Clinical heterogeneity of epilepsy and mutation spectrum of voltage-gated sodium channel genes

doi:10.21203/rs.3.rs-3803340/v1

Download PDF

Article

Clinical heterogeneity of epilepsy and mutation spectrum of voltage-gated sodium channel genes

https://doi.org/10.21203/rs.3.rs-3803340/v1

This work is licensed under a CC BY 4.0 License

Version 1

posted

You are reading this latest preprint version

Mutations in the genes encoding voltage-gated sodium channels (Na_v) family members are the most frequent cause of epilepsy. This study aims to screen Na_v genes (SCN1A, SCN1B, SCN2A, SCN3A, SCN8A, and SCN9A) to identify the sequence variations underlying epileptic phenotypes, including seizures, epileptic encephalopathies, and developmental delays. In this retrospective analysis, medical records of 1526 epilepsy patients were reviewed to extract all the patients who had the following genetic testing done: whole exome sequencing (WES), any next-generation sequencing (NGS) panel, and targeted single-gene testing were used to analyze the patients' genomic DNA sequences. Bioinformatics analysis was performed to analyze and detect the effect of variants on protein structure and stability. Sequence data analysis identified 25 heterozygous variants (4 protein-truncating variants and 21 missense variants) in SCN1A, SCN1B, SCN2A, SCN3A, SCN8A, and SCN9A genes, many of them are novel. Recurrent variants in SCN3A (c.2350A>G) and SCN9A (c.279A>C, c.1482G>T) in multiple individuals were also identified. Several therapeutic drugs, including bromide, phenytoin, oxcarbazepine, valproic acid, and ethosuximide were suggested based on Na_v variants identified, which indicates a possible personalized therapeutic approach. Novel variants identified in this work add to the mutation continuum of the Na_v genes in the epilepsy phenotype. Moreover, our findings emphasize the wide range of symptoms associated with variants in genes encoding Na_v channels, as well as the potential for personalized genomics and personalized therapies.

Biological sciences/Genetics/Development

Biological sciences/Genetics/Genotype

Biological sciences/Genetics/Medical genetics

Biological sciences/Genetics/Mutation

Developmental delay

Next-generation sequencing

Genetic testing

Precision medicine

Protein stability

Epilepsy is among the most common, chronic, and disabling neurological and systemic disorders. Epilepsy is caused by the sudden, excessive, hypersynchronous, and abnormal discharge of neurons, typically characterized by an enduring predisposition to generate recurrent and unconscious seizures [1,2]. The unremitting epileptic activity could contribute to progressive cerebral dysfunction, known as epileptic encephalopathy. Epileptic encephalopathy is a heterogeneous group of disorders that is characterized by both severe epileptic seizures and neurocognitive deterioration. Epileptic encephalopathy includes 8 syndromes, including early myoclonic encephalopathy, myoclonic status in non-progressive encephalopathy, epilepsy with continuous spike waves during sleep, Dravet syndrome (DS), Ohatahara syndrome, West syndrome, Lennox-Gastaut syndrome, and Landau-Kleffner syndrome [3-10]. Therefore, the underlying etiology of epileptic encephalopathy is diverse.

Advancement in human genetic studies have a significant clinical impact on understanding genetic predisposition to epilepsy. Genes involved in brain development, neuronal/cell signaling, and metabolism have been implicated in the pathogenesis of epilepsy. Studies reported several mutations in the genes encoding ion channels, including GABA receptors [11], potassium channels [12], calcium channels [13], voltage-gated sodium channels [14]. Therefore, epilepsy is also regarded as a “channelopathy”, a disorder caused by the dysfunction of the ion channels [15-22]. Voltage-gated sodium channels (VGSCs or Na_v) have a critical role in modulating neuronal excitability. The α-subunits of Na_v are the intrinsic transmembrane proteins, which are implicated in regulating the influx of Na⁺ across the cell membrane of excitable and non-excitable cells in response to membrane potential. In the mammalian genome, voltage-gated sodium channels α-subunits are localized on ten paralogous chromosomal regions [23]. The nine distinct Nav α-subunit proteins Nav1.1, Nav1.2, Nav1.3, Nav1.4, Nav1.5, Nav1.6, Nav1.7, Nav1.8, and Nav1.9 are encoded by SCNxA genes (i.e., SCN1A, SCN2A, SCN3A, SCN4A, SCN5A, SCN8A, SCN9A, SCN10A, and SCN11A, respectively). Within milliseconds after voltage-gated sodium channels α-subunits activation, the further flow of Na⁺ ions is occluded by the intracellular inactivation gate, allowing the membrane to return to resting potential. Na_v β-subunits regulate intracellular channel inactivation, consequently causing resting membrane potential [17,19,24,25]. Therefore, mutation in the SCNxA gene family (Na_v) result in hyperexcitability in the brain, i.e., epilepsy, and several other pathophysiological conditions. Diverse population studies reported that mutations in Na_vencoding genes is the most frequent cause of epilepsy [14,18,26,27]. Due to their high expression in the nervous system, pathogenic mutations in the SCN1A, SCN2A, SCN3A, SCN8A, SCN9A, and SCN1B genes have a significant role in the pathogenesis of epileptic encephalopathies. Therefore, the present study examines the incidence of pathogenic mutations in voltage-gated sodium channels α-subunits (SCNxA gene family) in a cohort of epilepsy patients. This study highlights the association between diverse phenotypes and comorbidities with mutations in the SCNxA gene family. Moreover, we also investigated the pathogenicity of variants, identified in this study, using bioinformatics.

2.1. Patient recruitment

This was a retrospective study that included patients diagnosed with epilepsy both clinically and using electroencephalography (EEG) at outpatient pediatric neurology, pediatric epilepsy, and pediatric neuromuscular clinics in the Department of Pediatric Neurology at King Fahad Specialist Hospital Dammam (KFSHD), Saudi Arabia, between January 2016 and January 2023. The KFSHD is a Ministry of Health Tertiary Care Center that accepts referrals from all around the country and accommodates mostly Saudi nationals. The medical records of all the patients with epilepsy were reviewed. Patients were not included in the study according to the following conditions:

1) No hypoxia, ischemia, infection of the central nervous system (CNS), or cranial trauma.

2) Acute symptomatic epilepsy, head trauma, brain tumors, and CNS infections

3) Clinical characteristics and neuroimaging revealed no evidence of typical hereditary epileptic phenotypes or related comorbidities.

Medical records of patients were reviewed to extract those who underwent genetic testing, including whole exome sequencing (WES), next-generation sequencing (NGS) panel, and targeted single-gene testing. The medical records of patients having mutations in Na_v encoding genes were further evaluated, including demographics, medical history, physical examination results, laboratory test results, electroencephalogram (EEG) data, radiological findings, and genetic results.

2.2.Genomic DNA Sequencing

For single gene sequencing and NGS panels, 2 ml of blood was collected in an EDTA- containing tube and transported in a cold pack to diagnostic laboratories (CGC Genetics, Portugal and Centogene, Germany) for genomic DNA extraction, polymerase chain reaction (PCR), and sequence analysis. Various approaches, depending on the phenotype of the patient, including next-generation sequencing panels, whole-exome sequencing, mitochondrial genome testing, and targeted single-gene molecular analysis, have been used to detect genetic defects in the DNA of patients. An Illumina instrument was used for next-generation sequencing. Oligonucleotide probes were used to capture the target areas of SCN genes (Human All Exon V6, Agilent Technologies). Following capture of target regions with oligonucleotide probes, next-generation sequencing (NextSeq, Illumina) of genomic DNA was performed using Agilent Technologies enrichment kits. Burrows-Wheeler Aligner (BWA) and Genome Analysis Toolkit (GATK) were used for alignment and base calling (UCSC hg19). Single nucleotide variants (SNV), insertions, deletions, and copy number variations (CNV) were called and annotated after the region was matched to the human reference genome (UCSC hg19). Variants found in the bordering exons and intronic regions (+8 bp) of the genes were also analyzed. The American College of Medical Genetics and Genomics guidelines have been used to categorize the variants (ACMG) [28]. Variants that likely explained the phenotype were independently confirmed using Sanger sequencing.

2.3. In silico Assessment of the Mutations to Identify Putative Pathogenic Mutations

In this study, we investigated the protein structures of human SCN1A, SCN1B, SCN2A, SCN8A, and SCN9A. The sequences of SCN1A (Entry: P35498), SCN1B (Entry: Q07699), SCN2A (Entry: Q99250), SCN3A (Entry: Q9NY46), SCN8A (Entry: Q9UQD0), and SCN9A (Entry: Q15858) were downloaded from UniProt (https://www.uniprot.org/). SWISS Model (https://swissmodel.expasy.org/) was used to construct wild type and mutated structures of proteins. UCLA-DOE LAB — SAVES v6.0 (https://saves.mbi.ucla.edu/) was used to validate, verify, and assess the changes in the stereochemical properties of protein structures due to variants. Pymol (https://pymol.org/) was used to generate structures of the mutated protein.

Various tools including SIFT (Sorting Intolerant From Tolerant) (https://sift.bii.a-star.edu.sg/), PolyPhen-2 (Polymorphism Phenotyping v2) (https://bio.tools/polyphen-2), Mutation Taster (https://www.genecascade.org/MutationTaster2021/#transcript), PROVEAN (Protein Variation Effect Analyzer) (http://provean.jcvi.org/index.php), MuPro (http://mupro.proteomics.ics.uci.edu/), and I-Mutant (https://folding.biofold.org/i-mutant/i-mutant2.0.html) were used to predict the potential functional effects of nonsynonymous variations . Variants having scored more than the threshold for each bioinformatics tool were considered pathogenic. DUET (http://biosig.unimelb.edu.au/duet/stability), which consolidates two complementary approaches (mCSM and SDM) in a consensus prediction, was used to predict the effects of mutations on protein stability and evaluate free energy (ΔΔG) differences between wild type and mutant Na_v proteins [29]. To study the protein-protein interaction of SCN1A, SCN1B, SCN2A, SCN8A, and SCN9A, Search Tool for the Retrieval of Interacting Genes (STRING) was used (http://stitch.embl.de/). STRING allows the discovery of relationships across disease genotype and creates protein-protein interaction network.

