Case Report: Novel Homozygous Likely Pathogenic SCN1A Variant With Autosomal Recessive Inheritance and Review of the Literature

Comprehensive genetic diagnosis and therapeutic perspectives in 155 children with developmental and epileptic encephalopathy

We studied a retrospective cohort of children with developmental and epileptic encephalopathy (DEE), a group of neurological conditions characterized by early onset epilepsy and severe developmental delay. Cases were recruited from three university hospitals based on clinical criteria, after a blinded cross-validation process, and most were subject to both array-CGH and exome-based gene panel analyses. 155 subjects were included. A genetic diagnosis was identified in 105 (68 %). A majority of patients (71 %) had onset of symptoms before the age of one year. In this age group a disease-causing variant was identified in 73 % of children, the highest proportion of cases reported so far. Genetic heterogeneity was high, involving 40 different genes. The most prevalent gene was SCN1A. Eight genes were identified in multiple patients and accounted for 50 % of all diagnoses. The remaining genes represented ultra-rare disorders. In many cases, molecular diagnosis leads to treatment adaptation and allows for genetic counseling. Those results highlight the growing importance of genetic investigations especially in children with symptoms onset before the age of 1. Finally, we evaluated the disease-causing variants in an intention-to-treat approach and found that almost half would theoretically be amenable to personalized therapy using antisense oligonucleotides (ASOs).

Biallelic SCN1A variants with divergent epilepsy phenotypes

PURPOSE

Pathogenic SCN1A variants most commonly cause autosomal dominant Dravet syndrome and genetic epilepsy with febrile seizures plus (GEFS+). However, rare homozygous SCN1A variants have also been reported. We report two new cases of homozygous SCN1A variants associated with divergent epilepsy phenotypes.

METHODS

We retrospectively reviewed the charts of two unrelated patients with different homozygous SCN1A variants. We also reviewed all published cases of biallelic SCN1A pathogenic variants, focusing on the epilepsy phenotypes.

RESULTS

Patient 1 had a homozygous c. 1676T>A, (p. Ile559Asn) variant of uncertain significance, inherited from asymptomatic parents. Patient 1 exhibited early afebrile seizures controlled by first-line anti-seizure medications and no febrile seizures or status epilepticus, as well as profound developmental delay, macrocephaly, and mild dysmorphic features. Patient 2 had a homozygous pathogenic c. 4970G>A, (p. Arg1657His) variant carried by asymptomatic parents. This patient presented with early, recurrent, and prolonged febrile seizures, moderate developmental delay, and motor dysfunction and was diagnosed with Dravet syndrome. We identified 16 further cases from the literature. Including our cases, 9/18 (50 %) were diagnosed with Dravet syndrome and 6/18 (33 %) with GEFS+. The mean age of seizure onset was 7 months (range 3-19 months). Phenotypes ranged from intact neurodevelopment with controlled epilepsy to profound developmental delay and refractory epilepsy.

CONCLUSION

These cases highlight and expand the phenotypic spectrum associated with biallelic SCN1A variants. While some patients present typically for Dravet/GEFS+, others may present with developmental delay in the absence of febrile seizures or status epilepticus. Further studies are needed to confirm genotype-phenotype relationships.

The Biallelic Inheritance of Two Novel SCN1A Variants Results in Developmental and Epileptic Encephalopathy Responsive to Levetiracetam

Loss-, gain-of-function and mixed variants in SCN1A (Nav1.1 voltage-gated sodium channel) have been associated with a spectrum of neurologic disorders with different severity and drug-responsiveness. Most SCN1A variants are heterozygous changes occurring de novo or dominantly inherited; recessive inheritance has been reported in a few cases. Here, we report a family in which the biallelic inheritance of two novel SCN1A variants, N935Y and H1393Q, occurs in two siblings presenting with drug-responsive developmental and epileptic encephalopathy and born to heterozygous asymptomatic parents. To assess the genotype-phenotype correlation and support the treatment choice, HEK 293 cells were transfected with different combinations of the SCN1A WT and mutant cDNAs, and the resulting sodium currents were recorded through whole-cell patch-clamp. Functional studies showed that the N935Y and H1393Q channels and their combinations with the WT (WT + N935Y and WT + H1393Q) had current densities and biophysical properties comparable with those of their respective control conditions. This explains the asymptomatic condition of the probands' parents. The co-expression of the N935Y + H1393Q channels, mimicking the recessive inheritance of the two variants in siblings, showed ~20% reduced current amplitude compared with WT and with parental channels. This mild loss of Nav1.1 function may contribute in part to the disease pathogenesis, although other mechanisms may be involved.

