Warsaw Genomics
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Genetic test

Epilepsy and epileptic encephalopathies

CAP & EMQN quality control
Price 2194 PLN 31 days from sample registration in laboratory 194 genes Sample Cheek swab or Venous blood or DNA
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Genetic testing with clinical consultation at Warsaw Genomics
~100 000
genomes in our reference database
CAP & EMQN
quality control
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our own laboratory, full control
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genetic data encrypted & protected

What's included in the price

  • NGS sequencing — analysis of the full coding sequence
  • In-house result interpretation by our own team
  • Material collection / delivery per instructions
  • Result available online in the patient portal (PDF)

A consultation with a clinical geneticist is available as a separate service. See the clinic

About this test

Epilepsy and epileptic encephalopathies are a wide group of disorders, in which 80% of cases have a genetic background. Based on the type of seizures, epilepsy can be divided into generalized, focal and epileptic encephalopathies.

Progressive encephalopathies can lead to a gradual loss of motor and cognitive functions concurrent with the deterioration of neurological disorders.

In this test, using novel technology of genome sequencing, full sequences of the 194 genes responsible for epilepsy and epileptic encephalopathies are analyzed.

Genes analysed (194)

Gene Inheritance Associated condition
ABCD1 X-linked Adrenoleukodystrophy, Adrenoleukodystrophy, Adrenoleukodystrophy, Adrenoleukodystrophy, Adrenoleukodystrophy
ADAR AD/AR Aicardi-Goutieres syndrome 1, Dyschromatosis symmetrica hereditaria 1
ADSL autosomal recessive Adenylosuccinase deficiency
AFG3L2 AD/AR Spastic ataxia 5, autosomal recessive
AGA autosomal recessive Aspartylglucosaminuria
AIMP1 autosomal recessive Leukodystrophy, hypomyelinating, 6
ALDH5A1 autosomal recessive Succinic semialdehyde dehydrogenase deficiency
ALDH7A1 autosomal recessive Epilepsy, pyridoxine-dependent
ALG13 X-linked Congenital disorder of glycosylation, type Ii
AMACR autosomal recessive Alpha-methylacyl-CoA racemase deficiency, Bile acid synthesis defect, congenital, 4
AMT autosomal recessive Glycine encephalopathy
ARG1 autosomal recessive Argininemia
ARHGEF9 X-linked Developmental and epileptic encephalopathy 1
ARSA autosomal recessive Metachromatic leukodystrophy
ARX X-linked Developmental and epileptic encephalopathy 1, Developmental and epileptic encephalopathy 1
ASAH1 autosomal recessive Farber lipogranulomatosis, Spinal muscular atrophy with progressive myoclonic epilepsy
ASPA autosomal recessive Canavan disease, Canavan disease, Canavan disease
ATP13A2 autosomal recessive Parkinson disease 19a, juvenile-onset
ATRX X-linked Alpha-Thalassemia myelodysplasia syndrome, Intellectual disability-hypotonic facies syndrome, X-linked
BTD autosomal recessive Biotinidase deficiencymultiple carboxylase deficiency, late-onset
CACNA1A autosomal dominant Migraine, familial hemiplegic, 1
CACNA1H autosomal dominant Childhood absence epilepsy
CACNB4 autosomal dominant Epilepsy, idiopathic generalized, susceptibility to, 9
CASK X-linked Intellectual developmental disorder, autosomal dominant 1
CASR autosomal dominant Hyperparathyroidism 2, Hypocalcemia, autosomal dominant 1, Hypocalciuric hypercalcemia, familial, type I
