Voltage-dependent sodium channels are heteromeric complexes that regulate sodium exchange between intracellular and extracellular spaces and are essential for the generation and propagation of action potentials in muscle cells and neurons. Each sodium channel is composed of a large pore-forming, glycosylated alpha subunit and two smaller beta subunits. This gene encodes a sodiu... See more...

Aliases for SCN1A Gene

Aliases for SCN1A Gene

  • Sodium Voltage-Gated Channel Alpha Subunit 1 2 3 5
  • Sodium Channel, Voltage-Gated, Type I, Alpha Subunit 2 3
  • Voltage-Gated Sodium Channel Subunit Alpha Nav1.1 3 4
  • Sodium Channel Protein Type 1 Subunit Alpha 3 4
  • Sodium Channel Protein Type I Subunit Alpha 3 4
  • SCN1 3 4
  • NAC1 3 4
  • Sodium Channel, Voltage-Gated, Type I, Alpha Polypeptide 3
  • Sodium Channel, Voltage Gated, Type I Alpha Subunit 2
  • Sodium Channel Voltage Gated Type 1 Alpha Subunit 3
  • Sodium Channel Protein, Brain I Alpha Subunit 3
  • Sodium Channel Protein Brain I Subunit Alpha 4
  • Febrile Convulsions 3 2
  • GEFSP2 3
  • Nav1.1 3
  • EIEE6 3
  • FEB3A 3
  • HBSCI 3
  • FHM3 3
  • SMEI 3
  • FEB3 3

External Ids for SCN1A Gene

Previous HGNC Symbols for SCN1A Gene

  • SCN1
  • FEB3

Previous GeneCards Identifiers for SCN1A Gene

  • GC02M164900
  • GC02M165387
  • GC02M166809
  • GC02M167048
  • GC02M166671
  • GC02M166553
  • GC02M158727

Summaries for SCN1A Gene

Entrez Gene Summary for SCN1A Gene

  • Voltage-dependent sodium channels are heteromeric complexes that regulate sodium exchange between intracellular and extracellular spaces and are essential for the generation and propagation of action potentials in muscle cells and neurons. Each sodium channel is composed of a large pore-forming, glycosylated alpha subunit and two smaller beta subunits. This gene encodes a sodium channel alpha subunit, which has four homologous domains, each of which contains six transmembrane regions. Allelic variants of this gene are associated with generalized epilepsy with febrile seizures and epileptic encephalopathy. Alternative splicing results in multiple transcript variants. The RefSeq Project has decided to create four representative RefSeq records. Three of the transcript variants are supported by experimental evidence and the fourth contains alternate 5' untranslated exons, the exact combination of which have not been experimentally confirmed for the full-length transcript. [provided by RefSeq, Oct 2015]

GeneCards Summary for SCN1A Gene

SCN1A (Sodium Voltage-Gated Channel Alpha Subunit 1) is a Protein Coding gene. Diseases associated with SCN1A include Epileptic Encephalopathy, Early Infantile, 6 and Generalized Epilepsy With Febrile Seizures Plus, Type 2. Among its related pathways are Neuropathic Pain-Signaling in Dorsal Horn Neurons and Interaction between L1 and Ankyrins. Gene Ontology (GO) annotations related to this gene include ion channel activity and voltage-gated sodium channel activity. An important paralog of this gene is SCN2A.

UniProtKB/Swiss-Prot Summary for SCN1A Gene

  • Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient. Plays a key role in brain, probably by regulating the moment when neurotransmitters are released in neurons. Involved in sensory perception of mechanical pain: activation in somatosensory neurons induces pain without neurogenic inflammation and produces hypersensitivity to mechanical, but not thermal stimuli.

Tocris Summary for SCN1A Gene

  • Voltage-gated sodium channels (NaV) are responsible for action potential initiation and propagation in excitable cells, including nerve, muscle, and neuroendocrine cell types. They are also expressed at low levels in non-excitable cells, where their physiological role is unclear.