3.1. Patient Characteristics

In this study, we found 24 variants in the voltage-gated sodium channels α-subunits (SCNxA gene family) and 1 mutation in β-subunit (SCN1B) in 23 epilepsy patients (8 males and 15 females), ranging in age from 4 to 23 years at the time of the most recent clinical evaluation (median: 11.5 years, STD: 5.4 years). 21 patients with heterozygous mutations in only one gene (SCN1A, SCN1B, SCN2A, SCN3A, SCN8A, and SCN9A), while 3 patients with heterozygous mutations in two genes (SCN1A + SCN1B, SCN1A + SCN3A, SCN8A + SCN3A, and SCN8A + SCN9A) were identified. In our cohort, epilepsy patients had global development delay (GDD), drug-resistant epilepsy, microcephaly, mental retardation, learning difficulties, or autism (Table 1). Of these patients, a spectrum of phenotypes of epileptic seizures with varying degrees of severity was clinically diagnosed, including refractory seizures, Hemi-convulsive seizures, focal seizures, epileptic spasms, frequent seizures with illness, generalized tonic-clonic, and myoclonic seizures. Some patients had other syndromes that include early infantile epileptic encephalopathy (IEE13), Dravet syndrome, and severe myoclonic epilepsy in infancy, or benign infantile familial seizures-5 (BFIS5). In addition, absence seizures were reported in some patients. In our cohort, 6 patients (25%) had a positive family history, and the remaining 18 (75%) were sporadic cases.

3.2. Na_v (SCN) Genes Variations Diversity

25 heterozygous mutations were found in SCN1A, SCN1B, SCN2A, SCN3A, SCN8A, and SCN9A genes. 4 frameshift mutations have been found that create premature stop codon, and produce truncated protein. These mutations induce their reduced expression by mRNA nonsense-mediated decoys. 3 truncating mutations were in the SCN1A gene, i.e., p.Pro1519Thrfs*18 (c.4554dup), p.Glu951Serfs*3 (c.2851del), and p.Lys1049Asnfs*6 (c.3147del), at cytoplasmic loop after S6 transmembrane domains III, pore of domain III, and cytoplasmic loop after S6 transmembrane domains III, respectively (Fig. 1). Glu951Serfs*3 and Lys1049Asnfs*6 mutations were reported as pathogenic and likely-pathogenic mutations, respectively. The other frameshift mutation, p.Glu209Valfs*85 (c.626_627del), was reported in the extracellular loop between S3 and S4 transmembrane domain I of the Na_v1.8 α-subunit protein encoded by SCN8A gene.

In SCN1A, 2 inherited missense mutations in cytoplasmic loops (p.Arg500Trp and p.Ser1122Thr), 2 de novo missense mutations, 1 in the pore-forming loop (p.Ala1429Pro), and 1 in the extracellular loop (p.Gly271Asp), were found in epilepsy patients. Novel mutations, i.e., c.812G > A, c.4285G > C, and, c.3147del have been found, which were not described in literature nor the population databases dbSNP or gnomAD. Also, c.4554dup and c.3364T > A were not described in literature nor in the population databases dbSNP but ClinVar and gnomAD, respectively. However, c.2851del and c.1498C > T were described in population databases, i.e., dbSNP (rs886042004, rs141188608), gnomAD (1498C > T: 0.00081%, including two heterozygotes) and ClinVar. Voltage-gated sodium channels are composed of one alpha and two beta subunits, where the α-subunit provides channel activity and the β-1 subunit modulates the kinetics of channel inactivation. SCN1B gene encodes a sodium channel β-1 subunit (Na_vβ1). 2 mutations were detected, p.Ala197Val (c.590C > T) and p.Cys211Tyr (c.632G > A), in the cytoplasmic domain of Na_vβ1 (Fig. 1). Both of these mutations were described in population databases, i.e., dbSNP (rs554201948, rs141188608), gnomAD (0.0016% and 0.039%) and ClinVar.

Only one missense heterozygous mutation, c.3457G > C (p.Glu1153Gln), was found in the SCN2A gene, which was located in the extracellular loop connecting domains II and III (Fig. 2) and was classified as a variant of unknown significance. Five missense heterozygous variants have been found in the SCN3A gene: three are in the extracellular loops (c.2350A > G, c.956T > C, and c.2350A > G) and two are in the cytoplasmic loops (c.3486C > A and c.44G > A) (Fig. 3). Variant c.2350A > G (p.Met784Val) is found in two patients, has not been described in literature nor in the population databases (dbSNP). However, it is present in gnomAD with very low frequency (0.0004%). c.44G > A (p.Arg15His) was described in population databases, i.e., dbSNP (rs139769668), gnomAD (0.021%, 57 heterozygous individuals reported) and ClinVar. In addition, c.956T > C (p.Ile319Thr) was also described in population databases, i.e., dbSNP (rs369361605), gnomAD (0.021%, 60 heterozygous individuals reported) and ClinVar.

In SCN8A (Na_v1.8), 1 frame-shift mutation and 6 missense mutations have been found in our cohort of epilepsy patients. The c.626_627del frame-shift mutation was located near S4 of domain I. A missense mutation, c.5113G > C (p.Ala1705Pro), was found in the pore-forming loop region, whereas, c.4594A > T (p.Ile1532Phe) mutation occurred in S1 of domain IV Na_v1.8 α-subunit. c.572G > A (p.Arg191Gln), c.2078G > A (p.Arg693Gln), and c.3422C > G (p.Pro1141Arg) were located in the cytoplasmic loop of Na_v1.8 (Fig. 4). c.3422C > G, c.2078G > A, c.5113G > C, c.626_627del, and c.4594A > T are not reported in literature nor in population database dbSNP and gnomAD. c.572G > A is not reported in the literature but in the population database gnomAD (0.00041%).

4 missense mutations in the cytoplasmic loops of Na_v1.9 α-subunits were detected. c.279A > C (Lys93Asn) occurred at the starting of the cytoplasmic loop. c.1482G > T (p.Lys494Asn) and c.1336G > A (p.Glu446Lys) were located on the cytoplasmic loop connecting domains I and II of Na_v1.9 (Fig. 5). c.1482G > T mutation is reported in population databases, i.e gnomAD (0.00081%, 2 heterozygous individuals reported) and ClinVar (ID: 331990). c.279A > C mutation was not described in literature nor in the population databases dbSNP or gnomAD. However, c.1336G > A was not described in the literature but in the population database dbSNP (rs1175228324).

3.3. Genotype-Phenotype correlation

In Table 1, the characteristics of SCN gene mutations reported in our cohort of epilepsy patients and clinical presentation of patients have been reported. The c.812G > A (p.Gly271Asp) (NM_001165963.1) mutation in SCN1A was reported in an 18 years old female having autism and refractory seizures but no family history. c.4554dup (p.Pro1519Thrfs*18) (NM_001165963.4) in the SCN1A was associated with severe myoclonic epilepsy in infancy in a 10 years female. c.2851del (p.Glu951Serfs*3) (NM_001165963.2) is a pathogenic mutation in the SCN1A gene that was detected in a 23 years old male with epilepsy and autism but no family history. Another likely-pathogenic mutation c.3147del (p.Lys1049Asnfs*6) (NM-001165963.2) was also detected in 5 years old female with hemibody convulsion, frequent seizures with illness and seizure, microcephaly, and Dravet syndrome. An 11 years old female of unrelated parents but with a positive family history of epilepsy and development delay harbors two mutations in SCN1A (c.4285G > C) and SCN3A (c.3486C > A) genes. Both of these mutations were heterozygous and were associated with microcephaly, epilepsy, and speech delay in the patient. Correspondingly, another 11-year-old female epilepsy patient with normal development and no family history also had two mutations in SCN1A (c.1498C > T) and SCN1B (c.590C > T) genes. A 5 years old female patient with drug-resistant epilepsy, global development delay, regression, hypotonia, and blindness had heterozygous c.3364T > A (p.Ser1122Thr) (NM_001165963.2) mutation in the SCN1A gene. Also, the patient had parental consanguinity and positive family history of seizures. The c.632G > A (p.Cys211Tyr) in SCN1B was also reported in a 14-year-old male patient with drug-resistant epilepsy, global development delay, and arrested hydrocephalus. Similarly, a 6 years old male patient with refractory seizures and global development had c.3457G > C (p.Glu1153Gln) (NM_021007.2) mutation in SCN2A gene. Another 19-year-old female patient also had global development delay, drug-resistant epilepsy, and mental retardation due to mutations in SCN8A (c.3422C > G) and SCN9A (c.279A > C). The c.2078G > A (p.Arg693Gln) in SCN8A causes severe developmental delay, mental retardation, hyperactive, and refractory epilepsy. 2 other mutations in SCN8A, i.e., c.572G > A and c.626_627del, were found to cause epilepsy, microcephaly, and global development delay in 12 years old and 4 years old females, respectively. Similar clinical presentations were also observed in a 13-year-old male patient with c.1482G > T (p.Lys494Asn) mutation in SCN9A. Therefore, a single voltage-gated sodium channel is not responsible for epileptic encephalopathies but SCN1A, SCN1B, SCN2A, SCN3A, SCN8A, and SCN9A are equally responsible for the pathogenesis of epilepsy.