SCN1A Channels a Wide Range of Epileptic Phenotypes: Report of Novel and Known Variants with Variable Presentations

SCN1A, the gene encoding for the Nav1.1 channel, exhibits dominant interneuron-specific expression, whereby variants disrupting the channel's function affect the initiation and propagation of action potentials and neuronal excitability causing various types of epilepsy. Dravet syndrome (DS), the first described clinical presentation of SCN1A channelopathy, is characterized by severe myoclonic epilepsy in infancy (SMEI). Variants' characteristics and other genetic or epigenetic factors lead to extreme clinical heterogeneity, ranging from non-epileptic conditions to developmental and epileptic encephalopathy (DEE). This current study reports on findings from 343 patients referred by physicians in hospitals and tertiary care centers in Greece between 2017 and 2023. Positive family history for specific neurologic disorders was disclosed in 89 cases and the one common clinical feature was the onset of seizures, at a mean age of 17 months (range from birth to 15 years old). Most patients were specifically referred for SCN1A investigation (Sanger Sequencing and MLPA) and only five for next generation sequencing. Twenty-six SCN1A variants were detected, including nine novel causative variants (c.4567A>Τ, c.5564C>A, c.2176+2T>C, c.3646G>C, c.4331C>A, c.1130_1131delGAinsAC, c.1574_1580delCTGAGGA, c.4620A>G and c.5462A>C), and are herein presented, along with subsequent genotype-phenotype associations. The identification of novel variants complements SCN1A databases extending our expertise on genetic counseling and patient and family management including gene-based personalized interventions.

Exome data of developmental and epileptic encephalopathy patients reveals de novo and inherited pathologic variants in epilepsy-associated genes

PURPOSE

In Developmental and Epileptic Encephalopathies (DEEs), identifying the precise genetic factors guides the clinicians to apply the most appropriate treatment for the patient. Due to high locus heterogeneity, WES analysis is a promising approach for the genetic diagnosis of DEE. Therefore, the aim of the present study is to evaluate the utility of WES in the diagnosis and treatment of DEE patients.

METHODS

The exome data of 29 DEE patients were filtrated for destructive and missense mutations in 1896 epilepsy-related genes to detect the causative variants and examine the genotype-phenotype correlations. We performed Sanger sequencing with the available DNA samples to follow the co-segregation of the variants with the disease phenotype in the families. Also, the structural effects of p.Asn1053Ser, p.Pro120Ser and p.Glu1868Gly mutations on KCNMA1, NPC2, and SCN2A proteins, respectively, were evaluated by molecular dynamics (MD) and molecular docking simulations.

RESULTS

Out of 29, nine patients (31%) harbor pathological (P) or likely pathological (LP) mutations in SCN2A, KCNQ2, ATP1A2, KCNMA1, and MECP2 genes, and three patients have VUS variants (10%) in SCN1A and SCN2A genes. Sanger sequencing results indicated that three of the patients have de novo mutations while eight of them carry paternally and/or maternally inherited causative variants. MD and molecular docking simulations supported the destructive effects of the mutations on KCNMA1, NPC2, and SCN2A protein structures.

CONCLUSION

Herein we demonstrated the effectiveness of WES for DEE with high locus heterogeneity. Identification of the genetic etiology guided the clinicians to adjust the proper treatment for the patients.

Prediction of molecular phenotypes for novel SCN1A variants from a Turkish genetic epilepsy syndromes cohort and report of two new patients with recessive Dravet syndrome

Dravet syndrome and genetic epilepsy with febrile seizures plus (GEFS+) are both epilepsy syndromes that can be attributed to deleterious mutations occurring in SCN1A, the gene encoding the pore-forming α-subunit of the NaV 1.1 voltage-gated sodium channel predominantly expressed in the central nervous system. In this research endeavor, our goal is to expand our prior cohort of Turkish patients affected by SCN1A-positive genetic epilepsy disorders. This will be accomplished by incorporating two recently discovered and infrequent index cases who possess a novel biallelic (homozygous) SCN1A missense variant, namely E158G, associated with Dravet syndrome. Furthermore, our intention is to use computational techniques to predict the molecular phenotypes of each distinct SCN1A variant that has been detected to date within our center. The correlation between genotype and phenotype in Dravet syndrome/GEFS+ is intricate and necessitates meticulous clinical investigation as well as advanced scientific exploration. Broadened mechanistic and structural insights into NaV 1.1 dysfunction offer significant promise in facilitating the development of targeted and effective therapies, which will ultimately enhance clinical outcomes in the treatment of epilepsy.