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SCN1A gene

sodium voltage-gated channel alpha subunit 1

Normal Function

The SCN1A gene belongs to a family of genes that provide instructions for making sodium channels. These channels, which transport positively charged sodium atoms (sodium ions) into cells, play a key role in a cell's ability to generate and transmit electrical signals.

The SCN1A gene provides instructions for making one part (the alpha subunit) of a sodium channel called NaV1.1. These channels are primarily found in the brain, where they control the flow of sodium ions into cells. NaV1.1 channels are involved in transmitting signals from one nerve cell (neuron) to another. Communication between neurons depends on chemicals called neurotransmitters, which are released from one neuron and taken up by neighboring neurons. The flow of sodium ions through NaV1.1 channels helps determine when neurotransmitters will be released.

Health Conditions Related to Genetic Changes

Familial hemiplegic migraine

At least seven mutations in the SCN1A gene have been identified in people with familial hemiplegic migraine type 3 (FHM3), a form of migraine headache that runs in families. Each of these mutations changes a single protein building block (amino acid) in the NaV1.1 channel, which alters the channel's structure. The abnormal channels stay open longer than usual, which increases the flow of sodium ions into neurons. This increase triggers the cell to release more neurotransmitters. The resulting changes in signaling between neurons make people with FHM3 more susceptible to developing these severe headaches.

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Genetic epilepsy with febrile seizures plus

Hundreds of mutations in the SCN1A gene have been found to cause genetic epilepsy with febrile seizures plus (GEFS+), which is a spectrum of seizure disorders of varying severity. These conditions include simple febrile (fever-associated) seizures, which start in infancy and usually stop by age 5, and febrile seizures plus (FS+). FS+ involves febrile and other types of seizures, including those not related to fevers (afebrile seizures), that continue beyond childhood. The GEFS+ spectrum also includes other conditions, such as Dravet syndrome (also known as severe myoclonic epilepsy of infancy or SMEI), that cause more serious seizures that last longer and may be difficult to control. These recurrent seizures (epilepsy) can worsen over time and are often accompanied by a decline in brain function.

The SCN1A gene mutations that underlie GEFS+ have a variety of effects on the function of the NaV1.1 channel. Some mutations change single amino acids in the channel, which alter the channel's structure. Others lead to the production of a nonfunctional version of the NaV1.1 channel or reduce the number of these channels produced in each cell. Still other mutations change single amino acids in critical regions of the channel. All of these genetic changes affect the ability of NaV1.1 channels to transport sodium ions into neurons. Some mutations are thought to reduce channel activity while others may increase it. It is unclear, however, how these genetic changes underlie the development of seizures or why they lead to a range of seizure disorders with varying severity.

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Lennox-Gastaut syndrome

MedlinePlus Genetics provides information about Lennox-Gastaut syndrome

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Malignant migrating partial seizures of infancy

MedlinePlus Genetics provides information about Malignant migrating partial seizures of infancy

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Other disorders

A common change (polymorphism) in the SCN1A gene has been associated with the effectiveness of certain anti-seizure medications. This polymorphism, which is written as ICS5N+5G>A, alters a single DNA building block (nucleotide) in the SCN1A gene. Studies suggest that this polymorphism is associated with the maximum safe amount (dose) of the anti-seizure drugs phenytoin and carbamazepine. These drugs treat epilepsy by blocking sodium channels (such as NaV1.1) in neurons. A dose that is too small may not control seizures effectively, while a dose that is too large may cause unwanted side effects. Researchers are hopeful that doctors will be able to test for the ICS5N+5G>A polymorphism to help determine the safest and most effective dose of anti-seizure medications for each individual.

Other Names for This Gene

  • GEFSP2
  • NAC1
  • Nav1.1
  • SCN1
  • sodium channel protein, brain I alpha subunit
  • sodium channel, voltage gated, type I alpha subunit
  • sodium channel, voltage-gated, type I, alpha
  • sodium channel, voltage-gated, type I, alpha polypeptide
  • sodium channel, voltage-gated, type I, alpha subunit

