Publications about genetic testing for neurological disorders
  1. NGS Panel – Genetic Testing for Early Infantile Epileptic Encephalopathy

Early Infantile Epileptic Encephalopathy

July 20, 2017

Disease synonyms

Early infantile epileptic encephalopathy, EIEE, Ohtahara syndrome, West syndrome, Infantile spasms, IS, Lennox–Gastaut syndrome, LGS, Severe myoclonic epilepsy in infancy, Dravet syndrome, Severe myoclonic epilepsy of infancy, SMEI, Early myoclonic encephalopathy, Malignant migrating partial seizures of infancy, MMPSI, Landau-Kleffner syndrome, LKS, Myoclonic status in non-progressive encephalopathies, MSNE


Inheritance pattern

Autosomal recessive, X-linked, autosomal dominant


Clinical features

Epileptic encephalopathies represent a group of severe epileptic diseases with an early onset, characterized by severe electroencephalographic abnormalities and resistance to standard anti-epileptic treatment. According to the International League Against Epilepsy (ILAE) 1, 43 epileptic encephalopathies (EEs) are defined as conditions in which the epileptiform abnormalities are believed to contribute to progressive disturbance in cerebral function, e.g. developmental delay and intellectual disability.

The main clinical features and signs of all epileptic encephalopathies are:

  • Refractory seizures
  • Severe EEG abnormalities
  • Developmental delay/regression or intellectual disability.

Depending on the severity, types of seizures, and prognosis, EEs can be classified into several major subtypes:

Early Infantile EE (EIEE) or Ohtahara Syndrome is one of the most severe forms of EE and is characterized by the following:

  • Presentation within first 3 months of life1, 42 or even earlier, e.g. in utero43
  • Tonic spasms, generalized or lateralized, occurring hundreds times per day and lasting >10s1, 42. About 30% of patients develops other seizure types, such as hemiconvulsions, motor seizures or generalized tonic-clonic seizures42.
  • The EEG is characterized by burst suppression during both wakefulness and sleep
  • Tonic spasms and partial (focal) seizures do not respond to anti-seizure medication
  • Many cases are caused by a brain malformation, metabolic disorder or genetic pathogenic variants
  • Ohtahara syndrome is very rare
  • Prognosis of the disease is poor, and patients usually die during infancy.

West syndrome or Infantile spasms (IS) is the most common type of EE and is characterized by a triad of symptoms: spasms, hypsarrhythmia, and developmental delay/regression.

  • IS spasms are brief seizures with flexion or extension of extremities and/or body that occur in clusters upon awakening
  • IS onset is between 3-7 months of age43
  • The estimated incidence is 2-3.5 per 10,000 live births1, 43
  • IS can be associated with malformations of cortical development and hypoxic-ischemic encephalopathy, as well as disorders including tuberous sclerosis and Down syndrome
  • Many patients develop other seizure types
  • The prognosis of the infantile spasms can be improved with early treatment.

Lennox–Gastaut syndrome (LGS) is a childhood onset severe epileptic encephalopathy characterized by multiple seizure types and is characterized by the following:

  • Tonic seizures are always present together with atonic and atypical absence seizures, and focal myoclonic and generalized tonic–clonic seizures
  • The onset of LGS is mostly between 3-5 years of age43
  • The incidence of LGS is estimated to be 1-10% of all childhood-onset epilepsies43
  • EEG shows fast activity paroxysms and generalized slow spike-and-wave discharges
  • Affected LGS patients have different degrees of developmental delay and they often develop autism and intellectual disability43
  • Patients react well to several antiepileptic drugs (clonazepam, felbamate, lamotrigine, topiramate, rufinamide, and clobazam)43.

Severe Myoclonic Epilepsy in Infancy or Dravet Syndrome is a severe form of EE with the following features:

  • Onset is commonly during the first year of life
  • Seizure types include myoclonus, prolonged convulsive seizures, frequent status epilepticus, and febrile seizures
  • The incidence of Dravet syndrome is 0.5–1/40,000 and accounts for up to 8 % of all epilepsies in the first 3 years of life43
  • Most commonly it is caused by pathogenic variants of SCN1A gene, encoding the neuronal voltage-gated sodium channel1,3,43.