Moreover, mutations in the SCN3A are associated with different types of epilepsy or seizures in our cohort of epileptic patients. The c.44G > A mutation was associated with Generalized tonic-clonic and myoclonic seizures in a patient with a family history of febrile seizures. In our cohort, a patient also had attention deficit hyperactivity disorder (ADHD) with learning difficulties and epilepsy due to c.956T > C mutation in SCN3A. Non-specific hyperintensity in white matter, bilateral thalamia, and caudate, with normal metabolic workup, was observed in a patient with c.956T > C mutation in SCN3A. However, mutations in the SCN3A gene also cause epilepsy with the absence of seizures, i.e., c.2350A > G in our cohort. The 10 years old female with c.2350A > G mutation in SCN3A had frequent starring episodes, corresponding to 3 Hz spike, and waves in EEG were reported. Also, a female with epilepsy (absence of seizure), learning difficulties, and benign infantile familial seizures-5 had mutations in the SCN3A (c.928A > T) and SCN8A (c.5113G > C) genes. Also, the c.4594A > T (p.Ile1532Phe) mutation in SCN8A was found in a patient with Infantile epileptic encephalopathy-13, neonatal seizure, hypotonia, and regression in development. In addition, SCN9A mutations, c.4702A > C, c.279A > C, and c.1336G > A, were also found to be associated with progressive myoclonic epilepsy, focal seizures, or new-onset epilepsy.

Table 1

Significance and characteristics of SCN gene mutations reported in our cohort of epilepsy patients and clinical presentation of patients.
Gene	Transcript	Age/Sex	Mutation	Protein change	Diagnosis
SCN1A	NM_001165963.1	18 y Female	c.812G > A	p.Gly271Asp	Refractory seizures and Autism
SCN1A	NM_001165963.4	10 y Female	c.4554dup	p.Pro1519Thrfs*18	Severe myoclonic epilepsy in infancy
SCN1A	NM_001165963.2	23 y Male	c.2851del	p.Glu951Serfs*3	Epilepsy and Autism
SCN1A SCN3A	NM_001165963.2 NM_006922.3	11 y Female	c.4285G > C c.3486C > A	p.Ala1429Pro p.Asp1162Glu	Microcephaly, Epilepsy, and Speech delay
SCN1A SCN1B	NM_001165963.1 NM_001037.4	11 y Female	c.1498C > T c.590C > T	p.Arg500Trp p.Ala197Val	Epilepsy; normal development
SCN1A	NM-001165963.2	5 y Female	c.3147del	p.Lys1049Asnfs*6	Hemibody convulsion, frequent seizures with illness and seizure, microcephaly, and Dravet syndrome
SCN1A	NM_001165963.2	5 y Female	c.3364T > A	p.Ser1122Thr	Drug-resistant epilepsy, Global development delay, regression, hypotonia, and blindness.
SCN1B	NM_001037.4	14 y Male	c.632G > A	p.Cys211Tyr	Global development delay, drug-resistant epilepsy, and arrested hydrocephalus
SCN2A	NM_021007.2	6 y Male	c.3457G > C	p.Glu1153Gln	Global development delay and refractory epilepsy
SCN3A	NM_006922.3	18 y Female	c.44G > A	p.Arg15His	Generalized tonic-clonic and myoclonic seizures
SNC3A	NM_006922.3	10 y Female	c.2350A > G	p.Met784Val	Absence epilepsy
SCN3A	NM_0069922.3	12 y Male	c.956T > C	p.Ile319Thr	Learning difficulties, epilepsy, and attention deficit hyperactivity disorder.
SCN3A	NM_006922.3	10 y Female	c.2350A > G	p.Met784Val	Childhood absence epilepsy
SCN8A	NM_014191.3	12 y Female	c.572G > A	p.Arg191Gln	Epilepsy, microcephaly, and Global development delay
SCN8A	NM_000335.5	19 y Male	c.2078G > A	p.Arg693Gln	Severe developmental delay, mental retardation, hyperactive and refractory epilepsy.
SCN8A SCN9A	NM_014191.4 NM_002977.3	19 y Female	c.3422C > G c.279A > C	p.Pro1141Arg p.Lys93Asn	Global development delay, drug-resistant epilepsy, and mental retardation
SCN8A SCN3A	NM-014191.3 NM_006922.3	15 y Female	c.5113G > C c.928A > T	p.Ala1705Pro p.Met310Leu	Epilepsy (absence of seizure), learning difficulties, and benign infantile familial seizures-5
SCN8A	NM_014191.3	4 y Female	c.626_627del	p.Glu209Valfs*85	Global development delay, epileptic spasms, and microcephaly
SCN8A	NM_001330260.1	6 y Female	c.4594A > T	p.Ile1532Phe	Neonatal seizure, hypotonia, regression in development, Infantile epileptic encephalopathy-13 (Ohtahara syndrome)
SCN9A	NM_002977.3	13 y Male	c.1482G > T	p.Lys494Asn	Epilepsy, microcephaly, and Global development delay
SCN9A	NM_002977.3	15 y Male	c.4702A > C	p.Asn1568His	Progressive myoclonic epilepsy, mental retardation, and ataxia
SCN9A	NM_002977.3	5 y Female	c.279A > C	Lys93Asn	Global development delay, infantile spasms, and microcephaly
SCN9A	NM_002977.3	17 y Male	c.1482G > T	p.Lys494Asn	Focal seizures
SCN9A	NM_002977.3	7 y Female	c.1336G > A	p.Glu446Lys	New-onset epilepsy

In our cohort of epilepsy patients and other neurological disorders of unknown etiology, mutations in different SCN genes were found to be associated with global development delay (GDD), i.e., SCN1A (c.3364T > A), SCN1B (c.632G > A), SCN2A (c.3457G > C), SCN8A (c.572G > A, c.2078G > A, and c.3422C > G), and SCN9A (c.1482G > T and c.279A > C). However, in our cohort, compared to other Na_v, SCN8A has the highest number of mutations (i.e., 3) to be associated with GDD, followed by SCN9A (2 mutations) in our cohort. Moreover, 2 patients harbor the same SCN9A mutation, c.279A > C, and interestingly have similar clinical features, i.e., global development delay, infantile spasms, and microcephaly in one patient and global development delay, drug-resistant epilepsy, and mental retardation in another patient. Similarly, an SCN3A mutation (c.2350A > G), reported in 2 different individuals, was found to cause absent epilepsy. In our cohort, 2 more same mutations, c.1482G > T, were also found in SCN9A and they were also associated with GDD, microcephaly, and epilepsy. Hence, we can say that the same missense mutations in an SCN gene in different individuals can cause similar epileptic phenotypes with similar symptoms but with varying degrees of severity.

3.4. Mutation Prediction and Verification of Functional Effects of Amino acid Variations

To predict the variant-caused secondary structure and protein stability change, Ramachandran plot was analyzed of each mutation. 6 different online bioinformatics approaches were used, which includes SIFT, PolyPhen-2, Mutation Taster, PROVEAN, MuPro, and I-Mutant to predict the potential functional effects of nonsynonymous amino acid variations. Mutations having scored more than the threshold for each bioinformatics tool were considered pathogenic. After combining the results of all tools in Table 2, we concluded that 18 mutations were highly pathogenic that significantly affects the protein structure and function of Na_v. Mutations having scored more than the threshold for each bioinformatics tool were considered pathogenic, i.e., for PROVEAN, variants with a score equal to or below − 2.5 are considered "deleterious,", while a score above − 2.5 are considered "neutral". For Polyphen-2, there’s a range from 0.00 to 1.00 for Benign to Damaging, respectively. The amino acid change reported to adversely affect the protein integrity in the majority of tools was concluded as pathogenic mutation. The mCSM, SDM, and DUET were also used to predict the change in protein stability due to amino acid variation in SCN1A, SCN1B, SCN2A, SCN8A, and SCN9A.

