Heterozygous SLC1A2 mutation in a child with early infantile seizures and global developmental delay

INTRODUCTION

The prenatal and early life periods are critical for brain development as it is involved in neurogenesis, neural migration, synaptogenesis, synaptic pruning and myelination, which are important for the normal brain growth.¹ Any insult during this period might cause severe cerebral impairment, developmental delay, intellectual disability and seizures.²

Anderson et al in 2010 in his study studied that a seizure insult prior to 3 years of age was associated with deficits in cognitive flexibility and working memory. Hence control of seizures is crucial for optimal neurodevelopment in a child.³

The aetiology of childhood epilepsy is diverse and can be due to various causes like fever, trauma, infections, metabolic disorder, hypoxic ischemic- encephalopathies. About 30% of the children with epilepsy have genetic etiology.⁴

Genetic epilepsies are usually suspected in children with early onset severe epilepsies and in those with recurrent seizures refractory to anticonvulsants.

Advancements in genetic technology, especially next generation sequencing has helped to pin point the specific pathogenic gene involved in genetic epilepsies, hence helps us to concentrate on the targeted therapy to control seizures and thereby improve cognitive development of such children.⁵

The authors report this case to emphasize the importance of genetic testing in evaluation of early infantile onset refractory seizures with global developmental delay or regression and its pivotal role in targeted therapy and better control of seizures which is crucial to cognitive development.

CASE REPORT

A 3 years 2 months old female child presented to Emergency Department with status epilepticus.

She was born term/IUGR to non-consanguineous parents with birth weight of 1.25 kg. Mother had PIH. She was kept in NICU for 10 days post-delivery and was breastfed after 4 days. There was no history of perinatal asphyxia. Mother noticed first episode of seizures at 40 days of life involving the upper limbs and was diagnosed as myoclonic seizures and treated with levetiracetam and clonazepam which was stopped after a year as she was seizure free during this period. MRI Brain done then was normal. EEG showed generalised epileptiform activity.

She had next episode of seizure at 1 year 7 months associated with fever, with generalised tonic-clonic seizures proceeding to status epilepticus and was treated with IV phenytoin. CT brain taken then was normal. Following this she was not on any anticonvulsants except for clobazam prophylaxis for febrile seizures. She started to have recurrent seizures from the age of 3 years after which she was started on syrup phenytoin and as the seizure episodes continued, levetiracetam was added. However, seizures are still recurrent and she has had more than 5 seizures in the last 3 months.

Mother noticed that child had motor delay at around 15 months of life when the child was unable to walk. Child was also noticed to have speech and language delay. She started walking at 2 years of age after physiotherapy exercises. Presently she has a speech corresponding to 18-24 months. No family history of seizures. There were no neuro-cutaneous markers. Her gait, tone, power, reflexes of both upper and lower limbs was normal. She had no focal neurological deficits. Seizures were treated with oxygen, inj. midazolam, fosphenytoin loading followed by maintenance after which seizures got controlled.

In the present episode, her electrolytes, liver function tests, ionised calcium was normal. MRI brain showed ill-defined flair hyperintensity in bilateral peri-trigonal and occipital white matter and paucity of bilateral parieto-occipital white matter which was suggested of periventricular leucomalacia. BERA was normal. Ophthalmological and ENT opinion was obtained and ruled out major concerns. She was discharged with oral phenytoin, levetiracetam, pyridoxine and clobazam.

In view of early onset of seizures at 40 days of age, recurrent persistent seizures with global developmental delay, MRI brain and EEG not contributory to aetiology, next generation sequencing was done to rule out genetic causes. A heterozygous missense variant (c.163A>T) in exon 3 of the SLC1A2 gene that results in the amino acid substitution from Isoleucine to Phenylalanine at codon 55 (p.Ile55Phe) was identified. SLC1A2 is an epileptic encephalopathy associated gene. The observed variant has a minor allele frequency of 0.0008% in genomAD database and not reported in 1000 genome database. The reference base is conserved across the species and in-silico predictions by polyphen and SIFT are damaging (Figure 1).

This mutation is classified as a variant of uncertain significance by American college of medical genetics (ACMG) classification. But we report this mutation in view of the clinical presentation of early onset recurrent refractory infantile seizures with global developmental delay and that SLC1A2 being classified as an epileptic encephalopathy associated gene. So further studies and research is indicated to establish its significance. We advised the parents to undergo Sanger sequencing for SLC1A2 gene in order to understand whether it is an inherited or de novo mutation.

DISCUSSION

A “seizure” is a paroxysmal alteration of neurologic function caused by the excessive, hypersynchronous discharge of neurons in the brain.⁶

‘Epilepsy’ is the condition of recurrent, unprovoked seizures. According to International league against epilepsy (ILAE), epilepsy is defined as 2 or more unprovoked afebrile seizures.⁷

Epilepsy affects about 0.5-0.8% children and the highest incidence rate is in the first year of life.⁴

Cognitive impairments that affect language, memory, attention and other abilities that are critical to normal development are common among people with epilepsy. Berg et al prospectively followed 198 children (aged <8 years) with new-onset epilepsy for 8-9 years and appropriately concluded that uncontrolled seizures impair cognitive function with effects being most severe in infancy.⁸

There are indications that early-life seizures independent of aetiology can lead to cognitive impairment.⁹

According to the international league against epilepsy (ILAE), the epileptic activity itself most likely contributes to severe cognitive and behavioural impairments, above and beyond expected from the underlying pathology alone.¹⁰

Hence it is extremely crucial to adequately control seizures as early as possible and prevent further recurrences.

