Developmental and epileptic encephalopathies (DEEs) are a group of clinically and genetically heterogeneous neurological disorders characterized by frequent epileptic activity and developmental impairment (Guerrini et al., 2023). DEEs represent the most severe forms of epilepsy, typically manifesting in neonates or children (Scheffer et al., 2021). Genetic factors play a significant role in the development of DEEs. To date, over 100 genes have been associated with DEEs due to rapid advances in diagnostic tools, significantly enhancing our understanding of their molecular basis (McTague et al., 2016; Guerrini et al., 2023).

Autosomal recessive variants of the SLC13A5 gene (MIM*608305) have been reported to cause developmental and epileptic encephalopathy 25 with amelogenesis imperfecta (DEE25, MIM #615905) in early infancy (Matricardi et al., 2020; Milosavljevic et al., 2022). The SLC13A5 gene is located on chromosome 17p13.1 and consists of 12 exons (Inoue et al., 2002a). It encodes a plasma membrane sodium-dependent citrate carrier known as the Na + -coupled citrate (NaCT) transporter, which is highly expressed in the brain, teeth, liver, and testis (Inoue et al., 2002b). Neurons are incapable of de novo synthesis of tricarboxylic acid cycle intermediates, therefore, the uptake of intermediates like citrate is crucial for maintaining energy status and neurotransmitter production (Hardies et al., 2015; Henke et al., 2020). Biallelic mutations, whether homozygous or compound heterozygous, in the SLC13A5 gene can impair citrate uptake, disrupting tricarboxylic acid cycle metabolism and resulting in neonatal epilepsy (Goodspeed et al., 2022). SLC13A5 was first identified as a causative gene of DEE25 in 2014 (Thevenon et al., 2014). To date, over 40 pathogenic variants have been reported in the SLC13A5 gene (Brown et al., 2021; Beltran, A.S., 2024). However, none of these variants have been reported in the Chinese population.

In our study, we identified a novel nonstop mutation in the SLC13A5 gene in a Chinese family affected by infant epilepsy and developmental delay. The patient exhibited a range of clinical features, including dental anomalies, intellectual disability, motor difficulties, and speech impairments, alongside abnormalities detected through neuroimaging. We conducted a thorough literature review on SLC13A5 variants to analyze their associated phenotypic characteristics.

Biallelic loss-of-function mutations in the SLC13A5 gene typically lead to DEE25, characterized by neurological manifestations such as epilepsy and psychomotor developmental delay (Alsemari et al., 2024). In this study, we identified a novel SLC13A5 nonstop variant (c.1705T>G) in a Chinese girl who began experiencing seizures shortly after birth. The phenotypic spectrum observed in our patient overlaps with previously reported cases, including early onset seizures, profound intellectual disability, global developmental delay, and dental abnormalities (Supplementary Table 1). Additionally, our patient exhibited auxiliary features such as brain MRI abnormalities and hypertonia. According to the literature, neuroimaging abnormalities are present in approximately one-third of SLC13A5-related DEE cases, with white matter abnormalities being the most common (Whitney et al., 2023). The affected patients may initially present with infantile hypotonia and later develop increased muscle tone, pyramidal signs, spasticity, dystonia, and/or ataxia. This range of symptoms reflects the clinical heterogeneity of the disease (Arvio and Lähdetie, 2020).

From the literature review (Supplementary Table 1), most SLC13A5 variants are missense mutations, though a smaller number of frameshift, splicing, insertion, and intronic mutations have also been reported. These variants are typically either homozygous or compound heterozygous and follow an autosomal recessive inheritance pattern. Patients with these mutations exhibit developmental impairments of varying severity, often accompanied by a range of neurological signs and symptoms, including axial hypotonia, peripheral hypertonia, dystonia, dyskinesia, spasticity, ataxia, choreoathetosis, and microcephaly. Current clinical and genetic data do not show consistent genotype-phenotype correlations (Matricardi et al., 2020). Even within families with more than one affected child, there is significant phenotype heterogeneity among siblings with identical genotypes (Anselm et al., 2017; Arvio and Lähdetie, 2020; Matricardi et al., 2020).

The human SLC13A5 protein consists of 568 amino acids and is located at the plasma membrane, where it mediates the transport of citrate from extracellular environment into the cell (Inoue et al., 2002a). Citrate is crucial for maintaining cellular metabolic homeostasis, particularly in energy production and neurotransmitter synthesis within the central nervous system (CNS) (Li and Wang, 2021). Secondary structure predictions indicate that SLC13A5 is predominantly α-helical, comprising approximately 65.3% α-helices, including 11 transmembrane α-helices, with 33% in loops and less than 2% in β-strands (Jaramillo-Martinez et al., 2021). The protein forms a homodimer, with each protomer containing a scaffold domain and a transport domain (Sauer et al., 2021). Mutations in SLC13A5 can disrupt citrate transport directly or affect protein expression and localization, depending on the position of the mutated residue (Jaramillo-Martinez et al., 2021; Beltran, 2024). Our case study presents a novel nonstop mutation that results in a C-terminally extended protein with an additional 174 residues (p.569Gluext174). Structural modeling revealed that this mutation introduces an α-helical domain and random coils not present in the wild-type protein. Functional research, such as citrate uptake assays, is needed to elucidate the underlying mechanisms of the mutation’s defects in SLC13A5-related epilepsy.

Nonstop variants, which convert stop codons into sense codons, are exceedingly rare mutations reported in various diseases (Hamby et al., 2011; Vaché et al., 2023), such as autosomal dominant Charcot-Marie-Tooth disease type 2 (Bock et al., 2018) and excessive hemorrhaging due to mutations in coagulation factor X (Ameri et al., 2007). When an alternative in-frame stop codon exists in the 3′untranslated region (UTR), translation can continue normally, resulting in the production of a C-terminally extended protein. The pathogenicity of these extra polypeptides has been investigated in a few cases. Studies have shown that these mutations can lead to altered subcellular localization in some instances (Sun et al., 2017) and accumulation of mutant proteins in others (Bock et al., 2018). These findings suggest that C-terminally extended proteins can confer a toxic gain-of-function, which contrasts with the loss-of-function effects typically seen in nonstop decay pathways. Further research is needed to fully understand the genetic mechanisms underlying C-terminal elongation in SLC13A5 and its implications for disease pathogenesis.

In summary, we identified the first SLC13A5 mutation (c.1705T>G, p.569Gluext174) in a Chinese population. This nonstop substitution is rare and broadens the mutational spectrum of the SLC13A5 gene. The discovery of this pathogenic variant will have significant implications for the proband’s family in terms of medical management and genetic counseling.