Table 2

Mutation prediction and verification of functional effects ad protein stabiltity change of amino acid variation in Na_v proteins reported in our cohort of epilepsy patients.
Gene	Mutation	PolyPhen-2 (Score)	PROVEAN	SIFT	MuPro (Delta G)	I-Mutant2.0	Mutation taster	mCSM	SDM	DUET	Remarks
SCN1A	G271D	Probably Damaging (1.000)	Deleterious (-6.840)	Not tolerated	Decrease stability (-0.66490151)	Decrease	Disease causing	-2.35 kcal/mol	-4.28 kcal/mol	-2.864 kcal/mol	Pathogenic
SCN1A	R500W	Probably damaging (0.999)	Deleterious (-7.073)	Not tolerated	Decrease stability (-1.2478423)	Decrease	Disease causing	-0.309 kcal/mol	0.2 kcal/mol	-0.351 kcal/mol	Pathogenic
SCN1A	A1429P	Probably Damaging (1.000)	Deleterious (-4.478)	Not tolerated	Decrease stability (-0.8849560)	Increase	Disease causing	0.754 kcal/mol	-3.91 kcal/mol	0.184 kcal/mol	Pathogenic
SCN1A	S1122T	Probably Damaging (0.981)	Deleterious (-2.847)	Not tolerated	Decrease stability (-0.82526636)	Decrease	Disease causing	-0.336 kcal/mol	0.68 kcal/mol	0.15 kcal/mol	Pathogenic
SCN1B	A197V	Probably damaging (0.997)	Neutral (-2.397)	Not tolerated	Decrease stability (-0.31094392)	Increase	Disease causing	-0.313 kcal/mol	-1.03 kcal/mol	-0.161 kcal/mol	Pathogenic
SCN1B	C211Y	Probably Damaging (0.995)	Deleterious (-4.765)	Not tolerated -	Decrease stability (-0.97743861)	Decrease	Disease causing	-	-	-	Pathogenic
SCN2A	E1153Q	Probably Damaging (0.956)	Neutral (-2.194)	Tolerated	Decrease stability (-0.49502662)	Decrease	Disease causing	0.479 kcal/mol	-0.7 kcal/mol	0.639 kcal/mol	Pathogenic
SCN3A	D1162E	Benign (0.001)	Neutral (-0.499)	Tolerated	Decrease stability (-0.5266769)	Increase	Disease causing	-0.184 kcal/mol	0.46 kcal/mol	0.243 kcal/mol	Non-pathogenic
SCN3A	R15H	Benign (0.007)	Neutral (-1.843)	Not tolerated	Decrease stability (-1.2066405)	Decrease	Disease causing	-1.117 kcal/mol	0.52 kcal/mol	-0.863 kcal/mol	Pathogenic
SNC3A	M784V	Probably Damaging (0.998)	Deleterious (-3.474)	Not tolerated	Decrease stability − 0.27632929 ()	Decrease	Disease causing	-1.65 kcal/mol	0.75 kcal/mol	-1.073 kcal/mol	Pathogenic
SCN3A	I319T	Benign (0.151)	Deleterious (-3.868)	Not tolerated	Decrease stability (-2.7533728)	Decrease	Disease causing	-1.001 kcal/mol	-0.41 kcal/mol	-0.63 kcal/mol	Pathogenic
SCN3A	M310L	Benign (0.000)	Neutral (-0.408)	Tolerated	Decrease stability (-0.2805257)	Decrease	Disease causing	0.086 kcal/mol	0.49 kcal/mol	0.64 kcal/mol	Non-pathogenic
SCN8A	R191Q	Probably Damaging (1.000)	Deleterious (-3.874)	Not tolerated	Decrease stability (-0.92873016)	Decrease	Disease causing	-0.487 kcal/mol	-0.8 kcal/mol	-0.409 kcal/mol	Pathogenic
SCN8A	P1141R	Probably Damaging (0.994)	Deleterious (-2.751)	Tolerated	Decrease stability (-0.5991921)	Decrease	Disease causing	-0.002 kcal/mol	-0.4 kcal/mol	0.169 kcal/mol	Pathogenic
SCN8A	A1705P	Probably Damaging (1.000)	Deleterious (-4.522)	Not tolerated	Decrease stability (-1.2896981)	Increase	Disease causing	-	-	-	Pathogenic
SCN9A	K93N	Probably Damaging (0.878)	Deleterious (-3.933)	Not-tolerated	Decrease stability (-0.7426442)	Decrease	Disease causing	-	-	-	Pathogenic
SCN8A	I1532F	Probably Damaging (0.997)	Deleterious (-3.719)	Not tolerated	Decrease stability (-1.2896981)	Decrease	Disease causing	-	-	-	Pathogenic
SCN8A	R693Q	Probably Damaging (0.997)	Neutral (-0.140)	Tolerated	Decrease stability (-1.3027849)	Decrease	Disease causing	0.079 kcal/mol	-0.47 kcal/mol	0.145 kcal/mol	Pathogenic
SCN9A	K494N	Possibly damaging (0.946)	Deleterious (-2.866)	Tolerated	Decrease stability (-0.4581563)	Increase	Disease causing	0.273 kcal/mol	-0.31 kcal/mol	0.318 kcal/mol	Pathogenic
SCN9A	N1568H	Probably Damaging (1.000)	Neutral (-0.885)	Not tolerated	Decrease stability (-0.013611302)	Decrease	Disease causing	-1.335 kcal/mol	0.55 kcal/mol	-0.977 kcal/mol	Pathogenic
SCN9A	E446K	Benign (0.061)	Neutral (-0.705)	Tolerated	Decrease stability (-0.5567253)	Decrease	Disease causing	0.504 kcal/mol	-0.36 kcal/mol	0.656 kcal/mol	Non-pathogenic

3.5. 3D-visualization of mutations in Na_v

Protein structure prediction is the prediction of a protein's three-dimensional (3D) structure based on its amino acid sequence. We studied 3D characteristics of Na_v proteins linked with pathogenic and benign variants, which revealed the mutations' molecular effect. The 3D amino acid sites altered in pathogenic and population variations in our cohort of epilepsy and associated illnesses (Fig. 1–5). Frameshift mutations (Glu951Serfs*3, Lys1049Asnfs*6, p.Glu209Valfs*85, and p.Glu209Valfs*85) had significantly altered the shape of proteins (i.e., SCN1A and SCN8A). Mapping mutations onto 3D structures allows for atomic-level assessments of protein locations that may be critical for protein stability or interaction formation; they may explain the effect of mutations and, in some situations, open the door to targeted medication development.

3.6. Protein-protein interation network

The Na_v genes were imported into the STRING database, species was described as Homo sapiens, and the minimum required interaction score was set as 0.7. The protein-protein interaction (PPI) network grid had 8 nodes and 12 connected edges, with an average node of degree 3 and an average clustering coefficient of 0.783. The enrichment PPI enrichment p-value was 1.47x10^− 06. The predicted functional partners of human SCN1A, SCN1B, SCN2A, SCN8A, and SCN9A were SCN2B, SCN4A, SCN4B, ANK3, and FGF14 (Fig. 6).

3.7. Approach towards Personalized Medicine

The current study looks at the prevalence of SCN gene mutations in a group of people who have epilepsy and other neurological illnesses. It emphasizes the wide range of diseases associated with mutations in Na_v, as well as the potential for personalized genomics and personalized treatments. The screening of Na_v genes mutation by NGS provides a better and more precise prognosis for epilepsy patients, leading to tailored therapy. NGS technologies have significant potential in deciding omics-based patient-specific treatment. In our cohort, several variants were detected that indicated possible personalized therapies (Table 3). Bromide is the most efficient and well-tolerated medication in the Dravet syndrome patients, particularly with mutations in the SCN1A gene [30, 31]. In patients with SCN1A mutations, Carbamazepine should be avoided [30]. Also, the ketogenic diet is suggested for refractory patients with and Dravet syndrome [32, 33]. In our cohort, SCN1B causes epilepsy and development delay, which can be treated with Phenytoin [34]. Patients with SCN2A variants could be treated with Oxcarbazepine [35]. Valproic acid and Ethosuximide are effective in the absence seizures [36], which is suggested for patients with SCN3A mutations in our study (Table 3). A patient having generalized tonic-clonic and myoclonic seizures due to the SCN3A variant could be treated with Oxcarbazepine [36]. Similarly, for SCN8A sodium channel blocking therapeutic agents could be effective, which include Lacosamide, Oxcarbazepine, and Phenytoin [37]. Furthermore, Oxcarbazepine can also exert potential therapeutic effects against SCN9A variants [37].

Table 3

Examples of precision medicine in our cohort
Gene variant	Disease description	Medicine	Reference
SCN1A	Dravet syndrome	Bromide	[30, 31]
SCN1A	Severe seizures and Dravet syndrome	Ketogenic diet	[32, 33]
SCN1B	Epilepsy	Phenytoin and Fenfluramine	[34, 38]
SCN2A	Epilepsy	Sodium channel blockers (Oxcarbazepine, Valproate, and Carbamazepine)	[35, 39]
SCN2A	Developmental and epileptic encephalopathy	Ketogenic diet	[40]
SCN3A	Absence seizures	Valproic acid and Ethosuximide	[36]
SCN3A	Generalized tonic-clonic and myoclonic seizures	Oxcarbazepine	[41]
SCN8A	Epilepsy	Lacosamide, Oxcarbazepine, and Phenytoin	[42]
SCN9A	Neonatal seizures and epileptic	Oxcarbazepine	[37]

Voltage-Gated Sodium Channels (VGSCs or Na_v) are the intrinsic transmembrane proteins, which are implicated in regulating the influx of Na⁺ across the cell membrane of excitable and non-excitable cells in response to membrane potential. Na_v generates action potential during neuronal synapses [43]. The mutation(s) in the SCN gene family results in hyperexcitability in the brain, i.e., epilepsy, and several other neurological disorders. Diverse population studies reported that mutations associated with Na_v most commonly cause epilepsy [14,18,26,27]. Epilepsy is the most common and devastating neurological disorder characterized by unprovoked, recurrent seizures, arising from excessive synchronized neuronal discharging. SCN1A, SCN2A, SCN3A, SCN8A, and SCN1B are of huge significance due to their high expression in the nervous system. This retrospective study reports the SCN gene mutations found in our cohort of patients with epilepsy and other neurological disorders. Our study highlights the diverse genotype-phenotype association, identify potential pathogenic mutation by in silico approaches, and discusses the potential roles of personalized treatments.

The goals of this research were to study the genetic factors that regulate the expression of neuronal Na_v, the underlying mechanism behind seizure generation in epilepsy, and the basis of variable severities in epilepsy patients. Next-generation sequencing technology was used to determine if mutation or variations in SCN1A, SCN1B, SCN2A, SCN3A, SCN8A, and SCN9A contribute to causing epilepsy. Moreover, bioinformatics and functional analysis were used to evaluate the significance of the SCN gene mutations and to identify putative pathogenic mutations. The medical records of patients were also reviewed to find the genotype-phenotype correlation.

4.1. SCN1A

SCN1A (OMIM# 182389) mutations are novel and primarily related to the different epilepsy-related phenotypes, including Dravet syndrome [44-46]. SCN1A mutations are considered common in epilepsy because of repeatedly reported [47]. Dravet syndrome (OMIM # 607208) was first discovered by Dravet [48], which is characterized by generalized, unilateral, tonic, clonic, or tonic-clonic seizures with febrile illness or fever. Dravet syndrome (DS) is an infantile-onset epileptic encephalopathy associated with developmental delay, intellectual disability, gait problems, and intractable epilepsy [45,49]. 80% of the Dravet syndrome cases have SCN1A mutation. [50,51]. Bjurulf, et al. [52] reported that 90% of children with DS have SCN1A variations. Missense or truncating mutations in the voltage sensor and pore domain of SCN1A are reported to be more common in DS patients, irrespective of differences in clinical presentation [53]. In line with this, we also found a c.3147del a frameshift mutation that create premature codon, producing a truncated protein in a 5-year-old female patient with Dravet syndrome and also other clinical presentations, including hemibody convulsion, frequent seizures with illness, and seizure, microcephaly. Frame-deletions in SCN1A disrupt protein residues and exert deleterious effects on Na_v1.1 [54]. In our cohort, we have 3 pathogenic frameshift mutations (c.4554dup, c.2851del, and c.3147del). Also, mutations on the homology domains result in earlier onset rather than mutations occurring in the linker domain of SCN1A [55]. SCN1A variants may also be common in patients with co-occurring epilepsy and autism spectrum disorders [56]. In our cohort, we also found two patients with autism having SCN1A mutations, a missense mutation in the extracellular loop (c.812G>A) and a frameshift mutation in the pore-forming unit of domain II (c.2851del). Moreover, we also found two SCN1A mutations (p.Lys1049Asnfs*6, and p.Ala1429Pro) to be associated with microcephaly.