CDKL5 X-linked Developmental and epileptic encephalopathy 1
CERS1 autosomal recessive Epilepsy, progressive myoclonic 7
CHD2 autosomal dominant Epileptic encephalopathy, early infantile, 31
CHRNA2 autosomal dominant Epilepsy, nocturnal frontal lobe, type 1
CHRNA4 autosomal dominant Epilepsy, nocturnal frontal lobe, type 1
CHRNB2 autosomal dominant Epilepsy, nocturnal frontal lobe, type 1
CLCN2 AD/AR Myoclonic epilepsy, juvenile, susceptibility to, 1
CLN3 autosomal recessive Ceroid lipofuscinosis, neuronal, 3, Ceroid lipofuscinosis, neuronal, 3
CLN5 autosomal recessive Ceroid lipofuscinosis, neuronal, 5
CLN6 autosomal recessive Ceroid lipofuscinosis, neuronal, 6
CLN8 autosomal recessive Ceroid lipofuscinosis, neuronal, 8
CNTNAP2 autosomal recessive Pitt-Hopkins like syndrome 1
COL4A1 autosomal dominant Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps, Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps, Anterior segment dysgenesis 1, Brain small vessel disease 1 with or without ocular anomalies, Brain small vessel disease 1 with or without ocular anomalies, Brain small vessel disease 1 with or without ocular anomalies, Retinal arteries, tortuosity of
COX15 autosomal recessive Mitochondrial complex IV deficiency, nuclear type 1, Mitochondrial complex IV deficiency, nuclear type 6
CPT2 autosomal recessive Carnitine palmitoyltransferase II deficiency, infantile
CSF1R autosomal dominant Leukoencephalopathy, diffuse hereditary, with spheroids
CSTB autosomal recessive Epilepsy, progressive myoclonic 1A (Unverricht and Lundborg)
CTSD autosomal recessive Ceroid lipofuscinosis, neuronal, 10
CTSF autosomal recessive Ceroid lipofuscinosis, neuronal, 13
CUL4B X-linked Intellectual developmental disorder, autosomal dominant 1, Intellectual developmental disorder, X-linked syndromic, Cabezas type
DARS2 autosomal recessive Leukoencephalopathy, diffuse hereditary, with spheroids
DCX X-linked Lissencephaly 2
DEPDC5 autosomal dominant Epilepsy, familial temporal lobe, 1
DNAJC5 autosomal dominant Ceroid lipofuscinosis, neuronal, 11, Ceroid lipofuscinosis, neuronal, 4B, autosomal dominant
DNM1 autosomal dominant Epileptic encephalopathy, early infantile, 31
DOCK7 autosomal recessive Epilepsy, familial temporal lobe, 1
DPYD AD/AR —
EARS2 autosomal recessive Combined oxidative phosphorylation deficiency 25
EEF1A2 autosomal dominant Epileptic encephalopathy, early infantile, 31
EFHC1 AD/AR Myoclonic epilepsy, juvenile, susceptibility to, 1
EIF2B1 autosomal recessive Leukoencephalopathy with vanishing white matter, Leukoencephalopathy with vanishing white matter
EIF2B2 autosomal recessive Leukoencephalopathy with vanishing white matter, Leukoencephalopathy with vanishing white matter
EIF2B3 autosomal recessive Leukoencephalopathy with vanishing white matter, Leukoencephalopathy with vanishing white matter
EIF2B4 autosomal recessive Leukoencephalopathy with vanishing white matter, Leukoencephalopathy with vanishing white matter
EIF2B5 autosomal recessive Leukoencephalopathy with vanishing white matter, Leukoencephalopathy with vanishing white matter
EPM2A autosomal recessive Myoclonic epilepsy of Lafora 2, Myoclonic epilepsy of Lafora 2
ETFA autosomal recessive Glutaricaciduria, type I, Multiple acyl-CoA dehydrogenation deficiency
ETFB autosomal recessive Glutaricaciduria, type I, Multiple acyl-CoA dehydrogenation deficiency
