Invitae Epilepsy Panel

Ordering
  • Test code: 03401
  • Turnaround time:
    10–21 calendar days (14 days on average)
  • Preferred specimen:
    3mL whole blood in a purple-top tube
  • Alternate specimens:
    DNA or saliva/assisted saliva
  • Sample requirements
  • Request a sample kit
Billing

Test description

The Invitae Epilepsy Panel analyzes up to 189 genes that are associated with both syndromic and nonsyndromic causes of epilepsy, a common neurological disease characterized by recurrent, unprovoked seizures. These genes were curated based on the available evidence to date in order to provide a comprehensive analysis for inherited epilepsy.

Given the clinical overlap between different epilepsy disorders, comprehensive testing allows for more efficient evaluation of multiple conditions based on a single indication for testing. Identification of the molecular basis of disease in an affected individual may confirm diagnosis, predict prognosis, and encourage testing of additional family members to inform reproductive risk.

Note: Invitae’s assay includes sequencing and deletion analysis of UBE3A but does not detect uniparental disomy or imprinting center defects.

Order test

Primary panel (125 genes)

ADSL ALDH5A1 ALDH7A1 ALG13 ARHGEF9 ARX ATP1A2 ATP1A3 ATRX BRAT1 C12orf57 CACNA2D2 CASK CDKL5 CHD2 CHRNA2 CHRNA4 CHRNB2 CLN2 (TPP1) CLN3 CLN5 CLN6 CLN8 CNTNAP2 CSTB CTSD DEPDC5 DNAJC5 DNM1 DYRK1A EEF1A2 EFHC1 EHMT1 EPM2A FOLR1 FOXG1 FRRS1L GABRA1 GABRB3 GABRG2 GAMT GATM GLRA1 GNAO1 GOSR2 GRIN1 GRIN2A GRIN2B HCN1 HNRNPU IER3IP1 IQSEC2 ITPA KANSL1 KCNA2 KCNB1 KCNC1 KCNH2 KCNJ10 KCNQ2 KCNQ3 KCNT1 KCTD7 KIAA2022 LGI1 LIAS MBD5 MECP2 MEF2C MFSD8 NGLY1 NHLRC1 NRXN1 PACS1 PCDH19 PIGA PIGN PIGO PLCB1 PNKD PNKP PNPO POLG PPT1 PRICKLE1 PRRT2 PURA QARS ROGDI SATB2 SCARB2 SCN1A SCN1B SCN2A SCN3A SCN8A SCN9A SERPINI1 SGCE SLC13A5 SLC19A3 SLC25A22 SLC2A1 SLC35A2 SLC6A1 SLC6A8 SLC9A6 SMC1A SNX27 SPATA5 SPTAN1 STX1B STXBP1 SYN1 SYNGAP1 SYNJ1 SZT2 TBC1D24 TCF4 TSC1 TSC2 UBE3A WWOX ZDHHC9 ZEB2

ARX: Analysis is validated to detect polyalanine expansions but sensitivity may be reduced in heterozygous females. Family variant testing in female individuals is available when there is a confirmed expansion in a male relative.
CLN3: Analysis includes the intronic variant NM_001042432.1; c.461-13G>C.
CSTB: Dodecamer repeat numbers in the 5' UTR are not determined.
KANSL1: Deletion/duplication analysis is not offered for exons 2-3.
KCNT1: Deletion/duplication analysis is not offered for exons 26 or 27.
PPT1: Analysis includes the large, mostly intronic deletion NM_000310.3:c.124+1215_235-102del3627 as well as the intronic variant NM_000310.3:c.125-15T>G.
SCN8A: Analysis includes exon 6 of NM_001330260.1.

Add-on Preliminary-evidence Genes for Epilepsy (58 genes)

Preliminary-evidence genes currently have early evidence of a clinical association with the specific disease covered by this test. Some clinicians may wish to include genes which do not currently have a definitive clinical association, but which may prove to be clinically significant in the future. These genes can be added at no additional charge. Visit our Preliminary-evidence genes page to learn more.

ABAT ARHGEF15 ATP6AP2 CACNA1A CACNA1H CACNB4 CARS2 CASR CBL CERS1 CLCN4 CNTN2 COQ4 CPA6 DIAPH1 DOCK7 FARS2 FASN GABBR2 GABRB2 GABRD GAL GPHN JMJD1C KCNA1 KCND2 KCNH5 KCNMA1 KPNA7 LMNB2 MTOR NECAP1 NEDD4L NPRL3 PIGG PIGQ PIK3AP1 PRDM8 PRICKLE2 PRIMA1 RBFOX1 RBFOX3 RELN RYR3 SCN5A SETD2 SIK1 SLC12A5 SLC25A12 SLC35A3 SNAP25 SRPX2 ST3GAL3 ST3GAL5 STRADA TBL1XR1 TPK1 WDR45

Add-on Genes for Glycine Encephalopathy (3 genes)

In addition to the primary panel, clinicians can choose to include three genes that are associated with glycine encephalopathy, which can cause encephalopathy, hypotonia, seizures, and elevated plasma and CSF glycine levels. If clinically indicated, these gene can be added at no additional charge.