In a Turkish cohort of GEFS+ (n=6) and DS (n=12), 17 variations in SCN1A were reported with 7 novel variations in DS cases (E1916G, I767L, M1R, M147T, N1319I, R1886G, and R1933Q) [57]. Similarly, 19 mutations in SCN1A genes with 12 novel mutations were also reported in another Turkish cohort of DS spectrum phenotypes patients (n=46) [58]. A study on a Chinese cohort of pediatric epilepsy patients reported 8 variants in SCN1A, with 6 novel mutations and 2 inherited [59]. In this study, 2 inherited missense mutations in cytoplasmic loops (p.Arg500Trp and p.Ser1122Thr), 2 de novo missense mutations, 1 in the pore-forming loop (p.Ala1429Pro), and 1 in the extracellular loop (p.Gly271Asp) of SCN1A gene, were found in epilepsy patients (Figure 1). Novel mutations, i.e., c.812G>A, c.4285G>C, and, c.3147del have been found, which were not described in literature nor the population databases dbSNP or gnomAD. Also, c.4554dup and c.3364T>A were not described in literature nor in the population databases dbSNP but ClinVar and gnomAD, respectively. However, c.2851del and c.1498C>T were described in population databases, i.e., dbSNP (rs886042004, rs141188608), gnomAD (1498C>T: 0.00081%, including two heterozygotes) and ClinVar. Previously, R500Q (c.1499G>A) mutation was reported in patients with epilepsy febrile seizures plus (EFS+) [60], whereas we have found R500W (c.1498C>T).

4.2. SCN1B

The mutated human SCN1B (OMIM# 600235) gene is also associated with a spectrum of epileptic phenotypes with variable severity. The first pathogenic epilepsy-related mutation in SCN1B was reported in GEFS+ patients who inherited p.C121W mutation in an autosomal dominant pattern [61]. This shows that β subunits of SCN genes may influence the normal activity of Na_v and contribute to the pathogenesis of epilepsy. Heterozygous SCN1B mutations have been reported in GEFS+ and temporal lobe epilepsy [61-63]. Also, a mutation in the SCN1B gene was reported in DS patients, but rarely [64]. Homozygous SCN1B mutations are uncommon [65]. However, homozygous Homozygous SCN1B mutation in three consanguineous families causes severe recessive developmental delay and epileptic encephalopathy [66]. A study from Taiwan reported the SCN1B variant (rs55742440) to be associated with not achieving seizure-free with sodium channel blockers [67]. A novel SCN1B mutation (N110S) was reported recently in a Chinese pediatric epilepsy patient [68]. However, we found 2 SCN1B mutations, p.Ala197Val (c.590C>T) and p.Cys211Tyr (c.632G>A), in the cytoplasmic domain of Na_vβ1. Both of these mutations were described in population databases, i.e., dbSNP (rs554201948, rs141188608), gnomAD (0.0016% and 0.039%) and ClinVar. One of the SCN1B mutations (c.1498C>T) occurred in comorbidity with SCN1A mutation (c.590C>T). Both of these mutations were considered pathogenic by the bioinformatics tools.

4.3. SCN2A

SCN2A (OMIM# 182390) mutations have been reported in several epileptic pathologies of different types, GEFS+, DS, epileptic encephalopathies, and benign familial neonatal infantile seizure [69]. SCN2A variants dependent epilepsies mostly onset in early childhood with a wide variety of phenotypic spectrums, which may also include intellectual disability, developmental delay, and epileptic encephalopathy [70]. SCN2A mutations are also considered a major cause of epilepsy in infancy with migrating focal seizures [71]. Melikishvili, et al. [72] reported three de novo mutations (D1487E, M136R, and M1545V) in the SCN2A gene in neonate patients with tonic spams, oculoclonic seizures, and epilepsy of infancy with migrating focal seizures [72]. SCN2A variations cause an early-infantile onset of seizures (up to 3 months of age) and infantile/childhood-onset (>3 months of age), with recognizable phenotypes (infantile spasms, partial migrating discharges, etc.) [58]. Zeng, et al. [73] also reported that half of the SCN2A mutated patients have seizures onset during the neonate period and 80% have seizures in the first 6 months of age. A novel mutation (A215T) in SCN2A also causes the onset of seizures immediately after birth [74]. Moreover, various SCN2A variations have also been reported, including A1316V, A1283D, N1393K, and G40T [75]. A1316V variant was also reported previously in patients with Ohtahara syndrome [76,77]. In this study, only one pathogenic missense heterozygous mutation, c.3457G>C (p.Glu1153Gln), was found in the SCN2A gene, which was located in the extracellular loop connecting domains II and III, causing refractory seizures and global.

4.4. SCN3A

Various missense and truncating variations have been reported in SCN3A (OMIM# 182391) gene, which could be associated with epilepsy and related epileptic encephalopathy. Homozygous SCN3A mutations could be associated with mild nonspecific forms of epilepsy. A heterozygous mutation K247P is reported to be associated with focal epilepsy and developmental delay. K247P variation in Na_v1.3 causes loss of function with decreased cell surface expression and current density [78-80]. Pathogenic variations in SCN3A result in childhood-onset of epilepsy and cortical development malformation [81]. Zaman, et al. [82] reported I875T de novo mutation in SCN3A to be associated with developmental and epileptic encephalopathy as well diffuse polymicrogyria. Polymicrogyria is the disorder of progenitor cell proliferation and migration. Similarly, Miyatake, et al. [83] also reported the reported I875T mutation in SCN3A in patients with developmental and epileptic encephalopathy as well diffuse polymicrogyria. SCN3A mutations are associated with development delay, refractory epilepsy, polymicrogyria, intellectual disability, autism spectrum disorder, and pharmacoresponsive epilepsy [84]. In our cohort, we also found that SCN3A missense mutations, c.3486C>A and c.956T>C, cause speech delay and learning difficulties. Vanoye, et al. [80] reported M1323V mutation, the first reported mutation site in focal seizure-related genes, in children with focal seizures and epilepsy. The damaging SCN3A mutation D1688Y was reported in patients with focal seizures plus [85]. The SCN3A variant N302S causes depolarizing shifts in voltage-dependent activation and inactivation, as well as a slow recovery from inactivation; therefore indicates a decrease in sodium channel activity [86].

However, in our cohort mutations in the SCN3A were associated with different types of epilepsy or seizures. The c.44G>A mutation was associated with Generalized tonic-clonic and myoclonic seizures in a patient with a family history of febrile seizures. A patient also had attention deficit hyperactivity disorder (ADHD) with learning difficulties and epilepsy due to c.956T>C mutation in SCN3A. Furthermore, mutations in the SCN3A gene also cause epilepsy with the absence of seizures, i.e., c.2350A>G in our cohort. Similarly, another study also found that SCN3A missense mutations (c.A1816G, p.Ser606Gly) were associated with childhood absence epilepsy [87]. Also, a female with epilepsy (absence of seizure), learning difficulties, and benign infantile familial seizures-5 had mutations in the SCN3A (c.928A>T) and SCN8A (c.5113G>C) genes. Also, the c.4594A>T (p.Ile1532Phe) mutation in SCN8A was found in a patient with Infantile epileptic encephalopathy-13, neonatal seizure, hypotonia, and regression in development. Zaman, et al. [88] reported the first association of SCN3B mutation (p.Ile875Thr) with the early infantile epileptic encephalopathy. In this study, we found the association of SCN8A mutation (Ile1532Phe) with infantile epileptic encephalopathy-13.

4.5. SCN8A

SCN8A gene (OMIM# 600702) is associated with a spectrum of epilepsy phenotypes with variable severity. Since the first epilepsy-causing mutation was reported in 2012 [89], hundreds of SCN8A variants have been reported to be associated with the pathogenesis and phenotypes of epilepsy and epileptic encephalopathies. SCN8 mutations are mostly associated with early-onset epilepsy and epileptic encephalopathies, early infantile epileptic encephalopathies, and sudden unexpected death in epilepsy [90]. In epilepsy, SCN8A mutations are typically heterogeneous and important in the pathogenesis of epileptic encephalopathies in the early first year. However, SCN8A was never reported to be mutated in neonatal-onset epileptic encephalopathies with suppression-burst. Approximately half of the SCN8A mutations in the neonatal period have myoclonic jerks [91]. The epilepsy-related SCN8A mutations are predominantly de novo mutations or inherited from unaffected parents. E1483K missense variation in the SCN8A gene causes benign infantile spasms and paroxysmal dyskinesia [92]. SCN8A mutations are also associated with co-occurrence of epilepsy and intellectual disability or autism spectrum disorder [93]. De novo and novel mutations (A890T, S1596, R850Q, L407F, and R1617Q) were reported in Chinese children with epilepsy and intellectual disability/developmental delay [94]. Various variations alter the structure of Na_v1.8, causing channel inactivation, and hyperexcitability [95]. In our study, we found that patients with SCN8A mutations significantly had developmental delays. Previously, p.Leu267Ser mutation in SCN8A was reported in a 4-years girl presenting seizures and development delays [96]. Similarly, another study also reported that SCN3A variation (p. Arg223Gly) is associated with developmental and epileptic encephalopathy [97].

