Identification of two rare NPRL3 variants in two Chinese families with familial focal epilepsy with variable foci 3: NGS analysis with literature review

Abstract

Background: The GAP Activity Towards Rags 1 (GATOR1) complex, which includes DEPDC5, NPRL2, and NPRL3, plays a key role in epilepsy. It has been reported that focal epilepsy is associated with mutations in the NPRL3 gene in some cases. We report two rare mutations in the NPRL3 gene in two unrelated Chinese families with focal epilepsy in this study.Methods: The proband and her brother in family E1 first experienced seizures at 1.5 and 6 years of age, respectively. Despite resection of epileptogenic foci, she still suffered recurrent seizures. The first seizure of a 20-year-old male proband in family E2 occurred when he was 2 years old. To identify pathogenic variants in these families, whole-exome sequencing (WES) was performed on genomic DNA from peripheral blood.Results: In family E1, the trio-WES analysis of the proband and her brother without apparent structural brain abnormalities identified a heterozygous variant in the NPRL3 gene (c.954C>A, p.Y318*, NM_001077350.3). In family E2, the proband carried a heterozygous NPRL3 mutation (c.1545-1G>C, NM_001077350.3). Surprisingly, the mothers of the two probands each carried the variants, but neither had an attack. Bioinformatics analysis predicted that the mutation (c.954C>A) was in the highly conserved amino acid residues of NPRL3, which affected the α-helix of NPRL3 protein, leading to a truncated protein. The splice variant (c.1545-1G>C) resulted in the loss of the last exon of the NPRL3 gene.Conclusion: The results of this study provide a foundation for diagnosing NPRL3-related epilepsy by enriching their genotypes and phenotypes and help us identify the genetic etiologies of epilepsy in these two families.

The clinical features of familial focal epilepsy with variable foci and NPRL3 gene variant

“…The clinical features of patients with different NPRL3 variants reported from published papers [ 6 , 9 , 10 ] and our study have been listed in Table 3 to deepen our understanding of the newly discovered gene variant. Most patients had adolescent-onset disease.…”

“…The MRI findings varied; they could be normal or abnormal. The genetic testing findings are as follows: Weckhuysen et al 2016 [ 6 ] found five patients had NPRL3 : c.1270C>T, p.Arg424* and four patients had NPRL3 : c.1070delC, p.Pro357Hisfs*56; Li et al 2021 [ 9 ] found five patients had NPRL3 : c316C>T, p. Q106*; Hu et al 2022 [ 10 ] found two patients had NPRL3 : c.954C>A, p.Y318* and one patient had NPRL3 : c.1545-1G>C.…”

“…Hu et al [ 10 ] identified another splicing variant, NPRL3 : c.1545-1G>C, in a Chinese family with FFEVF. FFEVF might be associated with abnormal splicing, resulting in the loss of the last exon of NPRL3 .…”

“…After the pathogenicity of the gene variant was predicted via in silico analysis, in vitro experiments (PCR, Western blotting, and immunohistochemistry) were conducted to analyze the gene transcription, protein expression, and subcellular localization of NPRL3 and related signaling molecules in the peripheral blood cells of the family members. Hu et al [ 10 ] identified NPRL3 : c.954C >A, p.Y318* and the splicing variant NPRL3 : c.1545-1G>C. After the pathogenicity of the gene variants was further assessed in different algorithms, the researchers used the Self-Optimized Prediction Method from Alignment (SOPMA) to predict the effect of the identified variant on the secondary structure of NPRL3 and SWISS-MODEL software to investigate the effect of the variant on the 3D structure of NPRL3.…”

“…However, few studies [ 9 , 10 ] on NPRL3 have been conducted in China. This study aimed to describe a new NPRL3 variant associated with FFEVF.…”