Mutations in SLC13A5 cause autosomal-recessive epileptic encephalopathy with seizure onset in the first days of life

Abstract

Epileptic encephalopathy (EE) refers to a clinically and genetically heterogeneous group of severe disorders characterized by seizures, abnormal interictal electro-encephalogram, psychomotor delay, and/or cognitive deterioration. We ascertained two multiplex families (including one consanguineous family) consistent with an autosomal-recessive inheritance pattern of EE. All seven affected individuals developed subclinical seizures as early as the first day of life, severe epileptic disease, and profound developmental delay with no facial dysmorphism. Given the similarity in clinical presentation in the two families, we hypothesized that the observed phenotype was due to mutations in the same gene, and we performed exome sequencing in three affected individuals. Analysis of rare variants in genes consistent with an autosomal-recessive mode of inheritance led to identification of mutations in SLC13A5, which encodes the cytoplasmic sodium-dependent citrate carrier, notably expressed in neurons. Disease association was confirmed by cosegregation analysis in additional family members. Screening of 68 additional unrelated individuals with early-onset epileptic encephalopathy for SLC13A5 mutations led to identification of one additional subject with compound heterozygous mutations of SLC13A5 and a similar clinical presentation as the index subjects. Mutations affected key residues for sodium binding, which is critical for citrate transport. These findings underline the value of careful clinical characterization for genetic investigations in highly heterogeneous conditions such as EE and further highlight the role of citrate metabolism in epilepsy.

Figure 1

Pedigrees of the Three Families with SLC13A5 Mutations Individuals for whom exome sequencing was performed are indicated by asterisks (^∗). The subject with a homozygous BCKDHB mutation is indicated by the symbol ¶. Detection of the identified SLC13A5 variants was performed in all available individuals. mut/mut and mut/− refer to compound heterozygous and heterozygous carriers of SLC13A5 mutations, respectively. −/− indicate individuals for whom no SLC13A5 mutation was identified.

Figure 2

Subject 2: Epileptic Activity with Long-Lasting Multifocal Bilateral Seizures during the First Week of Life (A) Schematic representation of the electrode placement according to the international standards in neonate (subject 2 at fifth day of life). (B) Longitudinal (lines 1–6) and transverse montage (lines 7–10) showing a typical seizure beginning in the right hemisphere, temporal region (dotted line), lasting around 100 s and immediately followed by a seizure originating in the left hemisphere, temporal lobe (full trace) beginning at around 100 s and lasting 130 s. Clinically, the discharge was not symptomatic initially, then the neonate displayed chewing movements (20^th s), discrete clonic jerks of the left limbs (50^th s), and discrete clonic jerks of the right limbs (130^th s).

Figure 3

In Silico Prediction of the Impact of SLC13A5 Mutations on Sodium Binding Left panel represents 3D model of VcINDY, SLC13A5 bacterial ortholog (PDB 4F35). Citrate molecule (yellow) and the first sodium-binding site (green) are shown. Right panels are 6 Å zoomed-in focuses of both wild-type and mutated residues. Protein structure data were loaded in the Swiss-PDB viewer and mutated residues introduced, with the most probable rotamer selected. Hydrogen bonds were computed by standard parameters.