Expanding SPTAN1 monoallelic variant associated disorders: From epileptic encephalopathy to pure spastic paraplegia and ataxia

Abstract

Purpose: Nonerythrocytic αII-spectrin (SPTAN1) variants have been previously associated with intellectual disability and epilepsy. We conducted this study to delineate the phenotypic spectrum of SPTAN1 variants.

Methods: We carried out SPTAN1 gene enrichment analysis in the rare disease component of the 100,000 Genomes Project and screened 100,000 Genomes Project, DECIPHER database, and GeneMatcher to identify individuals with SPTAN1 variants. Functional studies were performed on fibroblasts from 2 patients.

Results: Statistically significant enrichment of rare (minor allele frequency < 1 × 10^-5) probably damaging SPTAN1 variants was identified in families with hereditary ataxia (HA) or hereditary spastic paraplegia (HSP) (12/1142 cases vs 52/23,847 controls, p = 2.8 × 10^-5). We identified 31 individuals carrying SPTAN1 heterozygous variants or deletions. A total of 10 patients presented with pure or complex HSP/HA. The remaining 21 patients had developmental delay and seizures. Irregular αII-spectrin aggregation was noted in fibroblasts derived from 2 patients with p.(Arg19Trp) and p.(Glu2207del) variants.

Conclusion: We found that SPTAN1 is a genetic cause of neurodevelopmental disorder, which we classified into 3 distinct subgroups. The first comprises developmental epileptic encephalopathy. The second group exhibits milder phenotypes of developmental delay with or without seizures. The final group accounts for patients with pure or complex HSP/HA.

Keywords: Developmental delay; Developmental epileptic encephalopathy; Hereditary ataxia; Hereditary spastic paraplegia; SPTAN1.

Figure 1

Pedigrees of reported families with SPTAN1 variants showing disease segregation.

Figure 2

Schematic structure of SPTAN1 gene and its coding protein highlighting variants identified in this study. Coding exon numbers (NM_001130438.3) are reported on the gray bar. Truncating variants are indicated on the top. Missenses, in-frame deletion/insertion, and splice variants are on the bottom. Deletion 1, 3, and 5 (green) remain in frame, whereas predictions for deletions 2 and 4 (orange) are not available. p.Gln1448= (c.4344G>A) is predicted to affect exon 33 donor splice site, based on maxENTScan (predicting splice sites using ‘Maximum Entropy Principle’) (maxENT score wild-type 6.99 → 3.84 mutant). The splice altering variant (NC_000009.12(SPTAN1_v001):c.3519+2T>G) predicted to alter exon 25 canonical donor splice site (maxENT score wild-type 10.28 → 2.63 mutant). Variants identified in patients presenting with HSP/HA are highlighted in red. All other variants are represented in black.

Figure 3

Representative images of αII-spectrin protein expression and staining pattern in fibroblast cells derived from 2 patients and unrelated controls. A. Western blot. 1. Western blotting of protein extracted from fibroblast cell lines of patients 1 and 29 and 3 wild-type age-matched controls. 2. Densitometric analysis of western blot using BioRad Image Lab software after relative normalization to actin as a housekeeping protein. The analysis showed no change in protein expression in patient 1 but showed a quantitative reduction of protein expression in patient 29. B. Immunocytochemical staining of αII-spectrin expression in primary fibroblasts of patients 1 and 29 and unrelated control individual with Alexa Fluor 488 conjugated secondary antibody (green) and Hoescht 33342 nuclear staining (blue). Scale bar represents 50 μm. Immunocytochemical staining showed high immunofluorescence brightness and intense immunoreactivity and aggregation of αII-spectrin in both studied patients compared with the healthy unrelated control. Ctr, control.