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    SCN1A sodium voltage-gated channel alpha subunit 1 [ Homo sapiens (human) ]

    Gene ID: 6323, updated on 17-Jun-2024

    Summary

    Official Symbol
    SCN1Aprovided by HGNC
    Official Full Name
    sodium voltage-gated channel alpha subunit 1provided by HGNC
    Primary source
    HGNC:HGNC:10585
    See related
    Ensembl:ENSG00000144285 MIM:182389; AllianceGenome:HGNC:10585
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DEE6; DRVT; FEB3; FHM3; NAC1; SCN1; SMEI; DEE6A; DEE6B; EIEE6; FEB3A; HBSCI; GEFSP2; Nav1.1
    Summary
    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]
    Expression
    Biased expression in brain (RPKM 5.3), lung (RPKM 1.3) and 1 other tissue See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SCN1A in Genome Data Viewer
    Location:
    2q24.3
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (165984641..166149161, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (166442174..166606734, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (166841151..167005671, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100506124 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16729 Neighboring gene tetratricopeptide repeat domain 21B Neighboring gene TTC21B antisense RNA 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:166810301-166811050 Neighboring gene uncharacterized LOC102724058 Neighboring gene SCN1A and SCN9A antisense RNA 1 Neighboring gene RN7SK pseudogene 152 Neighboring gene sodium voltage-gated channel alpha subunit 9 Neighboring gene small nucleolar RNA U13

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2012-07-06)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2012-07-06)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Common variants associated with general and MMR vaccine-related febrile seizures.
    EBI GWAS Catalog
    Epilepsy, hippocampal sclerosis and febrile seizures linked by common genetic variation around SCN1A.
    EBI GWAS Catalog
    Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies.
    EBI GWAS Catalog
    Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32
    EBI GWAS Catalog
    Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in adult walking behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cardiac muscle cell action potential involved in contraction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cardiac muscle cell action potential involved in contraction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in detection of mechanical stimulus involved in sensory perception of pain ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in determination of adult lifespan IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in establishment of localization in cell IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in membrane depolarization during action potential IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in membrane depolarization during action potential ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in nerve development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuromuscular process controlling posture IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuronal action potential IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuronal action potential propagation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of presynaptic membrane potential IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sodium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in sodium ion transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in T-tubule IEA
    Inferred from Electronic Annotation
    more info
     
    located_in Z disc ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in axon initial segment IEA
    Inferred from Electronic Annotation
    more info
     
    located_in intercalated disc IEA
    Inferred from Electronic Annotation
    more info
     
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
     
    located_in node of Ranvier IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    part_of voltage-gated sodium channel complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    sodium channel protein type 1 subunit alpha
    Names
    sodium channel protein type I subunit alpha
    sodium channel protein, brain I alpha subunit
    sodium channel voltage gated type 1 alpha subunit
    sodium channel, voltage-gated, type I, alpha polypeptide
    sodium channel, voltage-gated, type I, alpha subunit
    voltage-gated sodium channel subunit alpha Nav1.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_011906.1 RefSeqGene

      Range
      820..89480
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_8

    mRNA and Protein(s)

    1. NM_001165963.4NP_001159435.1  sodium channel protein type 1 subunit alpha isoform 1

      See identical proteins and their annotated locations for NP_001159435.1

      Status: REVIEWED

      Source sequence(s)
      AC010127
      Consensus CDS
      CCDS54413.1
      UniProtKB/Swiss-Prot
      E9PG49, P35498, Q16172, Q585T7, Q8IUJ6, Q96LA3, Q9C008
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Related
      ENSP00000501589.1, ENST00000674923.1
      Conserved Domains (5) summary
      cd13433
      Location:14841536
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12171492
      Ion_trans; Ion transport protein
      pfam06512
      Location:10061213
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510705
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:18001863
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    2. NM_001165964.3NP_001159436.1  sodium channel protein type 1 subunit alpha isoform 3

      See identical proteins and their annotated locations for NP_001159436.1

      Status: REVIEWED

      Source sequence(s)
      AC010127
      Consensus CDS
      CCDS54414.1
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Conserved Domains (5) summary
      cd13433
      Location:14561508
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11891464
      Ion_trans; Ion transport protein
      pfam06512
      Location:9781185
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510677
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17721835
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    3. NM_001202435.3NP_001189364.1  sodium channel protein type 1 subunit alpha isoform 1

