Expanded clinical phenotype spectrum correlates with variant function in SCN2A-related disorders

Abstract

SCN2A-related disorders secondary to altered function in the voltage-gated sodium channel Nav1.2 are rare, with clinically heterogeneous expressions that include epilepsy, autism and multiple severe to profound impairments and other conditions. To advance understanding of the clinical phenotypes and their relationship to channel function, 81 patients (36 female, 44%, median age 5.4 years) with 69 unique SCN2A variants were systematically phenotyped and their Nav1.2 channel function systematically assessed. Participants were recruited through the FamileSCN2A Foundation. Primary phenotype (epilepsy of neonatal onset, n = 27; infant onset, n = 18; and later onset n = 24; and autism without seizures, n = 12) was strongly correlated with a non-seizure severity index (P = 0.002), which was based on presence of severe impairments in gross motor, fine motor, communication abilities, gastrostomy tube dependence and diagnosis of cortical visual impairment and scoliosis. Non-seizure severity was greatest in the neonatal-onset group and least in the autism group (P = 0.002). Children with the lowest severity indices were still severely impaired, as reflected by an average Vineland Adaptive Behavior composite score of 49.5 (>3 standard deviations below the norm-referenced mean of the test). Epileptic spasms were significantly more common in infant-onset (67%) than in neonatal (22%) or later-onset (29%) epilepsy (P = 0.007). Primary phenotype was also strongly correlated with variant function (P < 0.0001); gain-of-function and mixed function variants predominated in neonatal-onset epilepsy, shifting to moderate loss of function in infant-onset epilepsy and to severe and complete loss of function in later-onset epilepsy and autism groups. Exploratory cluster analysis identified five groups, representing: (i) primarily later-onset epilepsy with moderate loss-of-function variants and low severity indices; (ii) mostly infant-onset epilepsy with moderate loss-of-function variants but higher severity indices; and (iii) late-onset and autism only, with the lowest severity indices (mostly zero) and severe/complete loss-of-function variants. Two exclusively neonatal clusters were distinguished from each other largely on non-seizure severity scores and secondarily on variant function. The relationship between primary phenotype and variant function emphasizes the role of developmental factors in the differential clinical expression of SCN2A variants based on their effects on Nav1.2 channel function. The non-seizure severity of SCN2A disorders depends on a combination of the age at seizure onset (primary phenotype) and variant function. As precision therapies for SCN2A-related disorders advance towards clinical trials, knowledge of the relationship between variant function and clinical disease expression will be valuable for identifying appropriate patients for these trials and in selecting efficient clinical outcomes.

Keywords: Nav1.2; autism; automated patch clamp; developmental and epileptic encephalopathy; epilepsy.

Figure 1

Volcano plots of each of 10 biophysical parameters for SCN2A variants of participants in the Clinical Trials Readiness Study. Deviation from wild-type (WT) of disease-associated SCN2A variants recorded in the adult (upward triangles) and neonatal (downward triangles) splice isoforms. Only variants significantly different from WT are labelled with variant name, with the suffix -A or -N to indicate splice isoform. Blue symbols denote gain-of-function, and red symbols denote loss-of-function. The horizontal dotted line represents the statistical threshold of P = 0.05. Tau = time constant; V_½ = voltage at half-maximum.

Figure 2

Functional assessment of SCN2A Clinical Trials Readiness Study variants. Aggregate functional scores of disease-associated SCN2A variants characterized in adult (upward triangles) and neonatal (downward triangles) splice isoforms. Red triangles represent aggregate loss of function. Blue triangles represent aggregate gain-of-function. Purple triangles represent aggregate mixed function from equal, but opposite loss- and gain-of-function scores. Black triangles represent variants that show no functional divergence from wild-type channels. GOF = gain-of-function; LOF = loss-of-function; sLOF = severe loss-of-function; WTL = wild-type like.

Figure 3

Cluster analysis of clinical phenotypes, severity index, and functional impacts on variant. (A) Primary phenotype and severity index. (B) Primary phenotype and variant impact. (C) Non-seizure severity index and variant impact. (D) Three-dimensional representation of the three variables: Cluster 1 (orange circles) contains mostly later-onset epilepsy with mild non-seizure phenotype indices, moderate loss-of-function SCN2A variants. Cluster 2 (dark red circles) contains mostly infant-onset epilepsy, more severe non-seizure phenotypes and moderate loss-of-function. Cluster 3 (teal circles) is composed of all of the autism spectrum disorder or intellectual disability (ASD/ID) participants and many late-onset epilepsy cases with severe or complete loss of channel function and very low non-seizure severity indices. Clusters 4 and 5 are composed exclusively of neonatal-onset epilepsy cases. Cluster 4 (pink circles) contains those with milder non-seizure phenotypes and gain-of-function or mixed function variants, whereas as Cluster 5 (green circles) contains individuals with severe non-seizure phenotypes and a range of variant functions, including severe loss of function. Observations that were trimmed by the clustering algorithm are shown as dark grey diamonds.