Comprehensive Epilepsy Panel

SEQmethod-seq-icon Our Sequence Analysis is based on a proprietary targeted sequencing method OS-Seq™ and offers panels targeted for genes associated with certain phenotypes. A standard way to analyze NGS data for finding the genetic cause for Mendelian disorders. Results in 21 days. DEL/DUPmethod-dup-icon Targeted Del/Dup (CNV) analysis is used to detect bigger disease causing deletions or duplications from the disease-associated genes. Results in 21 days. PLUSmethod-plus-icon Plus Analysis combines Sequence + Del/Dup (CNV) Analysis providing increased diagnostic yield in certain clinical conditions, where the underlying genetic defect may be detectable by either of the analysis methods. Results in 21 days.

Test code: NE1001

The Blueprint Genetics Comprehensive Epilepsy Panel is a 194 gene test for genetic diagnostics of patients with clinical suspicion of epilepsy.

The panel covers generalized and focal genetic epilepsies, epileptic encephalopathies, progressive myoclonic epilepsies and epilepsies associated with X-linked mental retardation. Also other syndromes that include epileptic seizures as one of the main manifestation are included as well as hereditary metabolic diseases that manifest as epilepsy. We recommend the panel also to patients with sudden unexplained death. New genomic technologies have led to advances in understanding of the different genomic and genetic architectures across all the major classes of epilepsy, including uncovering a surprising overlap among seemingly different disorders (PMID: 26302787). There is an increasingly wide phenotypic spectrum associated with mutations in several eplepsy genes such as GABRA1, KCNQ2, KCNT1, SCN8A, TBC1D24, and DEPDC5. Thus using a comprehensive epilepsy panel is justifyed. Few studies have applied next generation sequencing technologies to analyze gene panels in unselected epilepsy patient cohorts (PMID: 22612257, 24848745). The reported total diagnostic yield has been 47-48% but the diagnostic yield per gene cannot be estimated from these studies due to small patient cohorts and variable number of genes tested (67 to 265). Recently, it was shown that 25% of sudden unexpected death in epilepsy (SUDEP) patients have mutations in epilepsy genes (PMID: 26704558). This Comprehensive Epilepsy Panel covers the following smaller panels: Idiopathic Generalized and Focal Epilepsy Panel, Epileptic Encephalopathy Panel, NCL and Progressive Myoclonic Epilepsy Panel, Leukodystrophy and Leukoencephalopathy Panel, Epilepsy and X-linked Mental Retardation Panel and Metabolic Epilepsy Panel.

About Epilepsy

Epilepsy is defined by recurrent, unprovoked seizures due to abnormal, synchronized neuronal firing in the brain. The condition is one of the most common neurological conditions. Approximately 20-30 % of epilepsy cases are caused by acquired conditions, but the remaining 70-80 % of cases are believed to be due to one or more genetic factors. The epilepsies can be broadly grouped into three classes: genetic generalized epilepsy (formerly idiopathic generalized epilepsy); focal epilepsy; and epileptic encephalopathy. There are then several specific syndromes within each class defined by differences in specific seizure types, electroencephalogram (EEG) patterns, age of onset and disease progression. Epilepsy is also one of the manifestations of many dysmorphology and multisystemic genetic syndromes and often occurs in neurodegenerative diseases.


Results in 3-4 weeks. We do not offer a maternal cell contamination (MCC) test at the moment. We offer prenatal testing only for cases where the maternal cell contamination studies (MCC) are done by a local genetic laboratory. Read more.