AMT GCSH GLDC

Add-on FLNA Gene (1 gene)

In addition to the primary Epilepsy panel, clinicians can choose to include the FLNA gene that is associated with disorders that are broadly categorized as neuronal migration disorders and otopalatodigital spectrum disorders. Periventricular nodular heterotopia is a neuronal migration disorder characterized by seizures and nodules lining the edges of the lateral cerebral ventricles, along with variable presence of persistent patent ductus arteriosus, coagulopathy, connective tissue and vascular anomalies, and/or gastrointestinal dysmotility (PMID: 15917206, 19917821). Periventricular nodular heterotopia predominantly affects females due to the severity of this condition in males (PMID: 15917206). If clinically indicated, this gene can be added at no additional charge.

FLNA

Add-on PTEN Gene (1 gene)

In addition to the primary Epilepsy panel, clinicians can choose to include the PTEN gene that is associated with PTEN-related autism spectrum disorder (ASD), with or without macrocephaly. ASDs are characterized by impairments in social interactions and communication, developmental delays, and restricted and/or repetitive behaviors. Autism is often associated with other neurological conditions including epilepsy (PMID: 20510557, 24580998). If clinically indicated, this gene can be added at no additional charge.

PTEN

PTEN: Deletion/duplication analysis covers the promoter region.

Add-on RANBP2 Gene (1 gene)

In addition to the primary panel, clinicians can choose to include the RANBP2 gene that is associated with infection-induced acute necrotizing encephalopathy, an environmentally triggered disease in which previously healthy children develop encephalopathy, seizures, and rapid progression to coma, typically within days of onset of a common febrile infection (PMID: 19118815). If clinically indicated, this gene can be added at no additional charge.

RANBP2

Alternative tests to consider

The Invitae Epilepsy panel includes a subset of genes associated with congenital, infantile and childhood onset neuronal ceroid lipofuscinoses (NCLs). NCLs are a group of inherited neurodegenerative lysosomal storage disorders that result in defective sphingolipid synthesis and the accumulation of autofluorescent ceroid lipopigments in the central nervous system and are characterized by progressive decline, which can include psychomotor and cognitive decline, seizures, epilepsy, and early death. In some NCLs, developmental delay, speech delay, ataxia, cerebellar and cerebral atrophy, visual decline, hand stereotypies, sleep disturbances, behavioral/psychiatric disturbances, or additional brain MRI findings may develop. Given clinical overlap of NCL with epilepsy disorders, comprehensive analysis of the genes associated with all clinical subtypes of NCL may be more appropriate. If clinically indicated, the Invitae Comprehensive Neuronal Ceroid Lipofuscinoses Panel should considered and can be ordered instead of this panel. See link below for more information about the Invitae Comprehensive NCL panel.

  • adenylosuccinate lyase deficiency
  • alpha-thalassemia X-linked intellectual disability (ATRX) syndrome
  • Angelman syndrome
    • Angelman-like syndrome
  • autosomal dominant childhood onset epilepsy
  • autosomal dominant lateral temporal lobe epilepsy
  • autosomal dominant mental retardation
  • autosomal dominant familial hemiplegic migraine
  • benign familial infantile seizures
  • benign familial neonatal seizures
  • benign familial neonatal-infantile seizures
  • cerebral creatine deficiency syndrome
  • cerebral folate deficiency
  • childhood absence epilepsy
  • CLN2 disease
  • congenital disorder of glycosylation type 1s
  • cortical dysplasia-focal epilepsy syndrome (CDFES)
  • Dravet syndrome
  • early infantile epileptic encephalopathy (EIEE)
  • familial paroxysmal kinesigenic dyskinesia
  • generalized epilepsy with febrile seizures plus (GEFS+)
  • Glass syndrome
  • GLUT1 deficiency syndrome
  • hyperphosphatasia with intellectual disability syndrome
  • idiopathic generalized epilepsy
  • intellectual disability
  • intractable childhood epilepsy with generalized tonic-clonic seizures
  • juvenile myoclonic epilepsy
  • Kleefstra syndrome
  • Kohlschütter-Tönz syndrome
  • Koolen-de Vries syndrome
  • MEF2C-related intellectual disability
  • microcephaly, epilepsy, and diabetes syndrome (MEDS)
  • Mowat-Wilson syndrome
  • multiple congenital anomalies-hypotonia-seizures syndrome 1 (MCAHS1)
  • neonatal-lethal rigidity and multifocal seizure syndrome (RFMSL)
  • neuronal ceroid lipofuscinosis
  • NGLY1-congenital disorder of glycosylation
  • Ohtahara syndrome
  • Phelan-McDermid syndrome
  • Pitt-Hopkins syndrome
    • Pitt-Hopkins-like syndrome
  • progressive microcephaly with seizures and cerebral and cerebellar atrophy
  • progressive myoclonic epilepsy
  • pyridoxal 5’-phosphate dependent epilepsy
  • pyridoxine-dependent epilepsy
  • pyruvate dehydrogenase complex deficiency
  • Rett syndrome
    • atypical Rett syndrome
    • congenital Rett syndrome
  • SCN8A-related early infantile epileptic encephalopathy
  • succinic semialdehyde dehydrogenase (SSADH) deficiency
  • sudden unexpected death in epilepsy (SUDEP)
  • tuberous sclerosis complex (TSC)
  • West syndrome