ETFDH autosomal recessive Glutaricaciduria, type I, Multiple acyl-CoA dehydrogenation deficiency
FAM126A autosomal recessive Leukodystrophy, hypomyelinating, 6
FH autosomal dominant Hereditary leiomyomatosis and renal cell cancer
FLNA X-linked Heterotopia, periventricular, X-linked dominant, Heterotopia, periventricular, X-linked dominant, Intestinal pseudoobstruction, neuronal, chronic idiopathic, X-linked, Intestinal pseudoobstruction, neuronal, chronic idiopathic, X-linked
FOLR1 autosomal recessive Neurodegeneration due to cerebral folate transport deficiency
FOXG1 autosomal dominant Rett syndrome
FOXRED1 autosomal recessive Mitochondrial complex I deficiency, nuclear type 19, Mitochondrial complex IV deficiency, nuclear type 1
GABRA1 autosomal dominant Myoclonic epilepsy, juvenile, susceptibility to, 1
GABRB3 autosomal dominant Epilepsy, childhood absence, susceptibility to, 5
GABRG2 autosomal dominant Epileptic encephalopathy, early infantile, 74
GALC autosomal recessive Krabbe disease, Krabbe disease
GAMT autosomal recessive Cerebral creatine deficiency syndrome 2
GCDH autosomal recessive Glutaricaciduria, type I
GCH1 AD/AR Dystonia, DOPA-responsive, with or without hyperphenylalaninemia, Dystonia, DOPA-responsive, with or without hyperphenylalaninemia, Dystonia, DOPA-responsive, with or without hyperphenylalaninemia
GFAP autosomal dominant Alexander disease
GJC2 AD/AR Leukodystrophy, hypomyelinating, 2, Spastic paralysis, infantile-onset ascending
GLDC autosomal recessive Glycine encephalopathy
GNAO1 autosomal dominant Epileptic encephalopathy, early infantile, 31
GNE AD/AR Nonaka myopathy
GOSR2 autosomal recessive Epilepsy, progressive myoclonic, 6
GPHN AD/AR Hyperekplexia 1, Molybdenum cofactor deficiency, complementation group A
GRIA3 X-linked Intellectual developmental disorder, autosomal dominant 1
GRIN2A autosomal dominant Epilepsy, focal, with speech disorder and with or without impaired intellectual development
GRIN2B autosomal dominant Epileptic encephalopathy, early infantile, 27
GRN AD/AR Ceroid lipofuscinosis, neuronal, 11, Frontotemporal lobar degeneration with TDP43 inclusions
HCN1 autosomal dominant Epileptic encephalopathy, early infantile, 31
HEPACAM AD/AR Megalencephalic leukoencephalopathy with subcortical cysts 2A
HNRNPU autosomal dominant Epileptic encephalopathy, early infantile, 54
HSD17B10 X-linked HSD10 mitochondrial disease
HSPD1 AD/AR Leukodystrophy, hypomyelinating, 2, Spastic paralysis, infantile-onset ascending
IQSEC2 X-linked Intellectual developmental disorder, autosomal dominant 1
KCNA1 autosomal dominant Episodic ataxia, type 1
KCNA2 autosomal dominant Epileptic encephalopathy, early infantile, 31
KCNB1 autosomal dominant Epileptic encephalopathy, early infantile, 31
KCNC1 autosomal dominant Epilepsy, progressive myoclonic 7
KCNQ2 autosomal dominant Epileptic encephalopathy, early infantile, 7
KCNQ3 autosomal dominant Epilepsy, benign neonatal, 2
KCNT1 autosomal dominant Developmental and epileptic encephalopathy 14
KCTD7 autosomal recessive Epilepsy, progressive myoclonic 3, with or without intracellular inclusions, Myoclonic epilepsy of Lafora 2
KDM5C X-linked Intellectual developmental disorder, autosomal dominant 1, Intellectual developmental disorder, X-linked syndromic, Claes-Jensen type
KIF1A AD/AR Neuropathy, hereditary sensory, type IIC, Spastic paralysis, infantile-onset ascending