Gene Wiki entry for SCN1A Gene

Additional gene information for SCN1A Gene

No data available for CIViC Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCN1A Gene

Genomics for SCN1A Gene

GeneHancer (GH) Regulatory Elements for SCN1A Gene

Promoters and enhancers for SCN1A Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J166149 Enhancer 0.5 Ensembl 500.7 +0.1 71 0.4 EP300 MAFK SMAD4 RARA NFIL3 MIER2 HLF PKNOX1 POLR2A REST SCN1A lnc-SCN1A-3 piR-32325-080 SCN1A-AS1
GH02J166125 Promoter/Enhancer 1.5 VISTA FANTOM5 Ensembl dbSUPER 14.2 +22.3 22315 3 CTCF TCF7 REST RAD21 TEAD1 SMC3 FOXA2 CEBPB NFIC ZNF384 lnc-SCN9A-72 SCN1A SCN1A-AS1 ENSG00000238813
GH02J166106 Enhancer 0.5 Ensembl 12.6 +42.6 42571 0.2 CTCF REST SMC3 RAD21 POLR2A ELF1 ZNF654 SMARCA4 ELF4 HLF SCN1A-AS1 SCN1A piR-36617 lnc-SCN9A-72 piR-55036-041
GH02J166034 Enhancer 0.2 FANTOM5 13.8 +115.0 114955 0.4 SCN1A SCN1A-AS1 TTC21B piR-55036-041 LOC102724058 piR-36617
GH02J166123 Enhancer 0.2 Ensembl 11.6 +26.0 25971 0.2 ENSG00000238813 SCN1A SCN1A-AS1 GALNT3 lnc-SCN9A-72 RF00994-532
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCN1A on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCN1A

Top Transcription factor binding sites by QIAGEN in the SCN1A gene promoter:
  • aMEF-2
  • AML1a
  • Cdc5
  • E47
  • FOXJ2
  • FOXJ2 (long isoform)
  • MEF-2A
  • Oct-B1
  • oct-B2
  • oct-B3

Genomic Locations for SCN1A Gene

Genomic Locations for SCN1A Gene
chr2:165,984,641-166,149,272
(GRCh38/hg38)
Size:
164,632 bases
Orientation:
Minus strand
chr2:166,845,670-167,005,642
(GRCh37/hg19)
Size:
159,973 bases
Orientation:
Minus strand

Genomic View for SCN1A Gene

Genes around SCN1A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCN1A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCN1A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCN1A Gene

Proteins for SCN1A Gene

  • Protein details for SCN1A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P35498-SCN1A_HUMAN
    Recommended name:
    Sodium channel protein type 1 subunit alpha
    Protein Accession:
    P35498
    Secondary Accessions:
    • E9PG49
    • Q16172
    • Q585T7
    • Q8IUJ6
    • Q96LA3
    • Q9C008

    Protein attributes for SCN1A Gene

    Size:
    2009 amino acids
    Molecular mass:
    228972 Da
    Quaternary structure:
    • The voltage-sensitive sodium channel consists of an ion conducting pore forming alpha-subunit regulated by one or more beta-1 (SCN1B), beta-2 (SCN2B), beta-3 (SCN3B) and/or beta-4 (SCN4B). Beta-1 (SCN1B) and beta-3 (SCN3B) are non-covalently associated with alpha, while beta-2 (SCN2B) and beta-4 (SCN4B) are covalently linked by disulfide bonds. Interacts with FGF13 (PubMed:21566136). Interacts with SCN1B (PubMed:17928445, PubMed:15525788). Interacts with the conotoxin GVIIJ (PubMed:24497506). Interacts with the spider beta/delta-theraphotoxin-Pre1a (PubMed:28428547).

    Alternative splice isoforms for SCN1A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCN1A Gene

Post-translational modifications for SCN1A Gene

  • Phosphorylation at Ser-1516 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents.
  • Glycosylation at Asn211, Asn284, Asn295, Asn301, Asn306, Asn338, Asn1378, Asn1392, and Asn1403
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SCN1A Gene

Domains & Families for SCN1A Gene

Gene Families for SCN1A Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Disease related genes
  • FDA approved drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Transporters
  • Voltage-gated ion channels

Protein Domains for SCN1A Gene

Blocks:
  • IQ calmodulin-binding region
  • Voltage-gated Na+ channel alpha subunit signature
  • Bacterial ribonuclease P protein
  • Voltage-gated Na+ channel alpha 1 subunit signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SCN1A Gene

GenScript: Design optimal peptide antigens:
  • Sodium channel voltage gated type 1 alpha subunit transcript variant 2 (F8T7W4_HUMAN)
  • Sodium channel voltage gated type 1 alpha subunit transcript variant 2 (F8T7W5_HUMAN)
  • Sodium channel voltage gated type 1 alpha subunit transcript variant 2 (F8T7W6_HUMAN)
  • Sodium channel voltage gated type 1 alpha subunit transcript variant 2 (F8T7W7_HUMAN)
  • Sodium channel voltage gated type 1 alpha subunit transcript variant 2 (F8T7W8_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P35498