Genes in the Comprehensive Epilepsy Panel and their clinical significance
GeneAssociated phenotypesInheritanceClinVarHGMD
ADARDyschromatosis symmetrica hereditaria, Aicardi-Goutières syndromeAD/AR16202
ADSLAdenylosuccinase deficiencyAR2253
AFG3L2*Spastic ataxia, Spinocerebellar ataxiaAD/AR1925
AIMP1Leukodystrophy, hypomyelinatingAR35
ALDH5A1Succinic semialdehyde dehydrogenase deficiencyAR867
ALDH7A1Epilepsy, pyridoxine-dependentAR29110
ALG13Congenital disorder of glycosylationXL36
AMACRAlpha-methylacyl-CoA racemase deficiency, Bile acid synthesis defectAR313
AMTGlycine encephalopathyAR2651
ARHGEF9Epileptic encephalopathy, early infantileXL311
ARSAMetachromatic leukodystrophyAR61212
ARXLissencephaly, Epileptic encephalopathy, Corpus callosum, agenesis of, with abnormal genitalia, Partington syndrome, Proud syndrome, Hydranencephaly with abnormal genitalia, Mental retardationXL5680
ASAH1Spinal muscular atrophy with progressive myoclonic epilepsy, Farber lipogranulomatosisAR1153
ASPAAspartoacylase deficiency (Canavan disease)AR1990
ATP13A2Parkinson disease (Kufor-Rakeb syndrome)AR1135
ATRXCarpenter-Waziri syndrome, Alpha-thalassemia/mental retardation syndrome, Holmes-Gang syndrome, Juberg-Marsidi syndrome, Smith-Fineman-Myers syndrome, Mental retardation-hypotonic facies syndromeXL42149
BTDBiotinidase deficiencyAR165231
CACNA1AMigraine, familial hemiplegic, Episodic ataxiaAD55181
CACNA1HChildhood absence epilepsyAD449
CACNB4Episodic ataxiaAD16
CASKMental retardation and microcephaly with pontine and cerebellar hypoplasia, FG syndrome, Mental retardationXL4380
CASRHypocalcemia, Neonatal hyperparathyroidism, Familial Hypocalciuric hypercalcemia with transient Neonatal hyperparathyroidismAD/AR78392
CDKL5Epileptic encephalopathy, early infantile, Rett syndrome, atypical, Angelman-like syndromeXL222254
CERS1Epilepsy, progressive myoclonicAR41
CHD2Epileptic encephalopathy, childhood-onsetAD4235
CHRNA2Epilepsy, nocturnal frontal lobeAD111
CHRNA4Epilepsy, nocturnal frontal lobeAD823
CHRNB2Epilepsy, nocturnal frontal lobeAD812
CLCN2Leukoencephalopathy with ataxia, EpilepsyAD/AR1829
CLN3Ceroid lipofuscinosis, neuronalAR6964
CLN5Ceroid lipofuscinosis, neuronalAR4042
CLN6Ceroid lipofuscinosis, neuronalAR2180
CLN8Ceroid lipofuscinosis, neuronalAR3135
CNTNAP2Pitt-Hopkins like syndrome, Cortical dysplasia-focal epilepsy syndromeAR2260
COL4A1Schizencephaly, Anterior segment dysgenesis with cerebral involvement, Retinal artery tortuosity, Porencephaly, Angiopathy, hereditary, with nephropathy, aneurysms, and muscle cramps, Brain small vessel diseaseAD2788
COX15Leigh syndrome, Cardioencephalomyopathy, fatal infantile, due to cytochrome c oxidase deficiencyAR65
CPT2Carnitine palmitoyltransferase II deficiencyAR36102
CSF1RLeukoencephalopathy, diffuse hereditary, with spheroidsAD4470
CSTBEpilepsy, progressive myoclonicAR1613
CTSDCeroid lipofuscinosis, neuronalAR1115
CTSFNeuronal ceroid lipofuscinosisAR79
CUL4BMental retardation, syndromic, CabezasXL934
DARS2Leukoencephalopathy with brain stem and spinal cord involvement and lactate elevationAR1556
DCXLissencephaly, Subcortical laminal heterotopiaXL117138
DEPDC5Epilepsy, familial focal, with variable fociAD5068
DNAJC5Kufs disease,, Ceroid lipofuscinosis, neuronal 4, ParryAD22
DNM1*Epileptic encephalopathy, early infantileAD815
DOCK7Epilepitic encephalopathyAR114
DPYD5-fluorouracil toxicityAD/AR1096
EARS2Combined oxidative phosphorylation deficiencyAR826
EEF1A2Epileptic encephalopathy, early infantile, Mental retardationAD610
EFHC1Epilepsy, myoclonic juvenile, Epilepsy, severe intractable, Epilepsy, juvenile absenceAD/AR317
EIF2B1Leukoencephalopathy with vanishing white matter, OvarioleukodystrophyAR79
EIF2B2Leukoencephalopathy with vanishing white matter, OvarioleukodystrophyAR825
EIF2B3Leukoencephalopathy with vanishing white matter, OvarioleukodystrophyAR520
EIF2B4Leukoencephalopathy with vanishing white matter, OvarioleukodystrophyAR629
EIF2B5Leukoencephalopathy with vanishing white matter, OvarioleukodystrophyAR1495
EPM2AEpilepsy, progressive myoclonicAR1274
ETFAGlutaric aciduria, Multiple acyl-CoA dehydrogenase deficiencyAR728