Additional Information & Resources

Tests Listed in the Genetic Testing Registry

Scientific Articles on PubMed

Gene and Variant Databases


  • Dichgans M, Freilinger T, Eckstein G, Babini E, Lorenz-Depiereux B, Biskup S, Ferrari MD, Herzog J, van den Maagdenberg AM, Pusch M, Strom TM. Mutation in the neuronal voltage-gated sodium channel SCN1A in familial hemiplegic migraine. Lancet. 2005 Jul 30-Aug 5;366(9483):371-7. doi: 10.1016/S0140-6736(05)66786-4. Citation on PubMed
  • Fujiwara T. Clinical spectrum of mutations in SCN1A gene: severe myoclonic epilepsy in infancy and related epilepsies. Epilepsy Res. 2006 Aug;70 Suppl 1:S223-30. doi: 10.1016/j.eplepsyres.2006.01.019. Epub 2006 Jun 27. Citation on PubMed
  • Gargus JJ, Tournay A. Novel mutation confirms seizure locus SCN1A is also familial hemiplegic migraine locus FHM3. Pediatr Neurol. 2007 Dec;37(6):407-10. doi: 10.1016/j.pediatrneurol.2007.06.016. Citation on PubMed or Free article on PubMed Central
  • Martin MS, Dutt K, Papale LA, Dube CM, Dutton SB, de Haan G, Shankar A, Tufik S, Meisler MH, Baram TZ, Goldin AL, Escayg A. Altered function of the SCN1A voltage-gated sodium channel leads to gamma-aminobutyric acid-ergic (GABAergic) interneuron abnormalities. J Biol Chem. 2010 Mar 26;285(13):9823-9834. doi: 10.1074/jbc.M109.078568. Epub 2010 Jan 25. Citation on PubMed or Free article on PubMed Central
  • Mulley JC, Scheffer IE, Petrou S, Dibbens LM, Berkovic SF, Harkin LA. SCN1A mutations and epilepsy. Hum Mutat. 2005 Jun;25(6):535-42. doi: 10.1002/humu.20178. Citation on PubMed
  • Pietrobon D. Familial hemiplegic migraine. Neurotherapeutics. 2007 Apr;4(2):274-84. doi: 10.1016/j.nurt.2007.01.008. Citation on PubMed
  • Spampanato J, Escayg A, Meisler MH, Goldin AL. Functional effects of two voltage-gated sodium channel mutations that cause generalized epilepsy with febrile seizures plus type 2. J Neurosci. 2001 Oct 1;21(19):7481-90. doi: 10.1523/JNEUROSCI.21-19-07481.2001. Citation on PubMed
  • Tate SK, Depondt C, Sisodiya SM, Cavalleri GL, Schorge S, Soranzo N, Thom M, Sen A, Shorvon SD, Sander JW, Wood NW, Goldstein DB. Genetic predictors of the maximum doses patients receive during clinical use of the anti-epileptic drugs carbamazepine and phenytoin. Proc Natl Acad Sci U S A. 2005 Apr 12;102(15):5507-12. doi: 10.1073/pnas.0407346102. Epub 2005 Apr 1. Citation on PubMed or Free article on PubMed Central
  • Tate SK, Singh R, Hung CC, Tai JJ, Depondt C, Cavalleri GL, Sisodiya SM, Goldstein DB, Liou HH. A common polymorphism in the SCN1A gene associates with phenytoin serum levels at maintenance dose. Pharmacogenet Genomics. 2006 Oct;16(10):721-6. doi: 10.1097/01.fpc.0000230114.41828.73. Citation on PubMed
  • Vanmolkot KR, Babini E, de Vries B, Stam AH, Freilinger T, Terwindt GM, Norris L, Haan J, Frants RR, Ramadan NM, Ferrari MD, Pusch M, van den Maagdenberg AM, Dichgans M. The novel p.L1649Q mutation in the SCN1A epilepsy gene is associated with familial hemiplegic migraine: genetic and functional studies. Mutation in brief #957. Online. Hum Mutat. 2007 May;28(5):522. doi: 10.1002/humu.9486. Citation on PubMed
  • Volkers L, Kahlig KM, Verbeek NE, Das JH, van Kempen MJ, Stroink H, Augustijn P, van Nieuwenhuizen O, Lindhout D, George AL Jr, Koeleman BP, Rook MB. Nav 1.1 dysfunction in genetic epilepsy with febrile seizures-plus or Dravet syndrome. Eur J Neurosci. 2011 Oct;34(8):1268-75. doi: 10.1111/j.1460-9568.2011.07826.x. Epub 2011 Aug 22. Citation on PubMed or Free article on PubMed Central
  • Yamakawa K. Na channel gene mutations in epilepsy--the functional consequences. Epilepsy Res. 2006 Aug;70 Suppl 1:S218-22. doi: 10.1016/j.eplepsyres.2005.11.025. Epub 2006 Jun 27. Citation on PubMed

The information on this site should not be used as a substitute for professional medical care or advice. Contact a health care provider if you have questions about your health.