As defined by the International League Against Epilepsy, epilepsy is a common neurological disease that is characterized by two or more unprovoked seizures occurring 24 hours apart. Erratic electrical activity in the brain results in seizures, which may present as abnormal movements such as convulsions or jerks or as behaviors such as staring blankly. The location of the abnormal electrical activity in the brain is used to classify seizures into two categories: generalized and partial. Generalized seizures occur due to abnormal electrical activity originating from both hemispheres of the brain and include absence, myoclonic, clonic, tonic, and atonic seizures. The types of movements or behaviors that occur are used to further classify the type of generalized seizure. Partial (focal) seizures are caused by abnormal electrical activity restricted to a localized region of the brain and are further categorized as simple (conscious), complex (unconscious) and partial with secondary generalization (initially maintains consciousness but evolves into a loss of consciousness). In some cases, focal seizures eventually evolve into generalized seizures. Epilepsy may present as an isolated finding or as part of a broader phenotype. Several syndromic neurodevelopmental disorders include epilepsy as a prominent feature.

The clinical sensitivity of this test is dependent on the patient’s underlying genetic condition. The percentage of clinical cases in which a pathogenic variant is expected to be identified through analysis of genes on this panel in association with EIEE and Rett/Angelman syndrome and related disorders can be found:

The estimated overall positive result rate is 20-25% with infantile epilepsy with the highest rate at 22% and childhood epilepsy rate at 10%. The Invitae Epilepsy Panel is expected to have a positive result rate at approximately 17% (PMID: 20100225, 19153375, 21481738).

Inherited epilepsy disorders can occur in several inheritance patterns, including autosomal dominant, autosomal recessive, and X-linked.

Epilepsy is the third-most-common neurological disorder, with a prevalence of 4-8 in 1000.

  1. Depienne, C, et al. Sporadic infantile epileptic encephalopathy caused by mutations in PCDH19 resembles Dravet syndrome but mainly affects females. PLoS Genet. 2009; 5(2):e1000381. PMID: 19214208
  2. Deprez, L, et al. Genetics of epilepsy syndromes starting in the first year of life. Neurology. 2009; 72(3):273-81. PMID: 19153375
  3. Fisher, RS, et al. ILAE official report: a practical clinical definition of epilepsy. Epilepsia. 2014; 55(4):475-82. PMID: 24730690
  4. Heron, SE, et al. Missense mutations in the sodium-gated potassium channel gene KCNT1 cause severe autosomal dominant nocturnal frontal lobe epilepsy. Nat. Genet. 2012; 44(11):1188-90. PMID: 23086396
  5. Kurahashi, H, Hirose, S. Autosomal Dominant Nocturnal Frontal Lobe Epilepsy. 2002 May 16. In: Pagon, RA, et al, editors. GeneReviews(®) (Internet). University of Washington, Seattle. PMID: 20301348
  6. Marini, C, et al. Protocadherin 19 mutations in girls with infantile-onset epilepsy. Neurology. 2010; 75(7):646-53. PMID: 20713952
  7. Ottman, R, et al. Genetic testing in the epilepsies--report of the ILAE Genetics Commission. Epilepsia. 2010; 51(4):655-70. doi: 10.1111/j.1528-1167.2009.02429.x. PMID: 20100225
  8. Pong, AW, et al. Developments in molecular genetic diagnostics: an update for the pediatric epilepsy specialist. Pediatr. Neurol. 2011; 44(5):317-27. PMID: 21481738
  9. Zara, F, et al. Genetic testing in benign familial epilepsies of the first year of life: clinical and diagnostic significance. Epilepsia. 2013; 54(3):425-36. PMID: 23360469

Assay and technical information

Invitae is a College of American Pathologists (CAP)-accredited and Clinical Laboratory Improvement Amendments (CLIA)-certified clinical diagnostic laboratory performing full-gene sequencing and deletion/duplication analysis using next-generation sequencing technology (NGS).

