splice sites, and most have not been functionally investigated. However, given its restricted expression pattern, functional analysis of splicing variants in the SCN1A gene could not be routinely performed. In this study, we conducted a comprehensive analysis of all reported SCN1A variants and their potential to impact SCN1A splicing and conclude that splicing variants are substantially misannotated and under-represented.We created a splicing reporter system consisting of 18 splicing vectors covering all 26 protein-coding exons with different genomic contexts and several promoters of varying strengths in order to reproduce the wild-type splicing pattern of the SCN1A gene, revealing cis-regulatory elements essential for proper recognition of SCN1A exons. Functional analysis of 95 SCN1A variants was carried out, including all 68 intronic variants reported in the literature, located outside of the splice sites canonical dinucleotides; 21 exonic variants of different classes (synonymous, missense, nonsense and in-frame deletion) and six variants observed in patients with epilepsy. Interestingly, almost 20% of tested intronic variants had no influence on SCN1A splicing, despite being reported as causative in the literature. Moreover, we confirmed that the majority of predicted exonic variants affect splicing unravelling their true molecular mechanism. We used functional data to perform genotype-phenotype correlation, revealing distinct distribution patterns for missense and splice-affecting ‘missense’ variants and observed no difference in the phenotype severity of variants leading to in-frame and out-of-frame isoforms, indicating that the Nav1.1 protein is highly intolerant to structural variations.Our work demonstrates the importance of functional analysis in proper variant annotation and provides a tool for high-throughput delineation of splice-affecting variants in SCN1A in a whole-gene manner.

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