Early myoclonic encephalopathy is a rare malignant epilepsy syndrome characterized by myoclonus with or without focal motor seizures:

  • Onset occurs very early, just a few hours after birth
  • Seizures are myoclonic, but other types of seizures are also common (partial seizures, massive myoclonia and tonic spasms)
  • The disease is most commonly inherited in an autosomal recessive manner
  • There is no effective treatment for early myoclonic encephalopathy and prognosis is very poor
  • The disease is very rare, with only 30 cases reported so far43
  • A common cause for the disease are pathogenic variants in the SLC25A22 gene1,3.

Malignant Migrating Partial Seizures of Infancy (MMPSI) also known as Early Infantile Epileptic Encephalopathy 14 (EIEE14) is a severe form of EE that begins very early in life. MMPSI is clinically characterized by the following:

  • Recurrent seizures in MMPSI commonly start within a few weeks of birth43
  • The seizures in MMPSI are partial or focal
  • Seizure activity can appear in multiple locations in the brain, or migrate from one region to another during an episode
  • Persistent seizures affect brain development and growth, leading to microcephaly43, profound developmental delay, and intellectual disability
  • Seizures are usually refractory to treatment and the majority of affected children do not survive past
  • The disease is very rare, with less than 100 reported cases42,43
  • Pathogenic variants in the KCNT1 gene are the most commonly known cause of MMPSI3,26.

Landau-Kleffner syndrome (LKS) is a less severe early epileptic encephalopathy syndrome of mid-childhood and is characterized by the gradual inability to understand and use spoken language43. Major clinical findings of LKS include the following:

  • Language regression
  • EEG abnormalities, including continuous or near-continuous spike-waves during slow wave sleep
  • The age of onset is between 3-7 years of age, boys are affected twice as often as girls43
  • Pathogenic variants in the GRIN2A gene have been reported as a major genetic cause of LKS18,19
  • LKS responds to anti-epileptic drugs.

Continuous Spike-Wave during Slow Sleep (CSWS) is an epileptic encephalopathy of childhood characterized by cognitive or behavioral impairment caused by interictal epileptiform discharges during sleep. CSWS seizures commonly present at 2-4 years of age.

  • The seizures are typically unilateral, tonic-clonic or clonic, occurring during the wake phases
  • At the age 5-6 years the seizures become more frequent, severe, and treatment-resistant
  • Developmental regression is common
  • Spontaneous improvement of disease symptoms can occur before adolescence, but most patients remain severely developmentally impaired.

Myoclonic status in nonprogressive encephalopathies (MSNE) is another type of EE and it is characterized by the early onset of continuous diffuse epileptiform abnormalities.

  • The prevalence of MSNE is estimated to be 0.5 %-1 % of all children with severe forms of epilepsy43
  • MSNE is frequently associated with Angelman syndrome, fetal/neonatal brain hypoxia and structural brain malformations
  • Prognosis of MSNE is poor, with progressive neurodegeneration
  • There is no effective treatment except for the benzodiazepines temporary interruptions of the myoclonic status epilepticus.

Development of new technologies in molecular diagnostics, including next generation sequencing (NGS), has resulted in the identification of a number of known monogenic causes underlying the epileptic encephalopathies. Different genetic causes and molecular pathways have been identified so far, including genes encoding the proteins of the ion channels, synaptic proteins, and others, involved in neuronal development, differentiation and other functions. The list of genes included in CENTOGENE´s Early infantile epileptic encephalopathy panel is presented in the table.

Table 1. Overview of genes included in Early infantile epileptic encephalopathy panel