      See identical proteins and their annotated locations for NP_001189364.1

      Status: REVIEWED

      Source sequence(s)
      AC010127, AC107082
      Consensus CDS
      CCDS54413.1
      UniProtKB/Swiss-Prot
      E9PG49, P35498, Q16172, Q585T7, Q8IUJ6, Q96LA3, Q9C008
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Related
      ENSP00000492945.1, ENST00000641603.1
      Conserved Domains (5) summary
      cd13433
      Location:14841536
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12171492
      Ion_trans; Ion transport protein
      pfam06512
      Location:10061213
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510705
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:18001863
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    4. NM_001353948.2NP_001340877.1  sodium channel protein type 1 subunit alpha isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC010127
      Consensus CDS
      CCDS54413.1
      UniProtKB/Swiss-Prot
      E9PG49, P35498, Q16172, Q585T7, Q8IUJ6, Q96LA3, Q9C008
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Conserved Domains (5) summary
      cd13433
      Location:14841536
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12171492
      Ion_trans; Ion transport protein
      pfam06512
      Location:10061213
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510705
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:18001863
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    5. NM_001353949.2NP_001340878.1  sodium channel protein type 1 subunit alpha isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC010127, AC107082
      Consensus CDS
      CCDS33316.1
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Related
      ENSP00000490799.1, ENST00000635750.1
      Conserved Domains (5) summary
      cd13433
      Location:14731525
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12061481
      Ion_trans; Ion transport protein
      pfam06512
      Location:9951202
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510694
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17891852
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    6. NM_001353950.2NP_001340879.1  sodium channel protein type 1 subunit alpha isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC010127, AC107082
      Consensus CDS
      CCDS33316.1
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Conserved Domains (5) summary
      cd13433
      Location:14731525
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12061481
      Ion_trans; Ion transport protein
      pfam06512
      Location:9951202
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510694
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17891852
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    7. NM_001353951.2NP_001340880.1  sodium channel protein type 1 subunit alpha isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC010127
      Consensus CDS
      CCDS33316.1
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Conserved Domains (5) summary
      cd13433
      Location:14731525
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12061481
      Ion_trans; Ion transport protein
      pfam06512
      Location:9951202
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510694
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17891852
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    8. NM_001353952.2NP_001340881.1  sodium channel protein type 1 subunit alpha isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC010127
      Consensus CDS
      CCDS33316.1
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Related
      ENSP00000518996.1, ENST00000713692.1
      Conserved Domains (5) summary
      cd13433
      Location:14731525
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12061481
      Ion_trans; Ion transport protein
      pfam06512
      Location:9951202
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510694
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17891852
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    9. NM_001353954.2NP_001340883.1  sodium channel protein type 1 subunit alpha isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC010127
      Consensus CDS
      CCDS86891.1
      UniProtKB/TrEMBL
      A0A1W2PPJ3, A0A286YF26
      Related
      ENSP00000492917.1, ENST00000641575.1
      Conserved Domains (5) summary
      cd13433
      Location:14721524
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12051480
      Ion_trans; Ion transport protein
      pfam06512
      Location:9941201
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:509693
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17881851
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    10. NM_001353955.2NP_001340884.1  sodium channel protein type 1 subunit alpha isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC010127
      Consensus CDS
      CCDS86891.1
      UniProtKB/TrEMBL
      A0A1W2PPJ3, A0A286YF26
      Conserved Domains (5) summary
      cd13433
      Location:14721524
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12051480
      Ion_trans; Ion transport protein
      pfam06512
      Location:9941201
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:509693
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17881851
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    11. NM_001353957.2NP_001340886.1  sodium channel protein type 1 subunit alpha isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC010127
      Consensus CDS
      CCDS54414.1
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Conserved Domains (5) summary
      cd13433
      Location:14561508
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11891464
      Ion_trans; Ion transport protein
      pfam06512
      Location:9781185
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510677
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17721835
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    12. NM_001353958.2NP_001340887.1  sodium channel protein type 1 subunit alpha isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC010127, AC107082
      Consensus CDS
      CCDS54414.1
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Related
      ENSP00000386312.1, ENST00000409050.2
      Conserved Domains (5) summary
      cd13433
      Location:14561508
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11891464
      Ion_trans; Ion transport protein
      pfam06512
      Location:9781185
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510677
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17721835
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    13. NM_001353960.2NP_001340889.1  sodium channel protein type 1 subunit alpha isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC010127
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Conserved Domains (1) summary
      cd13433
      Location:14551507
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    14. NM_001353961.2NP_001340890.1  sodium channel protein type 1 subunit alpha isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC010127
      Conserved Domains (4) summary
      cd13433
      Location:670722
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:403678
      Ion_trans; Ion transport protein
      pfam06512
      Location:192399
      Na_trans_assoc; Sodium ion transport-associated
      pfam16905
      Location:9861049
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    15. NM_006920.6NP_008851.3  sodium channel protein type 1 subunit alpha isoform 2

      See identical proteins and their annotated locations for NP_008851.3

      Status: REVIEWED

      Source sequence(s)
      AC010127
      Consensus CDS
      CCDS33316.1
      UniProtKB/TrEMBL
      A0A1W2PPJ3
      Related
      ENSP00000490780.1, ENST00000637988.1
      Conserved Domains (5) summary
      cd13433
      Location:14731525
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12061481
      Ion_trans; Ion transport protein
      pfam06512
      Location:9951202
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510694
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17891852
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated

    RNA

    1. NR_148667.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC010127
      Related
      ENST00000641996.1

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      165984641..166149161 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445392.1XP_047301348.1  sodium channel protein type 1 subunit alpha isoform X1

      UniProtKB/TrEMBL
      A0A1W2PPJ3
    2. XM_047445393.1XP_047301349.1  sodium channel protein type 1 subunit alpha isoform X2

      UniProtKB/TrEMBL
      A0A1B0GVX7
      Related
      ENSP00000490692.1, ENST00000635776.1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      166442174..166606734 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343301.1XP_054199276.1  sodium channel protein type 1 subunit alpha isoform X1

      UniProtKB/TrEMBL
      A0A1W2PPJ3
    2. XM_054343302.1XP_054199277.1  sodium channel protein type 1 subunit alpha isoform X2

      UniProtKB/TrEMBL
      A0A1B0GVX7