Genetic aetiology of seizures is suspected in severe early onset recurrent seizures below one year of age, seizures refractory to treatment, seizures with associated global developmental delay or intellectual disability, children suspected of having an underlying genetic syndrome due to dysmorphic facies, children with distinctive seizure types and children with strong family history of seizures.¹¹

A genetic epilepsy might be inherited or can occur de novo in a child without being present in either parent.

The application of genomic technologies, especially the development of next generation sequencing has a tremendous impact on the discovery of the genetic basis of epilepsy, and it is expected to play a pivotal role in the diagnosis and treatment of epilepsy.⁵

Common genetic mutations which are linked with EE are SCN1A, STXBP1, CDKL5.¹² In our study, we identified SLC1A2 which is an epileptic encephalopathy associated gene 41 according to Online Mendelian Inheritance in Man classification.¹³

Epileptic encephalopathies (EE) comprise a spectrum of disorders manifesting epilepsy and consequent psychomotor delay.¹⁴ In the latest classification of epilepsies (2017), the ILAE commission stated that “in an epileptic encephalopathy, the abundant epileptiform activity interferes with development resulting in cognitive slowing and often regression, and sometimes is associated with psychiatric and behavioural consequences”.⁵

The ILAE classification is based primarily on the age of seizure onset, and the particular pattern on electroencephalogram (EEG).¹⁰

On the other hand, Online Mendelian Inheritance in Man classifies early infantile EE exclusively according to the causative gene without relying on the phenotypes. This helps in concentrating on targeted therapy and hence achieve good seizure control.¹⁴

SLC1A2 encodes excitatory amino acid transporter 2 (EAAT2), which is one of major glutamate transporters expressed in astroglia and is responsible for clearing glutamate from the extracellular space at the synapse.¹⁵

Glutamate is the principal excitatory neurotransmitter of central nervous system, and its synaptic concentration is kept under tight control to prevent neuronal damage from excessive activation of glutamate receptor.¹⁶

Pan-knockout or astrocyte-specific knockout of Slc1a2 in mice results in neuronal excitotoxicity, epilepsy and premature death. However, mice heterozygote for the SLC1A2 deletion demonstrate no apparent clinical phenotype. Also, heterozygous deletion of SLC1A2 in humans is only rarely associated with epilepsy.¹⁷

However, in contrast to heterozygous SLC1A2 deletions, heterozygous SLC1A2 missense variants have recently been implicated in severe early-onset epilepsy.

The Epi4K project which is an international, multi-centre study that seeks to identify and characterize the genetic bases of complex epilepsies, in its publication in American journal of human genetics in 2016 summarised the denovo pathogenic variants associated with EE in previously identified mutations. They identified two individuals with de novo missense mutations in SLC1A2 establishing this as an epileptic encephalopathy associated gene. Previous to this observation, only a single individual with infantile spasm and a de novo missense mutation of this gene had been reported.¹³

Stergachis et al in 2019 summarised an extensive clinical phenotype feature of SLC1A2-related epilepsy based on seven independent cases reported till then, including: one new de novo dominant case; five previously reported de novo dominant cases; and one previously reported recessive case. All six de novo dominant cases had similar characteristics including early onset epilepsy between 2 days and 6 weeks of life, seizures in the form of focal motor events often tonic or myoclonic and progressed to multiple seizure types including epileptic spasms, myoclonic seizures, focal and generalized tonic seizures. All the cases were refractory to multiple medications. Brain MRIs were all normal for the first several months of life, but around 5 months of life began to show evidence of delayed myelination and EEG patterns demonstrated multifocal and generalized epileptiform discharges with abnormal background activity.¹⁷

Common clinical features included severe global developmental delay (6/6 cases), cortical visual impairment (3/6 cases), axial hypotonia (6/6 cases), spasticity and/or joint contractures (5/6 cases), and kyphoscoliosis (2/6 cases).¹⁷

The recessive type SLC1A2-related epilepsy appears milder, with seizure onset at 2 years of age that was controlled with a single medication and mild developmental delay.¹⁷

Our patient had a heterozygous missense mutation variant (c.163A>T) in exon 3 of the SLC1A2 gene. We have advised the parents for sanger sequencing of SLC1A2 gene to establish whether the gene was inherited. Further studies are needed to establish the significance of this mutation.

CONCLUSION

Early control of seizures is crucial for optimal cognitive development in a child. Suspect genetic causes in a child with early infantile onset refractory seizures with global developmental delay or regression. Genetic diagnosis limits the diagnostic odyssey, helps in targeted therapy and better control of seizures. SLC1A2 is classified as epileptic encephalopathy associated gene which codes for glutamate transporter. Further studies are warranted to establish the significance of heterozygous missense variant (163A>T) in exon 3 of the SLC1A2 gene in causation of refractory seizures with global developmental delay.

Funding: No funding sources

Conflict of interest: None declared

Ethical approval: Not required

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