NPRL3 (nitrogen permease regulator-like 3) variants are associated with focal epilepsy syndromes, including sleep-related hypermotor epilepsy (SHE) and familial focal epilepsy with variable foci (FFEVF), with or without focal cortical dysplasia (FCD). The NPRL3 gene encodes a protein that forms the GATOR1 complex, which regulates the mTOR signaling pathway.To characterize the epilepsy phenotype associated with NPRL3, assess treatment strategies, and evaluate patient prognosis.We conducted a multicenter, retrospective study using an online questionnaire to collect clinical data on seizure onset, crisis-like seizure exacerbations, MRI findings, neuropsychological assessment, treatment, and genetic variants. Variants were classified per ACMG guidelines. The study was part of the Network for Therapy in Rare Epilepsies (NETRE).Data from 37 patients with NPRL3-associated epilepsy were analyzed. Mean age at seizure onset was 3.7 years (median with interquartile range [IQR] 1.3-4.9). Over 1 to 45 years of follow-up (mean 13.6, IQR 5.4-18), 21/37 (57%) experienced crisis-like seizure exacerbations. MRI abnormalities were present in 10/36 (28%) cases: 8 FCD, 1 hippocampal sclerosis, and 1 hippocampal asymmetry. Persistent focal epileptiform discharges were present on serial EEGs in 20/37 patients (54%). Highest drug response rates were seen with lacosamide, followed by clobazam, carbamazepine/oxcarbazepine, and lamotrigine. Epilepsy surgery (n = 8) led to seizure freedom in four and significant reduction in one case.Crisis-like seizure exacerbations were common in NPRL3-associated epilepsy. Sodium channel blockers showed notable efficacy. Epilepsy surgery was beneficial even in MRI-negative cases. No distinct genotype-phenotype correlation was identified.

Familial focal epilepsy with variable foci 2 (FFEVF2), an autosomal dominant disorder caused by pathogenic heterozygous variants in the NPRL2 gene, is characterized by focal epilepsy originating in different cortical regions of the temporal, frontal, parietal, and occipital lobes of the brain. The study included a Chinese family in which proband had epilepsy, and her brother had autism, attention deficit hyperactivity disorder (ADHD), and mild intellectual disability (ID). Blood samples of the two children and their parents were collected for whole exome sequencing (WES). Proband was a 1-month-and-7-day-old baby girl with epilepsy manifesting as focal to bilateral tonic-clonic seizures and cranial magnetic resonance imaging showing focal cortical dysplasia or subcortical grey matter ectopia in the left anterior and posterior central gyrus. WES revealed a heterozygous variant of the NPRL2 gene [c.907delC (p. Gln303Serfs*11)]. Sanger sequencing confirmed that the variant was inherited from her unaffected mother. According to the ACMG, the variant was classified as likely pathogenic. Finally, she was diagnosed with FFEVF2. Her epilepsy type was only reported in one patient with FFEVF2 with multiple seizure types. Follow-up revealed that she had a global developmental delay and absent language, and despite numerous antiseizure medications, her seizures were uncontrolled. Her brother carried the same mutated gene, which manifested primarily as autism, ADHD, speech deficit, and mild ID. So far, he has had no seizures and a negative electroencephalogram. But he could have seizures in the future, and it’s worth following up. This study describes a family with a new NPRL2 variant, where affected members exhibited various neurological disorders including FFEVF2, autism, and ADHD, demonstrating incomplete penetrance.

Germline variants in DEPDC5 are a cause of familial focal epilepsy with variable foci. Affected individuals may have focal cortical dysplasia if a second brain somatic variant occurs. As access to brain tissue is limited, the second somatic hit in the brain is usually presumed if a clear pathogenic germline variant is present. Here, we present a patient with structural focal epilepsy due to focal cortical dysplasia. He underwent epilepsy surgery at age 2 months. Clinical genetic testing revealed a germline variant of uncertain significance (VUS) DEPDC5 c.920T>G, p. (Leu307Arg). We hypothesized that if the proband's germline DEPDC5 variant was disease-causal, a second somatic variant may be identifiable in affected cortical tissue. DNA was extracted from archived brain formalin-fixed paraffin-embedded tissue and subjected to deep gene panel analysis. This revealed an additional somatic pathogenic variant in DEPDC5, which was confirmed using droplet digital PCR. Identification of the second somatic hit in brain tissue (DEPDC5 c.982C>T, p.(Arg328*)) confirmed the two-hit situation in this patient and supported disease causality of the germline variant. In conclusion, testing tissue for somatic variants may be clinically relevant at a patient-specific level if a germline VUS affects a gene where a two-hit mechanism is known.

Familial focal epilepsy with variable foci-1 (FFEVF1) is a genetic epilepsy syndrome associated with a pathogenic mutation in the DEPDC5 gene. It has autosomal dominant inheritance, along with incomplete penetrance and a variable phenotype. We present a case of focal seizures that progressed to generalized tonic-clonic seizures within the span of one year in a 12-month-old male child. A family history of epilepsy was present in the mother and grandmother of the child. Generalized epilepsy was observed in the initial EEG, while the MRI of the brain was unremarkable. Levetiracetam was unable to control the seizures; however, they were partially responsive to sodium valproate, which was prescribed later. A heterozygous pathogenic variant was revealed in exon 26 during whole-exome sequencing of the DEPDC5 gene. Family history and genetic testing can play crucial roles in pediatric epilepsy diagnosis, particularly when lab investigations and neuroimaging are normal, as showcased in this case.

To explore the clinical manifestations and genetic etiology of a Chinese pedigree affected with Familial focal epilepsy with variable foci (FFEVF). A FFEVF pedigree presented at the Department of Medical Genetics of Linyi Maternal and Child Health Care Hospital on March 14, 2023 was selected as the study subject. The proband was subjected to whole exome sequencing (WES). Candidate variants were verified by Sanger sequencing of the proband and other affected members and bioinformatic analysis. This study was approved by the Linyi Maternal and Child Health Care Hospital (Ethics No. QTL-YXLL-2023048). WES revealed that the proband has harbored a heterozygous c.1642C>T (p.Arg548Cys) missense variant in exon 15 of the NPRL3 gene. Sanger sequencing confirmed that the variant was inherited from the proband's father, and multiple members of the pedigree had also harbored the same variant. Based on guidelines from the American College of Medical Genetics and Genomics (ACMG), the variant was classified as variant of unknown significance (PM2_supporting + PP3). The clinical phenotype of FFEVF patients caused by variants of NPRL3 gene is extensive, and the patients may present with neurological abnormality of autism spectrum disorder in addition to seizures.