ETFBGlutaric aciduria, Multiple acyl-CoA dehydrogenase deficiencyAR713
ETFDHGlutaric aciduria, Multiple acyl-CoA dehydrogenase deficiencyAR36168
FAM126ALeukodystrophy, hypomyelinatingAR612
FHHereditary leiomyomatosis and renal cell cancerAD89161
FLNAFrontometaphyseal dysplasia, Osteodysplasty Melnick-Needles, Otopalatodigital syndrome type 1, Otopalatodigital syndrome type 2, Terminal osseous dysplasia with pigmentary defectsXL86209
FOLR1Cerebral folate deficiencyAR424
FOXG1Rett syndrome, congenital variantAD68115
FOXRED1Leigh syndrome, Mitochondrial complex I deficiencyAR107
GABRA1Epileptic encephalopathy, early infantile, Epilepsy, childhood absence, Epilepsy, juvenile myoclonicAD1535
GABRB3Epilepsy, childhood absenceAD546
GABRG2Generalized epilepsy with febrile seizures plus, Familial febrile seizures, Dravet syndrome, Epilepsy, childhood absenceAD2123
GALCKrabbe diseaseAR35210
GAMTGuanidinoacetate methyltransferase deficiencyAR1253
GCDHGlutaric aciduriaAR36198
GCH1Dopa-Responsive Dystonia Hyperphenylalaninemia, BH4-deficient, GTP Cyclohydrolase 1-Deficient Dopa-Responsive DystoniaAD/AR25229
GFAPAlexander diseaseAD110112
GJC2Spastic paraplegia, Lymphedema, hereditary, Leukodystrophy, hypomyelinatingAD/AR1553
GLDCGlycine encephalopathyAR89214
GNAO1Epileptic encephalopathy, early infantileAD1220
GNEInclusion body myopathy, Nonaka myopathy, SialuriaAD/AR32193
GOSR2*Epilepsy, progessive myoclonicAR53
GPHNHyperekplexia, Molybdenum cofactor deficiencyAD/AR2520
GRIA3Mental retardationXL917
GRIN2AEpilepsy, focal, with speech disorderAD3775
GRIN2BEpileptic encephalopathy, early infantile, Mental retardationAD3841
GRNFrontotemporal lobar degeneration with TDP43 inclusions, GRN-related, Neuronal ceroid lipofuscinosisAD/AR24165
HCN1Epileptic encephalopathy, early infantileAD78
HEPACAMMegalencephalic leukoencephalopathy with subcortical cysts, remittingAD/AR923
HNRNPUIntellectual disability and seizuresAD434
HSD17B1017-beta-hydroxysteroid dehydrogenase X deficiency, Mental retardation, syndromicXL812
HSPD1*Spastic paraplegia, Leukodystrophy, hypomyelinatingAD/AR44
IQSEC2Mental retardationXL1636
KCNA1Episodic ataxia/myokymia syndromeAD2037
KCNA2Epileptic encephalopathy, early infantileAD510
KCNB1Early infantile epileptic encephalopathyAD69
KCNC1Epilepsy, progressive myoclonicAD11
KCNQ2Epileptic encephalopathy, early infantile, Benign familial neonatal seizures, MyokymiaAD240205
KCNQ3Seizures, benign neonatalAD1117
KCNT1Epilepsy, nocturnal frontal lobeAD1628
KCTD7*Epilepsy, progressive myoclonicAR1213
KDM5CMental retardation, syndromic, Claes-JensenXL2144
KIF1ASpastic paraplegia, Neuropathy, hereditary sensory, Mental retardationAD/AR3527
L2HGDHL-2-hydroxyglutaric aciduriaAR875
LGI1Epilepsy, familial temporal lobeAD1948
MARS2Combined oxidative phosphorylation deficiencyAR65
MBD5Mental retardationAD2172
MECP2Angelman-like syndrome, Autism, Rett syndrome, Encephalopathy, Mental retardationXL429937
MED12Ohdo syndrome, Mental retardation, with Marfanoid habitus, FG syndrome, Opitz-Kaveggia syndrome, Lujan-Fryns syndromeXL1719
MEF2CMental retardationAD2566
MFSD8Ceroid lipofuscinosis, neuronalAR1941
MLC1Megalencephalic leukoencephalopathy with subcortical cystsAR17111
MOCS1Molybdenum cofactor deficiencyAR732
MTHFRHomocystinuria due to MTHFR deficiencyAR51127
MTORSmith-Kingsmore syndromeAD710
NDUFAF5Mitochondrial complex I deficiencyAR810
NECAP1*Epileptic encephalopathy, early infantileAR11
NHLRC1Epilepsy, progressive myoclonicAR1470
NOTCH3Cerebral arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL)AD22313
NRXN1Pitt-Hopkins like syndrome, SchizophreniaAD/AR51290
OFD1Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndromeXL129148
OPHN1Mental retardation, with cerebellar hypoplasia and distinctive facial appearanceXL1334
PCDH19Epileptic encephalopathy, early infantileXL62141
PGK1Phosphoglycerate kinase 1 deficiencyXL1426
PHF6Borjeson-Forssman-Lehmann syndromeXL1527
PIGA*Multiple congenital anomalies-hypotonia-seizures syndromeXL1914
PLCB1Epileptic encephalopathy, early infantileAR510