UniProtKB/Swiss-Prot:

SCN1A_HUMAN :
  • The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1, S2, S3, S5, S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position.
  • Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.1/SCN1A subfamily.
Domain:
  • The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1, S2, S3, S5, S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position.
  • The S3b-S4 and S1-S2 loops of repeat IV are targeted by H.maculata toxins Hm1a and Hm1b, leading to inhibit fast inactivation of Nav1.1/SCN1A. Selectivity for H.maculata toxins Hm1a and Hm1b depends on S1-S2 loops of repeat IV.
Family:
  • Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.1/SCN1A subfamily.
genes like me logo Genes that share domains with SCN1A: view

Function for SCN1A Gene

Molecular function for SCN1A Gene

UniProtKB/Swiss-Prot Function:
Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient. Plays a key role in brain, probably by regulating the moment when neurotransmitters are released in neurons. Involved in sensory perception of mechanical pain: activation in somatosensory neurons induces pain without neurogenic inflammation and produces hypersensitivity to mechanical, but not thermal stimuli.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inactivation of this channel is specifically inhibited by the spider toxins Hm1a and Hm1b (H.maculata, AC P60992 and AC P0DOC5) in somatosensory neurons to elicit acute pain and mechanical allodynia.
GENATLAS Biochemistry:
sodium voltage-gated channel,type I,alpha polypeptide,expressed in brain

Phenotypes From GWAS Catalog for SCN1A Gene

Gene Ontology (GO) - Molecular Function for SCN1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity IEA --
GO:0005244 voltage-gated ion channel activity IEA --
GO:0005248 voltage-gated sodium channel activity NAS 10742094
GO:0005272 sodium channel activity IEA --
genes like me logo Genes that share ontologies with SCN1A: view
genes like me logo Genes that share phenotypes with SCN1A: view

Human Phenotype Ontology for SCN1A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SCN1A Gene

MGI Knock Outs for SCN1A:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCN1A

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SCN1A Gene

Localization for SCN1A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCN1A Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCN1A gene
Compartment Confidence
plasma membrane 5
nucleus 4
extracellular 2
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
cytosol 2
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCN1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001518 voltage-gated sodium channel complex IBA 21873635
GO:0005654 nucleoplasm IDA --
GO:0005886 plasma membrane IBA,IDA --
GO:0014704 intercalated disc IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with SCN1A: view

Pathways & Interactions for SCN1A Gene

PathCards logo

SuperPathways for SCN1A Gene

SuperPathway Contained pathways
1 Activation of cAMP-Dependent PKA
.77
.77
.56
2 Neuropathic Pain-Signaling in Dorsal Horn Neurons
.47
.47
.40
3 Developmental Biology
4 Cardiac conduction
5 Neuroscience
genes like me logo Genes that share pathways with SCN1A: view

Pathways by source for SCN1A Gene

7 Qiagen pathways for SCN1A Gene
  • Activation of cAMP-Dependent PKA
  • Aldosterone Signaling in Epithelial Cells
  • cAMP Pathway
  • Cholera Infection
  • GHRH Signaling
1 Cell Signaling Technology pathway for SCN1A Gene

SIGNOR curated interactions for SCN1A Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for SCN1A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006814 sodium ion transport NAS 10742094
GO:0007628 adult walking behavior IEA --
GO:0019227 neuronal action potential propagation IEA --
GO:0019228 neuronal action potential IBA 21873635
genes like me logo Genes that share ontologies with SCN1A: view

Drugs & Compounds for SCN1A Gene

(37) Drugs for SCN1A Gene - From: DrugBank, PharmGKB, ClinicalTrials, DGIdb, IUPHAR, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phenytoin Approved, Vet_approved Pharma Pore Blocker, Target, inhibitor, blocker 87
Carbamazepine Approved, Investigational Pharma Target, inhibitor Inhibitor of neuronal voltage-gated Na+ channels; anticonvulsant 103
Nitrazepam Approved Pharma Target, other/unknown, antagonist 10
Phenacemide Approved Pharma Target, inhibitor, blocker 0
Topiramate Approved Pharma Target, inhibitor, antagonist GluR5 receptor antagonist,anticonvulsant, GluR5 antagonist; inhibits carbonic anhydrase (CA) II and IV 273

(3) Additional Compounds for SCN1A Gene - From: HMDB, Novoseek, and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Na(+)
  • Na+
  • SODIUM ion
7440-23-5
3',4'-Dihydrodiol
Amiloride hydrochloride
2016-88-8