Our sequence analysis covers clinically important regions of each gene, including coding exons, +/- 10 base pairs of adjacent intronic sequence, and select noncoding variants. Our assay provides a Q30 quality-adjusted mean coverage depth of 350x (50x minimum, or supplemented with additional analysis). Variants classified as pathogenic or likely pathogenic are confirmed with orthogonal methods, except individual variants that have high quality scores and previously validated in at least ten unrelated samples.

Our analysis detects most intragenic deletions and duplications at single exon resolution. However, in rare situations, single-exon copy number events may not be analyzed due to inherent sequence properties or isolated reduction in data quality. If you are requesting the detection of a specific single-exon copy number variation, please contact Client Services before placing your order.

Assay notes

ARX: Analysis is validated to detect polyalanine expansions but sensitivity may be reduced in heterozygous females. Family variant testing in female individuals is available when there is a confirmed expansion in a male relative.

UBE3A: Analysis includes sequencing and deletion analysis but does not detect uniparental disomy or imprinting center defects.

Gene Transcript reference Sequencing analysis Deletion/Duplication analysis
ABAT NM_020686.5
ADSL NM_000026.2
ALDH5A1 NM_001080.3
ALDH7A1 NM_001182.4
ALG13 NM_001257230.1; NM_001099922.2
AMT NM_000481.3
ARHGEF15 NM_173728.3
ARHGEF9 NM_015185.2; NM_001173479.1
ARX* NM_139058.2
ATP1A2 NM_000702.3
ATP1A3 NM_152296.4
ATP6AP2 NM_005765.2
ATRX NM_000489.4
BRAT1 NM_152743.3
C12orf57 NM_138425.3
CACNA1A NM_001127221.1
CACNA1H NM_021098.2
CACNA2D2 NM_006030.3
CACNB4 NM_000726.3
CARS2 NM_024537.3
CASK NM_003688.3
CASR NM_000388.3
CBL NM_005188.3
CDKL5 NM_003159.2
CERS1 NM_021267.4
CHD2 NM_001271.3
CHRNA2 NM_000742.3
CHRNA4 NM_000744.6
CHRNB2 NM_000748.2
CLCN4 NM_001830.3
CLN2 (TPP1) NM_000391.3
CLN3* NM_001042432.1
CLN5 NM_006493.2
CLN6 NM_017882.2
CLN8 NM_018941.3
CNTN2 NM_005076.3
CNTNAP2 NM_014141.5
COQ4 NM_016035.4
CPA6 NM_020361.4
CSTB* NM_000100.3
CTSD NM_001909.4
DEPDC5 NM_001242896.1
DIAPH1 NM_005219.4
DNAJC5 NM_025219.2
DNM1 NM_004408.3
DOCK7 NM_001271999.1
DYRK1A NM_001396.3; NM_101395.2
EEF1A2 NM_001958.3
EFHC1 NM_018100.3
EHMT1 NM_024757.4
EPM2A NM_005670.3
FARS2 NM_006567.3
FASN NM_004104.4
FLNA NM_001456.3
FOLR1 NM_016725.2
FOXG1 NM_005249.4
FRRS1L NM_014334.2
GABBR2 NM_005458.7
GABRA1 NM_000806.5
GABRB2 NM_021911.2
GABRB3 NM_000814.5; NM_021912.4
GABRD NM_000815.4
GABRG2 NM_000816.3
GAL NM_015973.3
GAMT NM_000156.5
GATM NM_001482.2
GCSH NM_004483.4
GLDC NM_000170.2
GLRA1 NM_000171.3
GNAO1 NM_020988.2
GOSR2 NM_004287.3
GPHN NM_020806.4
GRIN1 NM_007327.3
GRIN2A NM_000833.4
GRIN2B NM_000834.3
HCN1 NM_021072.3
HNRNPU NM_031844.2
IER3IP1 NM_016097.4
IQSEC2 NM_001111125.2
ITPA NM_033453.3
JMJD1C NM_032776.2
KANSL1* NM_001193466.1