4.6. SCN9A

SCN9A gene (OMIM# 603415) mutations have been reported in epilepsy and autism-related disorders, which occurred alongside SCN1A mutations; therefore called “genes with modifying roles to SCN1A” [14,98]. Potentially pathogenic mutations (N641Y, Q10R, S490N, K655R, and I739V) in population allele frequencies are associated with monogenic seizure disorders [99]. Heterozygous rare variants in SCN9A were reported to be responsible for the epileptic syndrome [100]. R185H mutation in D I S2-S3 of Na_v1.9 was reported to be associated with focal seizures plus, inherited in horizontal pattern [85]. SCN9A mutations are also considered susceptible to epilepsy with febrile seizures plus [101]. SCN9A mutations could be the genetic modifier of Dravet syndrome caused by SCN1A mutation [102]. Other than febrile seizures, the G327E variant in SCN9A is reported to cause idiopathic focal epilepsy with Rolandic spikes in EEG [103]. Our study reports 4 missense mutations in the cytoplasmic loops of Nav1.9 α-subunits, which are c.279A>C (Lys93Asn), c.1482G>T (p.Lys494Asn), c.1336G>A (p.Glu446Lys), and c.4702A>C (p.Asn1568His) (Figure 5). c.1482G>T mutation is reported in population databases, i.e gnomAD (0.00081%, 2 heterozygous individuals reported) and ClinVar (ID: 331990). c.279A>C mutation was not described in literature nor in the population databases dbSNP or gnomAD. However, c.1336G>A was not described in the literature but in the population database dbSNP (rs1175228324). Also, we found that 2 patients had the same SCN9A mutation, c.279A>C, and expressed similar clinical features, i.e., global development delay, infantile spasms, and microcephaly in one patient and global development delay, drug-resistant epilepsy, and mental retardation in another patient. 2 more same mutations, c.1482G>T, were also found in SCN9A and they were also associated with GDD, microcephaly, and epilepsy.

SCN genes encode voltage-gated sodium channel proteins, which are involved in regulating the inflow of Na+ across the cell membrane of excitable and non-excitable cells in response to membrane potential and are hence responsible for neuronal excitability. The SCN genes are the most often mutated human epilepsy genes, and they are linked to a variety of symptoms with varying degrees of severity. This study suggested close relationships between genotype in sodium channel gene mutations and phenotype in epileptic encephalopathies. Since the prevalence of epilepsy may change over time, a longer follow-up period is required to characterize seizure characteristics. Along with phenotype data, functional analyses and the development of a database to record these data and results, maybe in collaboration with homologous sodium channels, will be required. Implementing methods for doing a high-throughput study of the influence of variations on channel function would significantly accelerate this procedure. Second, a whole-cell patch clamping investigation is required to confirm the function of the new SCN2A mutation. Electroencephalography, which directly monitors electrophysiological activity, may potentially indicate voltage-gated sodium channel impairment. Electrophysiological characterization of variants will evaluate whether the mutation is a gain-of-function or loss-of-function variant. Moreover, electrophysiological experiments under specific drugs influence will help in determining the omics-based personalized treatment.

This work illustrates the varied phenotypes related with Na_v mutations and the potential for precision treatment. SCN gene family mutation screening is clinically significant for detecting epilepsy and epilepsy-related disorders, such as GEFS+ and DS. However, gene sequencing of the large-sized SCN genes may be time-consuming and expensive. As a result, next-generation (exome- and genome-based) sequencing tools have transformed the discovery of functional mutations in epilepsy-causing genes such as the SCN family. Next-generation sequencing (NGS) technology is quick and inexpensive, and it has the potential to effectively replace traditional SCN mutation detection procedures. NGS screening for SCN mutations provides a more accurate prognosis for epileptic patients, leading to personalized therapy. NGS technology have enormous potential for determining patient-specific treatment. Follow-up of patients is critical for highlighting the effects of gene mutations on the development and prognosis of specific diseases, showing genotype-phenotype correlations, and suggesting novel treatment methods. Furthermore, the discovery of the molecular etiology allows the family to get effective genetic counselling for future pregnancies.

Ethical publication statement: We confirm that we have read the Journal’s position on issues involved in ethical publication and affirm that this report is consistent with those guidelines.

Acknowledgements:

The authors would like to thank Ms. Mary Joseph and Ms. Mylene Lamsen for their technical support.

Funding

No funding available for this work.

Availability of data and materials

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.

Ethics approval and consent to participate

The study was carried out in accordance with the code of international and local Ethics (Declaration of Helsinki). This study was reviewed and approved by the local ethics committee of the King Fahad Specialist Hospital Dammam (Dammam, Saudi Arabia).