PLP1Spastic paraplegia, Pelizaeus-Merzbacher diseaseXL41266
PNKPEpileptic encephalopathy, early infantile, Ataxia-oculomotorAR2116
PNPOPyridoxamine 5'-phosphate oxidase deficiencyAR1428
POLR3ALeukodystrophy, hypomyelinatingAR2167
POLR3BLeukodystrophy, hypomyelinatingAR1154
PPT1Ceroid lipofuscinosis, neuronalAR7277
PRICKLE1Epilepsy, progressive myoclonicAD/AR414
PRICKLE2Epilepsy, progessive myoclonicAD16
PRRT2Episodic kinesigenic dyskinesiaAD3291
PSAPKrabbe disease, atypical, Metachromatic leukodystrophy due to saposin-b deficiency, Combined saposin deficiency, Gaucher disease, atypical, due to saposin C deficiencyAR1524
PTSHyperphenylalaninemia, BH4-deficientAR1184
PURAMental retardationAD3623
QDPRHyperphenylalaninemia, BH4-deficientAR855
RAB39BWaisman parkinsonism-mental retardation syndrome, Mental retardationXL411
RELNLissencephaly, Epilepsy, familial temporal lobeAD/AR1731
RNASEH2AAicardi-Goutières syndromeAR1221
RNASEH2BAicardi-Goutières syndromeAR539
RNASEH2CAicardi-Goutières syndromeAR414
RNASET2Leukoencephalopathy, cystic, without megalencephalyAR611
SAMHD1Aicardi-Goutières syndromeAR2248
SCARB2Epilepsy, progressive myoclonicAR2222
SCN1AMigraine, familial hemiplegic, Epileptic encephalopathy, early infantile, Generalized epilepsy with febrile seizures plusAD4761282
SCN1BAtrial fibrillation, Brugada syndrome, Generalized epilepsy with febrile seizures plusAD1118
SCN2AEpileptic encephalopathy, early infantile, Seizures, benign familial infantileAD86131
SCN8ACognitive impairment, Epileptic encephalopathy, early infantileAD5655
SCN9AParoxysmal extreme pain disorderAD/AR34102
SERPINI1Encephalopathy, familial, with neuroserpin inclusion bodiesAD57
SIK1Epileptic encephalopathy, early infantileAD56
SLC2A1Stomatin-deficient cryohydrocytosis with neurologic defects, Epilepsy, idiopathic generalized, GLUT1 deficiency syndromeAD/AR65253
SLC6A1Myoclonic-astastic epilepsyAD612
SLC6A8*Creatine deficiency syndromeXL19127
SLC9A6Mental retardation, syndromic, ChristiansonXL2118
SLC12A5Epileptic encephalopathy, early infantileAR312
SLC13A5Epileptic encephalopathy, early infantileAR1014
SLC19A3Thiamine metabolism dysfunction syndromeAR1424
SLC25A15*Hyperornithinemia-hyperammonemia-homocitrullinemia syndromeAR1835
SLC25A22Epileptic encephalopathy, early infantileAR64
SLC35A2Congenital disorder of glycosylationXL713
SLC46A1Folate malabsorptionAR1719
SMSMental retardation, Snyder-RobinsonXL910
SNAP25Myasthenic syndrome, congenitalAD23
SOX10Peripheral demyelinating neuropathy, central dysmyelination, Waardenburg syndrome, and Hirschsprung diseaseAD31119
SPTAN1Epileptic encephalopathy, early infantileAD1515
ST3GAL3Epileptic encephalopathy, early infantile, Mental retardationAR33
ST3GAL5Ganglioside GM3 synthase deficiencyAR44
STX1BGeneralized epilepsy with febrile seizures plusAD79
STXBP1Epileptic encephalopathy, early infantileAD63156
SUMF1Multiple sulfatase deficiencyAR1851
SYN1Epilepsy, with variable learning disabilities and behavior disordersXL75
SYNGAP1Mental retardationAD2357
SZT2Epileptic encephalopathy, early infantileAR56
TBC1D24Deafness, Deafness, onychodystrophy, osteodystrophy, mental retardation, and seizures (DOORS) syndromeAD/AR2741
TCF4Corneal dystrophy, Fuchs endothelial, Pitt-Hopkins syndromeAD51129
TPP1Ceroid lipofuscinosis, neuronal, Spinocerebellar ataxiaAR33109
TREX1Vasculopathy, retinal, with cerebral leukodystrophy, Chilblain lupus, Aicardi-Goutières syndromeAD/AR2465
TSC1Lymphangioleiomyomatosis, Tuberous sclerosisAD61306
TSC2Lymphangioleiomyomatosis, Tuberous sclerosisAD141977
TUBB4A*Leukodystrophy, hypomyelinating, DystoniaAD3536
UBE2AMental retardation, syndromic, NascimentoXL421
UBE3A*Angelman syndromeAD143170
WDR45Neurodegeneration with brain iron accumulationXL2056
WWOXEpileptic encephalopathy, early infantile, Spinocerebellar ataxiaAR1935
ZEB2*Mowat-Wilson syndromeAD104247
  • * Some regions of the gene are duplicated in the genome leading to limited sensitivity within the regions. Thus, low-quality variants are filtered out from the duplicated regions and only high-quality variants confirmed by other methods are reported out. Read more.