Gene OMIM (Gene) Associated diseases (OMIM) Inheritance CentoMD® exclusive variant numbers (++)
AARS 601065 type 2N Charcot-Marie-Tooth disease; early infantile epileptic encephalopathy 29 AD, AR 6
ALG13 300776 congenital disorder of glycosylation type 1s XLD 5
ARHGEF9 300429 Epileptic encephalopathy, early infantile, 8 XLR 7
ARV1 611647 early infantile epileptic encephalopathy type 38 AR 1
ARX 300382 Proud syndrome; X-linked lissencephaly-2; ARX- related mental retardation; early infantile epileptic encephalopathy 1; Partington X-Linked Mental Retardation Syndrome XL, XLR 7
CACNA1A 601011 episodic ataxia type 2; familial hemiplegic migraine 1; spinocerebellar ataxia 6; early infantile epileptic encephalopathy, 42 AD 165
CDKL5 300203 early infantile epileptic encephalopathy 2 XLD 19
DNM1 602377 early infantile epileptic encephalopathy, 31 AD 6
DOCK7 615730 early infantile epileptic encephalopathy 23 AR 3
EEF1A2 602959 mental retardation- 38; early infantile epileptic encephalopathy type 33 AD 3
FRRS1L 604574 Epileptic encephalopathy, early infantile, 37 AR 2
GABRA1 137160 Epilepsy, Juvenile Myoclonic, Susceptibility To, 5; early infantile epileptic encephalopathy, 19 AD 8
GABRB3 137192 Epilepsy, Childhood Absence, Susceptibility To, 5 AD 14
GNAO1 139311 early infantile epileptic encephalopathy 17; neurodevelopmental disorder with involuntary movements AD 4
GRIN2B 138252 mental retardation- 6; early infantile epileptic encephalopathy 27 AD 19
GUF1 617064 early infantile epileptic encephalopathy, 40 AR 3
HCN1 602780 early infantile epileptic encephalopathy 24 AD 3
ITPA 147520 Epileptic encephalopathy, early infantile, 35 AR 4
KCNA2 176262 Epileptic encephalopathy, early infantile, 32 AD 4
KCNB1 600397 early infantile epileptic encephalopathy 26 AD 2
KCNQ2 602235 benign familial neonatal epilepsy; early-onset epileptic encephalopathy 7 AD 62
KCNT1 608167 early infantile epileptic encephalopathy 14; nocturnal frontal lobe epilepsy 5 AD 74
NECAP1 611623 early infantile epileptic encephalopathy 21 AR 0
PCDH19 300460 early infantile epileptic encephalopathy type 9 XL 12
PIGA 311770 Paroxysmal nocturnal hemoglobinuria 1; Multiple congenital anomalies-hypotonia-seizures syndrome 2 XLR 13
PLCB1 607120 early infantile epileptic encephalopathy 12 AR 45
PNKP 605610 early infantile epileptic encephalopathy 10 AR 28
SCN1A 182389 generalized epilepsy with febrile seizures plus 2; early infantile epileptic encephalopathy 6; familial hemiplegic migraine-3 AD 131
SCN2A 182390 benign familial neonatal-infantile seizures type 3; early infantile epileptic encephalopathy 11 AD 59
SCN8A 600702 Cognitive impairment with or without cerebellar ataxia; early infantile epileptic encephalopathy 13; Seizures, benign familial infantile, 5 AD 41
SCN9A 603415 primary erythermalgia; Paroxysmal extreme pain disorder; INDIFFERENCE TO PAIN, CONGENITAL; early infantile epileptic encephalopathy 6; generalized epilepsy with febrile seizures plus 7 AD, AR 74
SLC12A5 606726 early infantile epileptic encephalopathy type 34 AD, AR 8
SLC13A5 608305 early infantile epileptic encephalopathy 25 AR 2
SLC1A2 600300 early infantile epileptic encephalopathy type 41 AD 3
SLC25A12 603667 Epileptic encephalopathy, early infantile, 39 AR 1
SLC25A22 609302 early infantile epileptic encephalopathy 3 AR 10
SLC35A2 314375 congenital disorder of glycosylation type 2m XLD 4
SPTAN1 182810 Epileptic encephalopathy, early infantile, 5 AD 41
ST3GAL3 606494 mental retardation 12; early infantile epileptic encephalopathy, 15 AR 1
STXBP1 602926 early infantile epileptic encephalopathy 4 AD 21
SZT2 615463 Epileptic encephalopathy, early infantile, 18 AR 18
TBC1D24 613577 DOOR syndrome; Myoclonic epilepsy, infantile, familial; deafness type 86; Epileptic encephalopathy, early infantile, 16; deafness type 65 AD, AR 7
WWOX 605131 Esophageal cancer, somatic; autosomal recessive spinocerebellar ataxia 12; early infantile epileptic encephalopathy 28 AR 14

