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).