Patient consent for participation

The parents of the patient provided written informed consent for participation

Competing interests

Neither of the authors has any conflict of interest to disclose

Beghi, E. The Epidemiology of Epilepsy. Neuroepidemiology 54, 185-191, doi:10.1159/000503831 (2020).
Liu, G., Xiao, R., Xu, L. & Cai, J. Minireview of Epilepsy Detection Techniques Based on Electroencephalogram Signals. Frontiers in System Neurosciece 15, doi:10.3389/fnsys.2021.685387 (2021).
Engel Jr, J. A proposed diagnostic scheme for people with epileptic seizures and with epilepsy: report of the ILAE Task Force on Classification and Terminology. Epilepsia 42, 796-803 (2001).
Yamatogi, Y. & Ohtahara, S. Multiple independent spike foci and epilepsy, with special reference to a new epileptic syndrome of “severe epilepsy with multiple independent spike foci”. Epilepsy research 70, 96-104 (2006).
Hussain, S. A. Epileptic encephalopathies. CONTINUUM: Lifelong Learning in Neurology 24, 171-185 (2018).
Berg, A. T. et al. (Wiley Online Library, 2010).
Khan, S. & Al Baradie, R. Epileptic Encephalopathies: An Overview. Epilepsy Res Treat 2012, 403592, doi:10.1155/2012/403592 (2012).
Nabbout, R. & Dulac, O. Epileptic encephalopathies: a brief overview. Journal of Clinical Neurophysiology 20, 393-397 (2003).
Dulac, O. Epileptic encephalopathy. Epilepsia 42, 23-26 (2001).
Smith, M. C. & Hoeppner, T. J. Epileptic encephalopathy of late childhood: Landau-Kleffner syndrome and the syndrome of continuous spikes and waves during slow-wave sleep. Journal of Clinical Neurophysiology 20, 462-472 (2003).
Syed, P., Durisic, N., Harvey, R. J., Sah, P. & Lynch, J. W. Effects of GABAA Receptor α3 Subunit Epilepsy Mutations on Inhibitory Synaptic Signaling. Frontiers in molecular neurosciece 13, doi:10.3389/fnmol.2020.602559 (2020).
Khamdiyeva, O., Tileules, Z., Baratzhanova, G., Perfilyeva, A. & Djansugurova, L. The study of sodium and potassium channel gene single-nucleotide variation significance in non-mechanical forms of epilepsy. Egyptian Journal of Medical Human Genetics 22, 5, doi:10.1186/s43042-020-00123-y (2021).
Alehabib, E. et al. Clinical and molecular spectrum of P/Q type calcium channel Cav2.1 in epileptic patients. Orphanet Journal of Rare Diseases 16, 461, doi:10.1186/s13023-021-02101-y (2021).
Ademuwagun, I. A., Rotimi, S. O., Syrbe, S., Ajamma, Y. U. & Adebiyi, E. Voltage Gated Sodium Channel Genes in Epilepsy: Mutations, Functional Studies, and Treatment Dimensions. Frontiers in Neurology 12, doi:10.3389/fneur.2021.600050 (2021).
Catterall, W. A. Ion channel voltage sensors: structure, function, and pathophysiology. Neuron 67, 915-928, doi:10.1016/j.neuron.2010.08.021 (2010).
Hull, J. M. & Isom, L. L. Voltage-gated sodium channel β subunits: The power outside the pore in brain development and disease. Neuropharmacology 132, 43-57, doi:10.1016/j.neuropharm.2017.09.018 (2018).
Laedermann, C., Syam, N., Decosterd, I. & Abriel, H. β1- and β3- voltage-gated sodium channel subunits modulate cell surface expression and glycosylation of Nav1.7 in HEK293 cells. Frontiers in cellular neuroscience 7, doi:10.3389/fncel.2013.00137 (2013).
Menezes, L. F. S., Sabiá Júnior, E. F., Tibery, D. V., Carneiro, L. d. A. & Schwartz, E. F. Epilepsy-Related Voltage-Gated Sodium Channelopathies: A Review. Front Pharmacol 11, doi:10.3389/fphar.2020.01276 (2020).
Namadurai, S. et al. A new look at sodium channel β subunits. Open Biol 5, 140192-140192, doi:10.1098/rsob.140192 (2015).
O'Malley, H. A. & Isom, L. L. Sodium channel β subunits: emerging targets in channelopathies. Annual review of physiology 77, 481-504, doi:10.1146/annurev-physiol-021014-071846 (2015).
Helbig, I., Scheffer, I. E., Mulley, J. C. & Berkovic, S. F. Navigating the channels and beyond: unravelling the genetics of the epilepsies. The Lancet Neurology 7, 231-245 (2008).
Hildebrand, M. S. et al. Recent advances in the molecular genetics of epilepsy. Journal of medical genetics 50, 271-279 (2013).
Trimmer, J. S. & Rhodes, K. J. Localization of voltage-gated ion channels in mammalian brain. Annual review of physiology 66, 477-519, doi:10.1146/annurev.physiol.66.032102.113328 (2004).
Brackenbury, W. & Isom, L. Na+ Channel β Subunits: Overachievers of the Ion Channel Family. Front Pharmacol 2, doi:10.3389/fphar.2011.00053 (2011).
Lee, A. & Goldin, A. L. Role of the terminal domains in sodium channel localization. Channels (Austin) 3, 171-180, doi:10.4161/chan.3.3.8854 (2009).
Catterall, W. A. Sodium Channels, Inherited Epilepsy, and Antiepileptic Drugs. Annual Review of Pharmacology and Toxicology 54, 317-338, doi:10.1146/annurev-pharmtox-011112-140232 (2014).
Martin, M. S. et al. Altered Function of the SCN1A Voltage-gated Sodium Channel Leads to γ-Aminobutyric Acid-ergic (GABAergic) Interneuron Abnormalities*. Journal of Biological Chemistry 285, 9823-9834, doi:https://doi.org/10.1074/jbc.M109.078568 (2010).
Richards, S. et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genetics in medicine : official journal of the American College of Medical Genetics 17, 405-424, doi:10.1038/gim.2015.30 (2015).
Pires, D. E., Ascher, D. B. & Blundell, T. L. DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach. Nucleic Acids Res 42, W314-319, doi:10.1093/nar/gku411 (2014).
Shi, X. Y. et al. Efficacy of antiepileptic drugs for the treatment of Dravet syndrome with different genotypes. Brain & development 38, 40-46, doi:10.1016/j.braindev.2015.06.008 (2016).
Lotte, J., Haberlandt, E., Neubauer, B., Staudt, M. & Kluger, G. J. Bromide in patients with SCN1A-mutations manifesting as Dravet syndrome. Neuropediatrics 43, 17-21, doi:10.1055/s-0032-1307454 (2012).
Wang, Y.-Q., Fang, Z.-X., Zhang, Y.-W., Xie, L.-L. & Jiang, L. Efficacy of the ketogenic diet in patients with Dravet syndrome: A meta-analysis. Seizure 81, 36-42 (2020).
Dutton, S. B. et al. Protective effect of the ketogenic diet in Scn1a mutant mice. Epilepsia 52, 2050-2056, doi:10.1111/j.1528-1167.2011.03211.x (2011).
Zhu, Z. et al. SCN1B Genetic Variants: A Review of the Spectrum of Clinical Phenotypes and a Report of Early Myoclonic Encephalopathy. Children 9, 1507 (2022).
Reif, P. S., Tsai, M. H., Helbig, I., Rosenow, F. & Klein, K. M. Precision medicine in genetic epilepsies: break of dawn? Expert review of neurotherapeutics 17, 381-392, doi:10.1080/14737175.2017.1253476 (2017).
Strzelczyk, A. & Schubert-Bast, S. A Practical Guide to the Treatment of Dravet Syndrome with Anti-Seizure Medication. CNS drugs 36, 217-237, doi:10.1007/s40263-022-00898-1 (2022).
Zhang, S. et al. SCN9A Epileptic Encephalopathy Mutations Display a Gain-of-function Phenotype and Distinct Sensitivity to Oxcarbazepine. Neuroscience bulletin 36, 11-24, doi:10.1007/s12264-019-00413-5 (2020).
Dang, L. T., Quinonez, S. C., Becka, B. R., Isom, L. L. & Joshi, S. M. Dramatic Improvement in Seizures With Phenytoin Treatment in an Individual With Refractory Epilepsy and a SCN1B Variant. Pediatric neurology 108, 121-122, doi:10.1016/j.pediatrneurol.2020.03.012 (2020).
Adney, S. K. et al. Functional and pharmacological evaluation of a novel SCN2A variant linked to early-onset epilepsy. Annals of clinical and translational neurology 7, 1488-1501, doi:https://doi.org/10.1002/acn3.51105 (2020).
Tian, X. et al. Ketogenic Diet in Infants with Early-Onset Epileptic Encephalopathy and SCN2A Mutation. Yonsei medical journal 62, 370-373, doi:10.3349/ymj.2021.62.4.370 (2021).
Helbig, K. L. & Goldberg, E. M. SCN3A-Related Neurodevelopmental Disorder. (University of Washington, Seattle, 2021).
Hammer, M. F., Wagnon, J. L., Mefford, H. C. & Meisler, M. H. SCN8A-related epilepsy with encephalopathy. GeneReviews® (2016).
Chandler, W. K., Hodgkin, A. L. & Meves, H. The effect of changing the internal solution on sodium inactivation and related phenomena in giant axons. J Physiol 180, 821-836, doi:10.1113/jphysiol.1965.sp007733 (1965).
Tan, E. H., Yusoff, A. A. M., Abdullah, J. M. & Razak, S. A. Generalized epilepsy with febrile seizure plus (GEFS+) spectrum: Novel de novo mutation of SCN1A detected in a Malaysian patient. J Pediatr Neurosci 7, 123-125, doi:10.4103/1817-1745.102575 (2012).
Ragona, F. et al. Dravet syndrome: early clinical manifestations and cognitive outcome in 37 Italian patients. Brain & development 32, 71-77, doi:10.1016/j.braindev.2009.09.014 (2010).
Claes, L. et al. De novo mutations in the sodium-channel gene SCN1A cause severe myoclonic epilepsy of infancy. The American Journal of Human Genetics 68, 1327-1332 (2001).
Horák, O. et al. Next-generation sequencing in children with epilepsy: The importance of precise genotype–phenotype correlation. Epilepsy & Behavior 128, 108564, doi:https://doi.org/10.1016/j.yebeh.2022.108564 (2022).
Dravet, C. The core Dravet syndrome phenotype. Epilepsia 52, 3-9, doi:https://doi.org/10.1111/j.1528-1167.2011.02994.x (2011).
Genton, P., Velizarova, R. & Dravet, C. Dravet syndrome: the long-term outcome. Epilepsia 52 Suppl 2, 44-49, doi:10.1111/j.1528-1167.2011.03001.x (2011).
Depienne, C. et al. Spectrum of SCN1A gene mutations associated with Dravet syndrome: analysis of 333 patients. Journal of medical genetics 46, 183-191 (2009).
Tonekaboni, S. H. et al. Sodium Channel Gene Mutations in Children with GEFS+ and Dravet Syndrome: A Cross Sectional Study. Iran J Child Neurol 7, 31-36 (2013).
Bjurulf, B. et al. Dravet syndrome in children—A population-based study. Epilepsy research 182, 106922, doi:https://doi.org/10.1016/j.eplepsyres.2022.106922 (2022).
Gertler, T. S., Calhoun, J. & Laux, L. A single-center, retrospective analysis of genotype-phenotype correlations in children with Dravet syndrome. Seizure 75, 1-6, doi:10.1016/j.seizure.2019.12.009 (2020).
Wang, J.-Y. et al. Clinical and Functional Features of Epilepsy-Associated In-Frame Deletion Variants in SCN1A. Frontiers in molecular neurosciece 15, doi:10.3389/fnmol.2022.828846 (2022).
Usluer, S. et al. SCN1A gene sequencing in 46 Turkish epilepsy patients disclosed 12 novel mutations. Seizure 39, 34-43, doi:https://doi.org/10.1016/j.seizure.2016.05.008 (2016).
Long, S. et al. The Clinical and Genetic Features of Co-occurring Epilepsy and Autism Spectrum Disorder in Chinese Children. Front Neurol 10, 505, doi:10.3389/fneur.2019.00505 (2019).
Türkyılmaz, A., Tekin, E., Yaralı, O. & Çebi, A. H. Genetic Landscape of SCN1A Variants in a Turkish Cohort with GEFS+ Spectrum and Dravet Syndrome. Molecular Syndromology, doi:10.1159/000521330 (2022).
Wolff, M. et al. Genetic and phenotypic heterogeneity suggest therapeutic implications in SCN2A-related disorders. Brain : a journal of neurology 140, 1316-1336, doi:10.1093/brain/awx054 (2017).
Zhao, X. et al. Genetic analysis and identification of novel variations in Chinese patients with pediatric epilepsy by whole-exome sequencing. Neurological Sciences, doi:10.1007/s10072-022-05953-9 (2022).
Ma, H. et al. Mutations in the sodium channel genes <em>SCN1A, SCN3A</em>, and <em>SCN9A</em> in children with epilepsy with febrile seizures plus(EFS+). Seizure - European Journal of Epilepsy 88, 146-152, doi:10.1016/j.seizure.2021.04.006 (2021).
Wallace, R. H. et al. Febrile seizures and generalized epilepsy associated with a mutation in the Na+-channel beta1 subunit gene SCN1B. Nat Genet 19, 366-370, doi:10.1038/1252 (1998).
Scheffer, I. E. et al. Temporal lobe epilepsy and GEFS+ phenotypes associated with SCN1B mutations. Brain : a journal of neurology 130, 100-109, doi:10.1093/brain/awl272 (2007).
Audenaert, D. et al. A deletion in SCN1B is associated with febrile seizures and early-onset absence epilepsy. Neurology 61, 854-856, doi:10.1212/01.wnl.0000080362.55784.1c (2003).
Patino, G. A. et al. A functional null mutation of SCN1B in a patient with Dravet syndrome. The Journal of neuroscience : the official journal of the Society for Neuroscience 29, 10764-10778, doi:10.1523/jneurosci.2475-09.2009 (2009).
Kim, Y. O. et al. Do mutations in SCN1B cause Dravet syndrome? Epilepsy research 103, 97-100, doi:10.1016/j.eplepsyres.2012.10.009 (2013).
Ramadan, W. et al. Confirming the recessive inheritance of SCN1B mutations in developmental epileptic encephalopathy. Clinical genetics 92, 327-331, doi:10.1111/cge.12999 (2017).
Lin, C.-H., Ho, C.-J., Lu, Y.-T. & Tsai, M.-H. Response to Sodium Channel blocking Antiseizure medications and coding polymorphisms of Sodium Channel genes in Taiwanese epilepsy patients. BMC Neurology 21, 367, doi:10.1186/s12883-021-02395-2 (2021).
Miao, P. et al. Genotype and phenotype analysis using an epilepsy-associated gene panel in Chinese pediatric epilepsy patients. Clinical genetics 94, 512-520, doi:https://doi.org/10.1111/cge.13441 (2018).
Reid, C. A., Berkovic, S. F. & Petrou, S. Mechanisms of human inherited epilepsies. Progress in neurobiology 87, 41-57, doi:10.1016/j.pneurobio.2008.09.016 (2009).
Kim, H. J. et al. The phenotype and treatment of SCN2A-related developmental and epileptic encephalopathy. Epileptic disorders : international epilepsy journal with videotape 22, 563-570, doi:10.1684/epd.2020.1199 (2020).
Howell, K. B. et al. SCN2A encephalopathy: A major cause of epilepsy of infancy with migrating focal seizures. Neurology 85, 958-966, doi:10.1212/wnl.0000000000001926 (2015).
Melikishvili, G., Dulac, O. & Gataullina, S. Neonatal SCN2A encephalopathy: A peculiar recognizable electroclinical sequence. Epilepsy Behav 111, 107187, doi:10.1016/j.yebeh.2020.107187 (2020).
Zeng, Q. et al. SCN2A-Related Epilepsy: The Phenotypic Spectrum, Treatment and Prognosis. Front Mol Neurosci 15, 809951-809951, doi:10.3389/fnmol.2022.809951 (2022).
Penkl, A. et al. A mutation in the neonatal isoform of SCN2A causes neonatal-onset epilepsy. American Journal of Medical Genetics Part A 188, 941-947, doi:https://doi.org/10.1002/ajmg.a.62581 (2022).
Epifanio, R. et al. SCN2A Pathogenic Variants and Epilepsy: Heterogeneous Clinical, Genetic and Diagnostic Features. Brain sciences 12, 18 (2022).
Parrini, E. et al. Diagnostic Targeted Resequencing in 349 Patients with Drug-Resistant Pediatric Epilepsies Identifies Causative Mutations in 30 Different Genes. Hum Mutat 38, 216-225, doi:10.1002/humu.23149 (2017).
Lindy, A. S. et al. Diagnostic outcomes for genetic testing of 70 genes in 8565 patients with epilepsy and neurodevelopmental disorders. Epilepsia 59, 1062-1071, doi:10.1111/epi.14074 (2018).
Holland, K. D. et al. Mutation of sodium channel SCN3A in a patient with cryptogenic pediatric partial epilepsy. Neuroscience letters 433, 65-70, doi:10.1016/j.neulet.2007.12.064 (2008).
Lamar, T. et al. SCN3A deficiency associated with increased seizure susceptibility. Neurobiology of disease 102, 38-48, doi:10.1016/j.nbd.2017.02.006 (2017).
Vanoye, C. G., Gurnett, C. A., Holland, K. D., George, A. L., Jr. & Kearney, J. A. Novel SCN3A variants associated with focal epilepsy in children. Neurobiology of disease 62, 313-322, doi:10.1016/j.nbd.2013.10.015 (2014).
Zaman, T. et al. SCN3A-Related Neurodevelopmental Disorder: A Spectrum of Epilepsy and Brain Malformation. Annals of neurology 88, 348-362, doi:https://doi.org/10.1002/ana.25809 (2020).
Zaman, T. et al. Mutations in SCN3A cause early infantile epileptic encephalopathy. Annals of neurology 83, 703-717, doi:10.1002/ana.25188 (2018).
Miyatake, S. et al. Recurrent SCN3A p.Ile875Thr variant in patients with polymicrogyria. Annals of neurology 84, 159-161, doi:10.1002/ana.25256 (2018).
Inuzuka, L. M. et al. Neurodevelopmental disorder associated with de novo SCN3A pathogenic variants: two new cases and review of the literature. Brain & development 42, 211-216, doi:10.1016/j.braindev.2019.09.004 (2020).
Ma, H. et al. Mutations in the sodium channel genes SCN1A, SCN3A, and SCN9A in children with epilepsy with febrile seizures plus(EFS+). Seizure 88, 146-152, doi:https://doi.org/10.1016/j.seizure.2021.04.006 (2021).
Chen, Y.-J. et al. Electrophysiological differences between the same pore region mutation in SCN1A and SCN3A. Molecular neurobiology 51, 1263-1270 (2015).
Li, W. et al. Identification of a novel variant p.Ser606Gly in SCN3A associated with childhood absence epilepsy. Epilepsy research 175, 106682, doi:https://doi.org/10.1016/j.eplepsyres.2021.106682 (2021).
Zaman, T. et al. Mutations in SCN3A cause early infantile epileptic encephalopathy. Annals of neurology 83, 703-717, doi:https://doi.org/10.1002/ana.25188 (2018).
Veeramah, K. R. et al. De novo pathogenic SCN8A mutation identified by whole-genome sequencing of a family quartet affected by infantile epileptic encephalopathy and SUDEP. American journal of human genetics 90, 502-510, doi:10.1016/j.ajhg.2012.01.006 (2012).
Meisler, M. H. SCN8A encephalopathy: Mechanisms and models. Epilepsia 60 Suppl 3, S86-s91, doi:10.1111/epi.14703 (2019).
Denis, J. et al. Clinical study of 19 patients with SCN8A-related epilepsy: Two modes of onset regarding EEG and seizures. Epilepsia 60, 845-856, doi:10.1111/epi.14727 (2019).
Gardella, E. et al. Benign infantile seizures and paroxysmal dyskinesia caused by an SCN8A mutation. Annals of neurology 79, 428-436, doi:10.1002/ana.24580 (2016).
Butler, K. M. et al. De novo and inherited SCN8A epilepsy mutations detected by gene panel analysis. Epilepsy research 129, 17-25, doi:10.1016/j.eplepsyres.2016.11.002 (2017).
Kong, W. et al. SCN8A mutations in Chinese children with early onset epilepsy and intellectual disability. Epilepsia 56, 431-438, doi:10.1111/epi.12925 (2015).
Nguyen, H. M. & Goldin, A. L. Sodium channel carboxyl-terminal residue regulates fast inactivation. The Journal of biological chemistry 285, 9077-9089, doi:10.1074/jbc.M109.054940 (2010).
Malcolmson, J. et al. SCN8A mutation in a child presenting with seizures and developmental delays. Cold Spring Harb Mol Case Stud 2, a001073-a001073, doi:10.1101/mcs.a001073 (2016).
Liu, Y., Koko, M. & Lerche, H. A SCN8A variant associated with severe early onset epilepsy and developmental delay: Loss- or gain-of-function? Epilepsy research 178, 106824, doi:https://doi.org/10.1016/j.eplepsyres.2021.106824 (2021).
Aicardi, J. & Ohtahara, S. Severe neonatal epilepsies with suppression-burst pattern. Epileptic syndromes in infancy, childhood and adolescence, 39-52 (2005).
Fasham, J. et al. No association between SCN9A and monogenic human epilepsy disorders. PLoS genetics 16, e1009161, doi:10.1371/journal.pgen.1009161 (2020).
Banfi, P. et al. Lamotrigine induced Brugada-pattern in a patient with genetic epilepsy associated with a novel variant in SCN9A. Gene 754, 144847 (2020).
Zhang, T., Chen, M., Zhu, A., Zhang, X. & Fang, T. Novel mutation of SCN9A gene causing generalized epilepsy with febrile seizures plus in a Chinese family. Neurological Sciences 41, 1913-1917 (2020).
Singh, N. A. et al. A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome. PLoS genetics 5, e1000649 (2009).
Liu, Z. et al. G327E mutation in SCN9A gene causes idiopathic focal epilepsy with Rolandic spikes: a case report of twin sisters. Neurological Sciences 40, 1457-1460 (2019).