KCNA1 NM_000217.2
KCNA2 NM_004974.3
KCNB1 NM_004975.2
KCNC1 NM_001112741.1
KCND2 NM_012281.2
KCNH2 NM_000238.3; NM_172057.2
KCNH5 NM_139318.4
KCNJ10 NM_002241.4
KCNMA1 NM_002247.3
KCNQ2 NM_172107.2
KCNQ3 NM_004519.3
KCNT1* NM_020822.2
KCTD7 NM_153033.4
KIAA2022 NM_001008537.2
KPNA7 NM_001145715.1
LGI1 NM_005097.2
LIAS NM_006859.3
LMNB2 NM_032737.3
MBD5 NM_018328.4
MECP2 NM_004992.3; NM_001110792.1
MEF2C NM_002397.4
MFSD8 NM_152778.2
MTOR NM_004958.3
NECAP1 NM_015509.3
NEDD4L NM_015277.5
NGLY1 NM_018297.3
NHLRC1 NM_198586.2
NPRL3 NM_001077350.2
NRXN1 NM_001135659.1; NM_138735.2
PACS1 NM_018026.3
PCDH19 NM_001184880.1
PIGA NM_002641.3
PIGG NM_001127178.2
PIGN NM_176787.4
PIGO NM_032634.3
PIGQ NM_004204.3
PIK3AP1 NM_152309.2
PLCB1 NM_015192.3
PNKD NM_015488.4
PNKP NM_007254.3
PNPO NM_018129.3
POLG NM_002693.2
PPT1* NM_000310.3
PRDM8 NM_020226.3
PRICKLE1 NM_153026.2
PRICKLE2 NM_198859.3
PRIMA1 NM_178013.3
PRRT2 NM_145239.2
PTEN* NM_000314.4
PURA NM_005859.4
QARS NM_005051.2
RANBP2 NM_006267.4
RBFOX1 NM_145891.2; NM_018723.3
RBFOX3 NM_001082575.2
RELN NM_005045.3
ROGDI NM_024589.2
RYR3 NM_001036.4
SATB2 NM_015265.3
SCARB2 NM_005506.3
SCN1A NM_001165963.1
SCN1B NM_199037.3; NM_001037.4
SCN2A NM_021007.2
SCN3A NM_006922.3
SCN5A NM_198056.2
SCN8A* NM_014191.3; NM_001330260.1
SCN9A NM_002977.3
SERPINI1 NM_005025.4
SETD2 NM_014159.6
SGCE NM_003919.2
SIK1 NM_173354.3
SLC12A5 NM_020708.4
SLC13A5 NM_177550.4
SLC19A3 NM_025243.3
SLC25A12 NM_003705.4
SLC25A22 NM_024698.5
SLC2A1 NM_006516.2
SLC35A2 NM_001042498.2
SLC35A3 NM_012243.2
SLC6A1 NM_003042.3
SLC6A8 NM_005629.3
SLC9A6 NM_006359.2; NM_001042537.1
SMC1A NM_006306.3
SNAP25 NM_130811.2; NM_003081.3
SNX27 NM_030918.5
SPATA5 NM_145207.2
SPTAN1 NM_001130438.2
SRPX2 NM_014467.2
ST3GAL3 NM_006279.3
ST3GAL5 NM_003896.3
STRADA NM_001003787.2
STX1B NM_052874.4
STXBP1 NM_003165.3
SYN1 NM_133499.2
SYNGAP1 NM_006772.2
SYNJ1 NM_003895.3
SZT2 NM_015284.3
TBC1D24 NM_001199107.1
TBL1XR1 NM_024665.4
TCF4 NM_001083962.1; NM_001243232.1
TPK1 NM_022445.3
TSC1 NM_000368.4
TSC2 NM_000548.3
UBE3A NM_130838.1
WDR45 NM_007075.3
WWOX NM_016373.3
ZDHHC9 NM_016032.3
ZEB2 NM_014795.3

ARX: Analysis is validated to detect polyalanine expansions but sensitivity may be reduced in heterozygous females. Family variant testing in female individuals is available when there is a confirmed expansion in a male relative.
CLN3: Analysis includes the intronic variant NM_001042432.1; c.461-13G>C.
CSTB: Dodecamer repeat numbers in the 5' UTR are not determined.
KANSL1: Deletion/duplication analysis is not offered for exons 2-3.
KCNT1: Deletion/duplication analysis is not offered for exons 26 or 27.
PPT1: Analysis includes the large, mostly intronic deletion NM_000310.3:c.124+1215_235-102del3627 as well as the intronic variant NM_000310.3:c.125-15T>G.
PTEN: Deletion/duplication analysis covers the promoter region.
SCN8A: Analysis includes exon 6 of NM_001330260.1.