(3) Tocris Compounds for SCN1A Gene

Compound Action Cas Number
Amiloride hydrochloride Na+ channel blocker; also I2 imidazoline ligand 2016-88-8
Carbamazepine Inhibitor of neuronal voltage-gated Na+ channels; anticonvulsant 298-46-4
Vinpocetine Na+ channel blocker 42971-09-5
genes like me logo Genes that share compounds with SCN1A: view

Transcripts for SCN1A Gene

mRNA/cDNA for SCN1A Gene

15 REFSEQ mRNAs :
20 NCBI additional mRNA sequence :
23 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCN1A

Alternative Splicing Database (ASD) splice patterns (SP) for SCN1A Gene

No ASD Table

Relevant External Links for SCN1A Gene

GeneLoc Exon Structure for
SCN1A

Expression for SCN1A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCN1A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCN1A Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x9.2), Brain - Cortex (x5.9), and Brain - Anterior cingulate cortex (BA24) (x5.7).

Protein differential expression in normal tissues from HIPED for SCN1A Gene

This gene is overexpressed in Breast (24.0), Frontal cortex (22.9), and Blymphocyte (17.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SCN1A Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCN1A

SOURCE GeneReport for Unigene cluster for SCN1A Gene:

Hs.22654

Evidence on tissue expression from TISSUES for SCN1A Gene

  • Nervous system(4.8)
  • Muscle(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SCN1A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • immune
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • head
  • skull
Thorax:
  • chest wall
  • esophagus
Abdomen:
  • abdominal wall
  • stomach
Limb:
  • lower limb
  • upper limb
General:
  • blood
  • peripheral nerve
  • peripheral nervous system
  • spinal cord
  • white blood cell
genes like me logo Genes that share expression patterns with SCN1A: view

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for SCN1A Gene

Orthologs for SCN1A Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCN1A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCN1A 31 30
  • 99.57 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SCN1A 31
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SCN1A 31 30
  • 94.09 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SCN1A 31 30
  • 93.63 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Scn1a 17 31 30
  • 90.44 (n)
rat
(Rattus norvegicus)
Mammalia Scn1a 30
  • 89.96 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SCN1A 31
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCN1A 30
  • 83.09 (n)
lizard
(Anolis carolinensis)
Reptilia SCN1A 31
  • 89 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii scn1lab 31
  • 78 (a)
OneToMany
Species where no ortholog for SCN1A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCN1A Gene

ENSEMBL:
Gene Tree for SCN1A (if available)
TreeFam:
Gene Tree for SCN1A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCN1A: view image

Paralogs for SCN1A Gene

(17) SIMAP similar genes for SCN1A Gene using alignment to 6 proteins:

  • SCN1A_HUMAN
  • F8T7W4_HUMAN
  • F8T7W5_HUMAN
  • F8T7W6_HUMAN
  • F8T7W7_HUMAN
  • F8T7W8_HUMAN
genes like me logo Genes that share paralogs with SCN1A: view

Variants for SCN1A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCN1A Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
12888 Pathogenic: Severe myoclonic epilepsy in infancy 166,052,887(-) ACT/A FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR_VARIANT
12901 Pathogenic: Severe myoclonic epilepsy in infancy 166,013,839(-) AT/A FRAMESHIFT_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
206747 Uncertain Significance: Early infantile epileptic encephalopathy 166,051,905(-) C/T MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT,FIVE_PRIME_UTR_VARIANT
579103 Pathogenic: Early infantile epileptic encephalopathy 166,051,316(-) GGGGTAGAAATACCAA SPLICE_ACCEPTOR_VARIANT,SPLICE_DONOR_VARIANT
638433 Likely Pathogenic: Generalized epilepsy with febrile seizures plus, type 1; Epileptic encephalopathy, early infantile, 1 166,043,692(-) C/G MISSENSE_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for SCN1A Gene