No competing interests reported.

Download PDF

Version 1

posted

You are reading this latest preprint version

Clinical heterogeneity of epilepsy and mutation spectrum of voltage-gated sodium channel genes

Status:

Version 1

Abstract

Figures

1. Introduction

2. Methods

2.1. Patient recruitment

2.2.Genomic DNA Sequencing

2.3. In silico Assessment of the Mutations to Identify Putative Pathogenic Mutations

3. Results

3.1. Patient Characteristics

3.2. Na_v (SCN) Genes Variations Diversity

3.3. Genotype-Phenotype correlation

3.4. Mutation Prediction and Verification of Functional Effects of Amino acid Variations

3.5. 3D-visualization of mutations in Na_v

3.6. Protein-protein interation network

3.7. Approach towards Personalized Medicine

4. DISCUSSION

4.1. SCN1A

4.2. SCN1B

4.3. SCN2A

4.4. SCN3A

4.5. SCN8A

4.6. SCN9A

Conclusions & Future Perspectives

Declarations

References

Additional Declarations

Status:

Version 1

Clinical heterogeneity of epilepsy and mutation spectrum of voltage-gated sodium channel genes

Status:

Version 1

Abstract

Figures

1. Introduction

2. Methods

2.1. Patient recruitment

2.2.Genomic DNA Sequencing

2.3. In silico Assessment of the Mutations to Identify Putative Pathogenic Mutations

3. Results

3.1. Patient Characteristics

3.2. Nav (SCN) Genes Variations Diversity

3.3. Genotype-Phenotype correlation

3.4. Mutation Prediction and Verification of Functional Effects of Amino acid Variations

3.5. 3D-visualization of mutations in Nav

3.6. Protein-protein interation network

3.7. Approach towards Personalized Medicine

4. DISCUSSION

4.1. SCN1A

4.2. SCN1B

4.3. SCN2A

4.4. SCN3A

4.5. SCN8A

4.6. SCN9A

Conclusions & Future Perspectives

Declarations

References

Additional Declarations

Status:

Version 1

3.2. Na_v (SCN) Genes Variations Diversity

3.5. 3D-visualization of mutations in Na_v