L2HGDH autosomal recessive L-2-hydroxyglutaric aciduria
LGI1 autosomal dominant Epilepsy, familial temporal lobe, 1
MARS2 autosomal recessive Combined oxidative phosphorylation deficiency 25
MBD5 autosomal dominant Intellectual developmental disorder, autosomal dominant 1
MECP2 X-linked Rett syndrome
MED12 X-linked Intellectual developmental disorder, autosomal dominant 1, Ohdo syndrome, X-linked, Opitz-Kaveggia syndrome
MEF2C autosomal dominant Intellectual developmental disorder, autosomal dominant 1
MFSD8 autosomal recessive Ceroid lipofuscinosis, neuronal, 7
MLC1 autosomal recessive Megalencephalic leukoencephalopathy with subcortical cysts 2A
MOCS1 autosomal recessive Molybdenum cofactor deficiency, complementation group A
MTHFR autosomal recessive Homocystinuria-megaloblastic anemia, cbl E type
MTOR autosomal dominant Smith-Kingsmore syndrome
NDUFAF5 autosomal recessive Mitochondrial complex I deficiency, nuclear type 16
NECAP1 autosomal recessive Epileptic encephalopathy, early infantile, 31
NEU1 autosomal recessive Neuraminidase deficiency
NHLRC1 autosomal recessive Myoclonic epilepsy of Lafora 2, Myoclonic epilepsy of Lafora 2
NOTCH3 autosomal dominant Myofibromatosis, infantile 2
NRXN1 AD/AR Pitt-Hopkins-Like syndrome 2
OFD1 X-linked Joubert syndrome 13, Orofaciodigital syndrome VI, Retinitis pigmentosa, Simpson-Golabi-Behmel syndrome, type 2
OPHN1 X-linked Intellectual developmental disorder, autosomal dominant 1
PCDH19 X-linked Epileptic encephalopathy, early infantile, 9, Epileptic encephalopathy, early infantile, 9
PGK1 X-linked Phosphoglycerate kinase 1 deficiency
PHF6 X-linked Borjeson-Forssman-Lehmann syndrome
PIGA X-linked Multiple congenital anomalies-hypotonia-seizures syndrome 2
PLCB1 autosomal recessive Developmental and epileptic encephalopathy 12
PLP1 X-linked Leukodystrophy, hypomyelinating, 2, Pelizaeus-Merzbacher disease
PNKP autosomal recessive Microcephaly, seizures, and developmental delay
PNPO autosomal recessive Pyridoxamine 5-prime-phosphate oxidase deficiency
POLR3A autosomal recessive Leukodystrophy, hypomyelinating, 6
POLR3B autosomal recessive Leukodystrophy, hypomyelinating, 6
PPT1 autosomal recessive Ceroid lipofuscinosis, neuronal, 1
PRICKLE1 AD/AR Epilepsy, progressive myoclonic 7
PRICKLE2 autosomal dominant Epilepsy, progressive myoclonic 7
PRODH autosomal recessive Hyperprolinemia, type I
PRRT2 autosomal dominant Convulsions, familial infantile, with paroxysmal choreoathetosis
PSAP autosomal recessive Gaucher disease, type II, Krabbe disease, Metachromatic leukodystrophy
PTS autosomal recessive Dystonia, DOPA-responsive, with or without hyperphenylalaninemia
PURA autosomal dominant Intellectual developmental disorder, autosomal dominant 1
QDPR autosomal recessive Dystonia, DOPA-responsive, with or without hyperphenylalaninemia
RAB39B X-linked Waisman syndrome
RELN AD/AR Epilepsy, familial temporal lobe, 7, Lissencephaly 2
RNASEH2A autosomal recessive Aicardi-Goutieres syndrome 1
RNASEH2B autosomal recessive Aicardi-Goutieres syndrome 1
RNASEH2C autosomal recessive Aicardi-Goutieres syndrome 1
RNASET2 autosomal recessive Leukoencephalopathy, diffuse hereditary, with spheroids
SAMHD1 autosomal recessive Aicardi-Goutieres syndrome 1
SCARB2 autosomal recessive Epilepsy, progressive myoclonic, 4, with or without renal failure
SCN1A autosomal dominant Epileptic encephalopathy, early infantile, 6 (Dravet syndrome), Epileptic encephalopathy, early infantile, 6 (Dravet syndrome)