Structural Variations from Database of Genomic Variants (DGV) for SCN1A Gene

Variant ID Type Subtype PubMed ID
dgv1181e212 CNV loss 25503493
dgv2085n106 CNV deletion 24896259
dgv63n17 CNV loss 16327808
esv2357676 CNV deletion 18987734
esv2721076 CNV deletion 23290073
esv2721077 CNV deletion 23290073
esv2721078 CNV deletion 23290073
esv2721079 CNV deletion 23290073
esv2721080 CNV deletion 23290073
esv3560478 CNV deletion 23714750
esv3584150 CNV loss 25503493
esv3593246 CNV gain 21293372
nsv1127778 CNV deletion 24896259
nsv1143007 CNV deletion 24896259
nsv1149312 CNV insertion 26484159
nsv1153442 CNV deletion 26484159
nsv459936 CNV loss 19166990
nsv478361 CNV novel sequence insertion 20440878
nsv583584 CNV loss 21841781
nsv834445 CNV gain+loss 17160897
nsv956697 CNV deletion 24416366
nsv961904 CNV duplication 23825009

Variation tolerance for SCN1A Gene

Residual Variation Intolerance Score: 2.38% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.65; 45.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCN1A Gene

Human Gene Mutation Database (HGMD)
SCN1A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCN1A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCN1A Gene

Disorders for SCN1A Gene

MalaCards: The human disease database

(91) MalaCards diseases for SCN1A Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SCN1A in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SCN1A_HUMAN
  • Generalized epilepsy with febrile seizures plus 2 (GEFS+2) [MIM:604403]: A rare autosomal dominant, familial condition with incomplete penetrance and large intrafamilial variability. Patients display febrile seizures persisting sometimes beyond the age of 6 years and/or a variety of afebrile seizure types. This disease combines febrile seizures, generalized seizures often precipitated by fever at age 6 years or more, and partial seizures, with a variable degree of severity. {ECO:0000269 PubMed:10742094, ECO:0000269 PubMed:11254444, ECO:0000269 PubMed:11254445, ECO:0000269 PubMed:11524484, ECO:0000269 PubMed:11756608, ECO:0000269 PubMed:12535936, ECO:0000269 PubMed:12576172, ECO:0000269 PubMed:12919402, ECO:0000269 PubMed:14672992, ECO:0000269 PubMed:15525788, ECO:0000269 PubMed:15694566, ECO:0000269 PubMed:15715999, ECO:0000269 PubMed:16525050, ECO:0000269 PubMed:17347258, ECO:0000269 PubMed:17507202, ECO:0000269 PubMed:17561957, ECO:0000269 PubMed:17927801, ECO:0000269 PubMed:17928445, ECO:0000269 PubMed:18251839, ECO:0000269 PubMed:18413471, ECO:0000269 PubMed:18566737, ECO:0000269 PubMed:19339291, ECO:0000269 PubMed:19464195, ECO:0000269 PubMed:19522081, ECO:0000269 PubMed:20117752, ECO:0000269 PubMed:20550552, ECO:0000269 PubMed:20600615, ECO:0000269 PubMed:20729507, ECO:0000269 PubMed:21248271, ECO:0000269 PubMed:21864321}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Epileptic encephalopathy, early infantile, 6 (EIEE6) [MIM:607208]: A severe form of epileptic encephalopathy characterized by generalized tonic, clonic, and tonic-clonic seizures that are initially induced by fever and begin during the first year of life. Later, patients also manifest other seizure types, including absence, myoclonic, and simple and complex partial seizures. Psychomotor development delay is observed around the second year of life. Some patients manifest a borderline disease phenotype and do not necessarily fulfill all diagnostic criteria for core EIEE6. EIEE6 is considered to be the most severe phenotype within the spectrum of generalized epilepsies with febrile seizures-plus. {ECO:0000269 PubMed:11359211, ECO:0000269 PubMed:12083760, ECO:0000269 PubMed:12566275, ECO:0000269 PubMed:12754708, ECO:0000269 PubMed:12821740, ECO:0000269 PubMed:14504318, ECO:0000269 PubMed:14672992, ECO:0000269 PubMed:14738421, ECO:0000269 PubMed:15087100, ECO:0000269 PubMed:15944908, ECO:0000269 PubMed:16122630, ECO:0000269 PubMed:16458823, ECO:0000269 PubMed:16713920, ECO:0000269 PubMed:17054684, ECO:0000269 PubMed:17054685, ECO:0000269 PubMed:17129991, ECO:0000269 PubMed:17347258, ECO:0000269 PubMed:17561957, ECO:0000269 PubMed:18413471, ECO:0000269 PubMed:18639757, ECO:0000269 PubMed:18930999, ECO:0000269 PubMed:19522081, ECO:0000269 PubMed:19563458, ECO:0000269 PubMed:19589774, ECO:0000269 PubMed:19783390, ECO:0000269 PubMed:20110217, ECO:0000269 PubMed:20431604, ECO:0000269 PubMed:20452746, ECO:0000269 PubMed:20522430, ECO:0000269 PubMed:20729507, ECO:0000269 PubMed:21248271, ECO:0000269 