Abbreviations for Table 1: EIEE – Early infantile epileptic encephalopathy; Lennox-Gastaut syndrome, West syndrome, CDG – Congenital disorder of glycosylation, MRX – X-linked mental retardation; LISX - Lissencephaly, PRTS – Partington syndrome; Proud syndrome; EA - Episodic ataxia; FHM – Familial hemiplegic migraine; EE – Epileptic encephalopathy; MRD- Mental retardation autosomal dominant; EJM – Juvenile myoclonic epilepsy; ECA – Childhood absence epilepsy; BFNS – Benign familial neonatal seizures; ENFL – Epilepsy nocturnal frontal lobe; PNH - Paroxysmal nocturnal hemoglobinuria; AOA – Ataxia-oculomotor apraxia; MCSZ – Microcephaly seizures and developmental delay; GEFSP – Generalized epilepsy with febrile seizures plus; CIAT – Cognitive impairment with or without cerebellar ataxia; SFN - Small fiber neuropathy; CIP – Congenital insensitivity to pain; PEPD – Paroxysmal extreme pain disorder; EIG – Epilepsy idiopathic generalized; MRT – Mental retardation autosomal recessive; FIME – Familial infantile myoclonic epilepsy; DOORS – DOOR syndrome; DFNA – Deafness autosomal dominant; DFNB – Deafness autosomal recessive.

Even though there are numerous anti-epileptic drugs routinely used for the treatment of epileptic encephalopathies, Ohtahara syndrome seizures are usually difficult to control. Commonly used medications include clobazam, clonazepam, topiramate, phenobarbital, valproate, and others. Some affected children have displayed a good response to steroid therapy with ACTH or prednisone. In addition, epilepsy-related surgery may be helpful in children with localized/focal seizures.

CENTOGENE offers sequencing and deletion/duplication analysis for the Early infantile epileptic encephalopathy panel (genes: AARS, ALG13, ARHGEF9, ARV1, ARX, CACNA1A, CDKL5, DNM1, DOCK7, EEF1A2, FGF12, FRRS1L, GABRA1, GABRB1, GABRB3, GNAO1, GRIN2B, GRIN2D, GUF1, HCN1, ITPA, KCNA2, KCNB1, KCNQ2, KCNT1, NECAP1, PCDH19, PIGA, PLCB1, PNKP, SCN1A, SCN2A, SCN8A, SCN9A, SIK1, SLC12A5, SLC13A5, SLC1A2, SLC25A12, SLC25A22, SLC35A2, SPTAN1, ST3GAL3, STXBP1, SZT2, TBC1D24, UBA5, WWOX).


Differential diagnosis

The differential diagnosis of early infantile epileptic encephalopathy-related disorders – depending on the major symptoms in the initial case – includes the following diseases:

  • Benign childhood epilepsy
  • Complex partial seizures
  • Epilepsia partialis continua
  • Generalized tonic-clonic seizures
  • Autism
  • Acquired epileptic aphasia
  • Absence seizures
  • Temporal lobe epilepsy

Testing strategy

CENTOGENE offers an advanced, fast and cost-effective strategy to test large NGS panels and diagnose complex phenotypes based on PCR-free whole genome sequencing and NGS technology. This approach offers an unparalleled advantage by reducing amplification/capture biases and providing sequencing of the entire gene with more uniform coverage.

To confirm/establish the diagnosis, CENTOGENE offers the following testing strategy for early infantile epileptic encephalopathy using NGS Panel Genomic targeted towards this specific phenotype

Step 1: Whole genome sequencing from a single filter card.The sequencing covers the entire gene (coding region, exon/intron boundaries, intronic and promoter) for all the genes included in the Early infantile epileptic encephalopathy panel. Copy Number Variants analysis derived from NGS data is also included.

Step 2: If no pathogenic variant is identified after analysis of the Early infantile epileptic encephalopathy panel, we further recommend continuing the bioinformatics analysis of the data using whole genome sequencing to cover those genes which are either implicated in an overlapping phenotype or could be involved in a similar pathway but are not strongly clinically implicated based on the current information in literature.


Referral reasons

The following individuals are candidates for early infantile epileptic encephalopathy testing:

  • Individuals with a family history of early infantile epileptic encephalopathy and presentation of the most common symptoms, including early onset seizures
  • Individuals without a positive family history of EIEE, but with symptoms resembling epileptic encephalopathy
  • Individuals with a negative but suspected family history of EIEE, in order to perform proper genetic counseling.

Test utility

Sequencing, deletion/duplication of the panel genes should be performed in all individuals suspected of having early infantile epileptic encephalopathy and suspected phenotypes. In parallel, other genes reported to be related with this clinical phenotype should also be analyzed for the presence of pathogenic variants, due to the overlap in many clinical features caused by those particular genes.

Confirmation of a clinical diagnosis through genetic testing can allow for genetic counseling and may direct medical management. Genetic counseling can provide a patient and/or family with the natural history of the early infantile epileptic encephalopathy and related disorders identify at-risk family members, provide disease risks as well as appropriate referral for patient support and/or resources.