SCN1B autosomal dominant Brugada syndrome 1, Generalized epilepsy with febrile seizures plus, type 1
SCN2A autosomal dominant Epileptic encephalopathy, early infantile, 11
SCN8A autosomal dominant Epileptic encephalopathy, early infantile, 13
SCN9A AD/AR Epileptic encephalopathy, early infantile, 6 (Dravet syndrome)
SERPINI1 autosomal dominant Encephalopathy, familial, with neuroserpin inclusion bodies
SIK1 autosomal dominant Epileptic encephalopathy, early infantile, 31
SLC12A5 autosomal recessive Epileptic encephalopathy, early infantile, 31
SLC13A5 autosomal recessive Epileptic encephalopathy, early infantile, 25, with amelogenesis imperfecta
SLC19A3 autosomal recessive —
SLC25A15 autosomal recessive Hyperornithinemia-hyperammonemia-homocitrullinemia syndrome
SLC25A22 autosomal recessive Epileptic encephalopathy, early infantile, 3
SLC2A1 AD/AR GLUT1 deficiency syndrome 1, infantile onset, severe
SLC35A2 X-linked Congenital disorder of glycosylation, type Ii
SLC46A1 autosomal recessive Folate malabsorption, hereditary
SLC6A1 autosomal dominant Epilepsy, progressive myoclonic 7
SLC6A8 X-linked Cerebral creatine deficiency syndrome 1
SLC9A6 X-linked Intellectual developmental disorder, autosomal dominant 1
SMS X-linked Intellectual developmental disorder, autosomal dominant 1, Intellectual developmental disorder, X-linked syndromic, Snyder-Robinson type
SNAP25 autosomal dominant Myasthenic syndrome, congenital, 5
SOX10 autosomal dominant Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung disease, Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung disease, Waardenburg syndrome, type 2E
SPTAN1 autosomal dominant Epileptic encephalopathy, early infantile, 5
ST3GAL3 autosomal recessive Developmental and epileptic encephalopathy 15
ST3GAL5 autosomal recessive Salt and pepper developmental regression syndrome
STX1B autosomal dominant Generalized epilepsy with febrile seizures plus, type 9
STXBP1 autosomal dominant Developmental and epileptic encephalopathy 4
SUMF1 autosomal recessive Multiple sulfatase deficiency
SUOX autosomal recessive Sulfite oxidase deficiency
SYN1 X-linked Epileptic encephalopathy, early infantile, 31
SYNGAP1 autosomal dominant Intellectual developmental disorder, autosomal dominant 1
SZT2 autosomal recessive Developmental and epileptic encephalopathy 18
TBC1D24 AD/AR Developmental and epileptic encephalopathy 16
TCF4 autosomal dominant ciężkie napady padaczkowe z dysfunkcją autonomicznego układu nerwowego, Pitt-Hopkins syndrome, Pitt-Hopkins syndrome
TPP1 autosomal recessive Ceroid lipofuscinosis, neuronal, 2
TREX1 AD/AR Aicardi-Goutieres syndrome 1, Vasculopathy, retinal, with cerebral leukodystrophy, Vasculopathy, retinal, with cerebral leukodystrophy
TSC1 autosomal dominant LYMPHANGIOLEIOMYOMATOSIS, Tuberous sclerosis-2
TSC2 autosomal dominant LYMPHANGIOLEIOMYOMATOSIS, Tuberous sclerosis-2
TUBB4A autosomal dominant Leukodystrophy, hypomyelinating, 6, Leukodystrophy, hypomyelinating, 6
UBE2A X-linked Intellectual developmental disorder, autosomal dominant 1, Intellectual developmental disorder, X-linked syndromic, Nascimento type
UBE3A autosomal dominant Angelman syndrome
WDR45 X-linked Neurodegeneration with brain iron accumulation 5
WWOX autosomal recessive Developmental and epileptic encephalopathy 28
ZEB2 autosomal dominant Mowat-Wilson syndrome

