Genotypic and phenotypic analysis of epilepsy associated with NPRL2/NPRL3 genes

Summary and analysis of clinical phenotypes, genotypes, and their correlations in epilepsy patients associated with NPRL2 and NPRL3 gene variants.

Retrospective analysis and statistical investigation of clinical phenotypes and genotype-phenotype correlations in children with NPRL2/NPRL3 gene variants, combining clinical data from Shandong University Affiliated Children's Hospital and Beijing Children's Hospital, Capital Medical University, with literature review.

Our institution collected 8 epilepsy patients with NPRL2 variants, and 32 additional cases were identified from the literature, resulting in a total cohort of 40 patients. Among the available clinical data, 20 patients (54.3 %) were male and 16 (45.7 %) were female. The median age of seizure onset was 21.0 months (2.5-55.0 months). Twenty-five distinct variant types were identified, with nonsense variants (8/25, 32.0 %) being the most prevalent. Focal seizures were observed in 26 patients (75.8 %). Cortical developmental abnormalities Malformations of Cortical Development (MCD) were present in 15 patients (51.7 %), normal cortical structure in 12 (41.4 %), tumor in 1 (3.4 %), and hippocampal sclerosis in 1 (3.4 %). Regarding treatment, 18 patients (69.2 %) had drug-resistant epilepsy (DRE), while seizures were pharmacologically controlled in 8 (30.8 %). Thirteen patients underwent epilepsy surgery, and 8 achieved postoperative seizure freedom. Our institution collected 11 epilepsy patients with NPRL3 variants, combined with 145 cases reported in the literature, totaling 156 cases. A total of 67 variant sites and 6 variant types were identified, with frameshift variants (20/67, 29.9 %) being the most common. The cohort included 87 males (60 %) and 58 females (40 %), with a median age of onset of 48.0 months (12.0-120.0 months). Focal seizures were observed in 95 patients (79.2 %). MRI results showed normal findings in 69 patients (63.3 %) and MCD in 38 (34.9 %), including 30 cases of focal cortical dysplasia (FCD). DRE was reported in 52 patients (54.2 %), with 20 achieving seizure control through monotherapy. Twenty-nine patients underwent surgical resection, and 15 (51.7 %) achieved postoperative seizure freedom. Among 4 drug-resistant epilepsy patients treated with ketogenic diet therapy (KDT), 2 showed no response, 1 achieved seizure control, and 1 experienced recurrence after discontinuing KDT and undergoing surgery. Five patients received rapamycin therapy, with 4 showing no improvement. Comparative analysis between MCD and non-MCD groups revealed significant differences in age of onset and proportion of drug-resistant epilepsy (P = 0.001, 0.033, and < 0.001, respectively). When comparing NPRL2 and NPRL3 variant cohorts, significant differences were observed in age of onset (P = 0.030) and presence of MCD (P = 0.046). No significant differences were found in sex, family history of epilepsy, epilepsy syndrome, variant type, number of anti-seizure medications (ASMs), drug resistance rates, or surgical outcomes.

Patients with NPRL2/NPRL3-related epilepsy commonly present with focal seizures, frequently accompanied by MCD, and are predominantly drug-resistant. Pathogenic variants include protein-truncating variants such as nonsense and frameshift mutations, primarily driven by loss-of-function (LOF) mechanisms, with a predominance of germline variants. In NPRL2-related epilepsy, variants associated with MCD cluster in the Longin and CTD domains, while NPRL3-related epilepsy cases with MCD show variant enrichment in the Longin and INT domains. Copy number variants (CNVs) represent a novel genotype in NPRL2-related epilepsy, whereas infantile epileptic spasms syndrome (IESS) emerges as a new phenotype in NPRL3-related epilepsy. Compared to NPRL3-related epilepsy, NPRL2-related epilepsy manifests earlier (typically within 2 years of age) and demonstrates a stronger association with MCD. Sodium channel blockers such as oxcarbazepine are commonly effective ASMs for monotherapy in both NPRL2/NPRL3-related epilepsies. For NPRL2/NPRL3-related epilepsy with MCD, surgical resection proves beneficial, with postoperative pathology predominantly revealing focal cortical dysplasia type II (FCD II).