Gene, refers to HGNC approved gene symbol; Inheritance to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR) and X-linked (XL); ClinVar, refers to a number of variants in the gene classified as pathogenic or likely pathogenic in ClinVar (; HGMD, refers to a number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD, The list of associated (gene specific) phenotypes are generated from CDG ( or Orphanet ( databases.

Blueprint Genetics offers a Comprehensive Epilepsy Panel that covers classical genes associated with epilepsy, leukoencephalopathy, metabolic epilepsy, neuronal ceroid lipofuscinosis and sudden unexpected death. The genes are carefully selected based on the existing scientific evidence, our experience and most current mutation databases. Candidate genes are excluded from this first-line diagnostic test. The test does not recognise balanced translocations or complex inversions, and it may not detect low-level mosaicism. The test should not be used for analysis of sequence repeats or for diagnosis of disorders caused by mutations in the mitochondrial DNA.

Analytical validation is a continuous process at Blueprint Genetics. Our mission is to improve the quality of the sequencing process and each modification is followed by our standardized validation process. Average sensitivity and specificity in Blueprint NGS Panels is 99.3% and 99.9% for detecting SNPs. Sensitivity to for indels vary depending on the size of the alteration: 1-10bps (96.0%), 11-20 bps (88.4%) and 21-30 bps (66.7%). The longest detected indel was 46 bps by sequence analysis. Detection limit for Del/Dup (CNV) analysis varies through the genome depending on exon size, sequencing coverage and sequence content. The sensitivity is 71.5% for single exon deletions and duplications and 99% for three exons’ deletions and duplications. We have validated the assays for different starting materials including EDTA-blood, isolated DNA (no FFPE) and saliva that all provide high-quality results. The diagnostic yield varies substantially depending on the used assay, referring healthcare professional, hospital and country. Blueprint Genetics’ Plus Analysis (Seq+Del/Dup) maximizes the chance to find molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be cost-effective first line test if your patient’s phenotype is suggestive for a specific mutation profile.