Click a gene to see a single-gene test.

How the test works

  1. 1

    Order online

    No referral needed. You order online.

  2. 2

    Collect the sample

    Sample: Cheek swab or Venous blood or DNA.

  3. 3

    Result

    Available in 31 days from sample registration in laboratory, online.

Methodology
Methodology
Information on the test method:

At first, deoxyribonucleic acid (DNA) is isolated from a blood sample or paraffin embedded tissue block. The quantity and quality of the material is determined in spectrophotometric and fluorometric assays. From mechanically or enzymatically fragmented DNA a library is made to be used for determination, sequencing and examination of selected genes. The library is sequenced on a new generation sequencer. Afterwards, sequencing results are subjected to bioinformatics analysis and clinical interpretation. Genetic variants are identified using BurrowsWheeler Aligner. The test detects 100% of substitutions and 95% of small insertions and deletions.

Information on variant classification:

The study report provides information on variants classified as ‘potentially pathogenic’ and ‘pathogenic’ depending on their suspected clinical significance. The identified variants are classified under the following categories:

Pathogenic variant: the detected change in the gene sequence directly associates with disease development. At the same time, some pathogenic changes may not have full penetration, meaning that a single mutation may not be enough to cause a full-blown disease.

Potentially pathogenic variant: the detected change in the gene sequence may be, with a great probability, associated with disease development however it is not possible to prove this association on the basis of currently available scientific data. Variant pathogenicity confirmation would require additional tests and evidence; it cannot be excluded that further tests might prove that the change has limited or no clinical significance.

Variant of unknown pathogenicity: based on the currently available scientific data it is not possible to determine the significance of the detected change.

Potentially benign variant: the detected change in the gene sequence most probably does not associate with disease development, however based on the currently available scientific data the benignity of the mutation cannot be confirmed. Confirmation of the clinical significance of the variant would require additional tests and evidence; it cannot be excluded that further tests might prove that the detected mutation has clinical significance and would cause disease development.

Benign variant: the detected change does not associate with disease development.

The identified genetic variants are classified based on the guidelines of the American College of Medical Genetics and Genomics and the American Association for Molecular Pathology (S. Richards, Genet Med. 2015 May; 17(5):405-24). In variant classification the following criteria are considered:

  • Previous variant identification in persons burdened with the disease
  • Variant impact of functional gene product synthesis determined through bioinformatics analyses, confirmed by in vitro/in vivo studies
  • Variant location (exon/intron, functional domain)
  • De novo/hereditary change
  • Variant incidence in general population (each variant with incidence >5% in line with Exome Sequencing Project, 1000 Genomes Project or Exome Aggregation Consortium is classified as benign change)

Variant incidence in general population with relation to patient population The final classification of variants is made on the basis of the total of the above-mentioned criteria. The data bases include: 1000GP, ClinVar, ConsensusPathDB, Exome Aggregation Consortium, Exome Variant Server, FATHMM, GO (Gene Ontology), GTEx (Genotype-Tissue Expression), GWAS (Genome Wide Association Study), HGMD, KEGG, MetaLR, MetaSVM, MutationAssessor, MutationTaster, OMIM, PolyPhen-2, PROVEAN, SIFT, SnpEff, dbNSFP, UniProt, VEP (Variant Effect Predictor).

Test limitations:

All sequencing technologies have some limitations. Our tests use new generation sequencing (NGS) to examine coding and splicing regions of disease-associated genes. Sequencing techniques and subsequent bioinformatics analyses are aimed at limiting the significance of pseudo-gene sequences, however presence of highly homologous gene sequences may still occasionally disturb the identification of pathogenic alleles, deletions/duplications. The Sanger sequencing method is used to confirm variants with lower quality parameters. Deletion/duplication analyses show qualitative changes in DNA covering at least one exon and always require confirmation with other methods (qPCR or MLPA). The analyses are not designed for detecting certain types of genomic changes, such as translocations, inversions, dynamic mutations (e.g. increased number of trinucleotide repetitions) or mutations in regulatory or intronic regions. In case increased numbers of di- or trinucleotide repetitions are reported, it should be assumed that the exact number of repetitions is not precise. The test is not intended to detect somatic mosaicism and somatic mutation analyses should be made in the context of the germinal DNA sequence.

It is not possible to exclude mutations in genes and regions other than those covered by the test as well as alternations in the gene copy number. The test report includes information on changes in gene sequence identified on the basis of a comparison against current reference sequences maintained in NCBI Nucleotide and Ensembl databases. Tests are developed by Warsaw Genomics for clinical objectives. All test results collected are interpreted and analysed by scientific and medical experts of Warsaw Genomics.

Frequently asked questions

How long does the Epilepsy and epileptic encephalopathies test take?

The result is usually available within 31 days from sample registration in laboratory.

Do I need a referral?

No. You can order this genetic test online without a referral.

How many genes does this panel cover?

The panel analyses 194 genes.

How much does the test cost?

The price of the test is 2194 PLN.

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