PubMed:21864321, ECO:0000269 PubMed:22092154, ECO:0000269 PubMed:22612257, ECO:0000269 PubMed:23195492, ECO:0000269 PubMed:23662938, ECO:0000269 PubMed:23708187, ECO:0000269 PubMed:25818041, ECO:0000269 PubMed:26993267, ECO:0000269 PubMed:27864847, ECO:0000269 PubMed:28544625}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Intractable childhood epilepsy with generalized tonic-clonic seizures (ICEGTC) [MIM:607208]: A disorder characterized by generalized tonic-clonic seizures beginning usually in infancy and induced by fever. Seizures are associated with subsequent mental decline, as well as ataxia or hypotonia. ICEGTC is similar to SMEI, except for the absence of myoclonic seizures. {ECO:0000269 PubMed:12566275, ECO:0000269 PubMed:16210358, ECO:0000269 PubMed:17507202, ECO:0000269 PubMed:23195492, ECO:0000269 PubMed:23708187}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Migraine, familial hemiplegic, 3 (FHM3) [MIM:609634]: A subtype of migraine associated with transient blindness in some families. Migraine is a disabling symptom complex of periodic headaches, usually temporal and unilateral. Headaches are often accompanied by irritability, nausea, vomiting and photophobia, preceded by constriction of the cranial arteries. The two major subtypes are common migraine (migraine without aura) and classic migraine (migraine with aura). Classic migraine is characterized by recurrent attacks of reversible neurological symptoms (aura) that precede or accompany the headache. Aura may include a combination of sensory disturbances, such as blurred vision, hallucinations, vertigo, numbness and difficulty in concentrating and speaking. {ECO:0000269 PubMed:16054936, ECO:0000269 PubMed:17397047, ECO:0000269 PubMed:18021921, ECO:0000269 PubMed:19332696}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Febrile seizures, familial, 3A (FEB3A) [MIM:604403]: Seizures associated with febrile episodes in childhood without any evidence of intracranial infection or defined pathologic or traumatic cause. It is a common condition, affecting 2-5% of children aged 3 months to 5 years. The majority are simple febrile seizures (generally defined as generalized onset, single seizures with a duration of less than 30 minutes). Complex febrile seizures are characterized by focal onset, duration greater than 30 minutes, and/or more than one seizure in a 24 hour period. The likelihood of developing epilepsy following simple febrile seizures is low. Complex febrile seizures are associated with a moderately increased incidence of epilepsy. {ECO:0000269 PubMed:16326807, ECO:0000269 PubMed:19522081}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=SCN1A mutations may be involved in Panayiotopoulos syndrome, a benign age-related focal seizure disorder occurring in early and mid-childhood. It is characterized by seizures, often prolonged, with predominantly autonomic symptoms, and by an electroencephalogram that shows shifting and/or multiple foci, often with occipital predominance. Autonomic seizures in Panayiotopoulos syndrome consist of episodes of disturbed autonomic function with emesis as the predominant symptom. Cardiorespiratory arrest is exceptional. {ECO:0000269 PubMed:17679682, ECO:0000269 PubMed:19339291, ECO:0000269 PubMed:19522081}.

Additional Disease Information for SCN1A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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Publications for SCN1A Gene

  1. Spectrum of SCN1A gene mutations associated with Dravet syndrome: analysis of 333 patients. (PMID: 18930999) Depienne C … LeGuern E (Journal of medical genetics 2009) 3 4 23 41 54
  2. The spectrum of SCN1A-related infantile epileptic encephalopathies. (PMID: 17347258) Harkin LA … Scheffer IE (Brain : a journal of neurology 2007) 3 4 23 41 54
  3. A common polymorphism in the SCN1A gene associates with phenytoin serum levels at maintenance dose. (PMID: 17001291) Tate SK … Liou HH (Pharmacogenetics and genomics 2006) 3 23 26 41 54
  4. Spectrum of SCN1A mutations in severe myoclonic epilepsy of infancy. (PMID: 12821740) Nabbout R … Zara F (Neurology 2003) 3 4 23 41 54
  5. A novel SCN1A mutation associated with generalized epilepsy with febrile seizures plus--and prevalence of variants in patients with epilepsy. (PMID: 11254445) Escayg A … Meisler MH (American journal of human genetics 2001) 3 4 23 41 54

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