The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. The highest relevance in the reported variants is achieved through elimination of false positive findings based on variability data for thousands of publicly available human reference sequences and validation against our in-house curated mutation database as well as the most current and relevant human mutation databases. Reference databases currently used are the 1000 Genomes Project (, the NHLBI GO Exome Sequencing Project (ESP;, the Exome Aggregation Consortium (ExAC;, ClinVar database of genotype-phenotype associations ( and the Human Gene Mutation Database ( The consequence of variants in coding and splice regions are estimated using the following in silico variant prediction tools: SIFT (, Polyphen (, and Mutation Taster (

Through our online ordering and statement reporting system, Nucleus, the customer can access specific details of the analysis of the patient. This includes coverage and quality specifications and other relevant information on the analysis. This represents our mission to build fully transparent diagnostics where the customer gains easy access to crucial details of the analysis process.

In addition to our cutting-edge patented sequencing technology and proprietary bioinformatics pipeline, we also provide the customers with the best-informed clinical report on the market. Clinical interpretation requires fundamental clinical and genetic understanding. At Blueprint Genetics our geneticists and clinicians, who together evaluate the results from the sequence analysis pipeline in the context of phenotype information provided in the requisition form, prepare the clinical statement. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals, even without training in genetics.

Variants reported in the statement are always classified using the Blueprint Genetics Variant Classification Scheme modified from the ACMG guidelines (Richards et al. 2015), which has been developed by evaluating existing literature, databases and with thousands of clinical cases analyzed in our laboratory. Variant classification forms the corner stone of clinical interpretation and following patient management decisions. Our statement also includes allele frequencies in reference populations and in silico predictions. We also provide PubMed IDs to the articles or submission numbers to public databases that have been used in the interpretation of the detected variants. In our conclusion, we summarize all the existing information and provide our rationale for the classification of the variant.

A final component of the analysis is the Sanger confirmation of the variants classified as likely pathogenic or pathogenic. This does not only bring confidence to the results obtained by our NGS solution but establishes the mutation specific test for family members. Sanger sequencing is also used occasionally with other variants reported in the statement. In the case of variant of uncertain significance (VUS) we do not recommend risk stratification based on the genetic finding. Furthermore, in the case VUS we do not recommend use of genetic information in patient management or genetic counseling. For some cases Blueprint Genetics offers a special free of charge service to investigate the role of identified VUS.

We constantly follow genetic literature adapting new relevant information and findings to our diagnostics. Relevant novel discoveries can be rapidly translated and adopted into our diagnostics without delay. These processes ensure that our diagnostic panels and clinical statements remain the most up-to-date on the market.

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ICD & CPT codes

CPT codes


ICD codes

Commonly used ICD-10 codes when ordering the Comprehensive Epilepsy Panel


Accepted sample types

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 5μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

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