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    SCN2A sodium voltage-gated channel alpha subunit 2 [ Homo sapiens (human) ]

    Gene ID: 6326, updated on 12-Mar-2017
    Official Symbol
    SCN2Aprovided by HGNC
    Official Full Name
    sodium voltage-gated channel alpha subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:10588
    See related
    Ensembl:ENSG00000136531 MIM:182390; Vega:OTTHUMG00000044172
    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
    HBA; NAC2; BFIC3; BFIS3; BFNIS; HBSCI; EIEE11; HBSCII; Nav1.2; SCN2A1; SCN2A2; Na(v)1.2
    Summary
    Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with four repeat domains, each of which is composed of six membrane-spanning segments, and one or more regulatory beta subunits. Voltage-gated sodium channels function in the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family. Allelic variants of this gene are associated with seizure disorders and autism spectrum disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
    Orthologs
    Location:
    2q24.3
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 2 NC_000002.12 (165208056..165392310)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (165986659..166248820)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 38 member 11 Neighboring gene sodium voltage-gated channel alpha subunit 3 Neighboring gene MAPRE1 pseudogene 3 Neighboring gene cysteine and serine rich nuclear protein 3 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 3

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Benign familial neonatal-infantile seizures
    MedGen: C1843140 OMIM: 607745 GeneReviews: Not available
    Compare labs
    Early infantile epileptic encephalopathy 11
    MedGen: C3150987 OMIM: 613721 GeneReviews: Not available
    Compare labs
    SCN2A-related generalized epilepsy with febrile seizures plus
    MedGen: CN120574 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2013-02-21)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2013-02-21)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    Common variants associated with general and MMR vaccine-related febrile seizures.
    NHGRI GWA Catalog
    Genome-wide association study of chronic periodontitis in a general German population.
    NHGRI GWA Catalog
    • Axon guidance, organism-specific biosystem (from REACTOME)
      Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
    • Cardiac conduction, organism-specific biosystem (from REACTOME)
      Cardiac conduction, organism-specific biosystemThe normal sequence of contraction of atria and ventricles of the heart require activation of groups of cardiac cells. The mechanism must elicit rapid changes in heart rate and respond to changes in ...
    • Developmental Biology, organism-specific biosystem (from REACTOME)
      Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
    • Interaction between L1 and Ankyrins, organism-specific biosystem (from REACTOME)
      Interaction between L1 and Ankyrins, organism-specific biosystemAnkyrins are a family of adaptor proteins that couple membrane proteins such as voltage gated Na+ channels and the Na+/K+ anion exchanger to the spectrin actin cytoskeleton. Ankyrins are encoded by t...
    • L1CAM interactions, organism-specific biosystem (from REACTOME)
      L1CAM interactions, organism-specific biosystemThe L1 family of cell adhesion molecules (L1CAMs) are a subfamily of the immunoglobulin superfamily of transmembrane receptors, comprised of four structurally related proteins: L1, Close Homolog of L...
    • Muscle contraction, organism-specific biosystem (from REACTOME)
      Muscle contraction, organism-specific biosystemIn this module, the processes by which calcium binding triggers actin - myosin interactions and force generation in smooth and striated muscle tissues are annotated.
    • Phase 0 - rapid depolarisation, organism-specific biosystem (from REACTOME)
      Phase 0 - rapid depolarisation, organism-specific biosystemPhase 0 is the rapid depolarisation phase in which electrical stimulation of a cell initiates events involving the influx and efflux of ions resulting in the production of a cell's action potential. ...
    • Taste transduction, organism-specific biosystem (from KEGG)
      Taste transduction, organism-specific biosystemFive basic tastes are recognized by humans and most other animals - bitter, sweet, sour, salty and umami. In vertebrates, taste stimuli are detected by taste receptor cells (TRCs). At least three dis...
    • Taste transduction, conserved biosystem (from KEGG)
      Taste transduction, conserved biosystemFive basic tastes are recognized by humans and most other animals - bitter, sweet, sour, salty and umami. In vertebrates, taste stimuli are detected by taste receptor cells (TRCs). At least three dis...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    voltage-gated sodium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    voltage-gated sodium channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    intrinsic apoptotic signaling pathway in response to osmotic stress IEA
    Inferred from Electronic Annotation
    more info
     
    membrane depolarization during action potential IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    myelination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    neuron apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    neuronal action potential IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    regulation of ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of postsynaptic membrane potential IEA
    Inferred from Electronic Annotation
    more info
     
    sodium ion transmembrane transport ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    sodium ion transport TAS
    Traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    T-tubule IEA
    Inferred from Electronic Annotation
    more info
     
    axon TAS
    Traceable Author Statement
    more info
    PubMed 
    integral component of plasma membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    intercalated disc IEA
    Inferred from Electronic Annotation
    more info
     
    intracellular IEA
    Inferred from Electronic Annotation
    more info
     
    intrinsic component of plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    node of Ranvier ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    paranode region of axon IEA
    Inferred from Electronic Annotation
    more info
     
    sodium channel complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    voltage-gated sodium channel complex IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    sodium channel protein type 2 subunit alpha
    Names
    HBSC II
    sodium channel protein brain II subunit alpha
    sodium channel protein type II subunit alpha
    sodium channel protein, brain type 2 alpha subunit
    sodium channel, voltage-gated, type II, alpha 1 polypeptide
    sodium channel, voltage-gated, type II, alpha 2 polypeptide
    sodium channel, voltage-gated, type II, alpha subunit
    voltage-gated sodium channel subtype II
    voltage-gated sodium channel subunit alpha Nav1.2
    voltage-gated sodium channel type II alpha subunit

    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_008143.1 RefSeqGene

      Range
      5001..157909
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001040142.1NP_001035232.1  sodium channel protein type 2 subunit alpha isoform 1

      See identical proteins and their annotated locations for NP_001035232.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AC011303, BP199510, BP311214, BU729783, DA232976, M94055
      Consensus CDS
      CCDS33314.1
      UniProtKB/Swiss-Prot
      Q99250
      Related
      ENSP00000364586, ENST00000375437
      Conserved Domains (5) summary
      cd13433
      Location:14741526
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12251482
      Ion_trans; Ion transport protein
      pfam06512
      Location:9971203
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:514630
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17981853
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    2. NM_001040143.1NP_001035233.1  sodium channel protein type 2 subunit alpha isoform 2

      See identical proteins and their annotated locations for NP_001035233.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (2) contains one amino acid substitution relative to isoform 1.
      Source sequence(s)
      AC011303, BU729783
      Consensus CDS
      CCDS33313.1
      UniProtKB/Swiss-Prot
      Q99250
      Related
      ENSP00000364576, ENST00000375427
      Conserved Domains (5) summary
      cd13433
      Location:14741526
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12251482
      Ion_trans; Ion transport protein
      pfam06512
      Location:9971203
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:514630
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17981853
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    3. NM_021007.2NP_066287.2  sodium channel protein type 2 subunit alpha isoform 1

      See identical proteins and their annotated locations for NP_066287.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AC011303, BP311214, BU729783, DA232976, M94055
      Consensus CDS
      CCDS33314.1
      UniProtKB/Swiss-Prot
      Q99250
      Related
      ENSP00000283256, OTTHUMP00000041049, ENST00000283256, OTTHUMT00000102659
      Conserved Domains (5) summary
      cd13433
      Location:14741526
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12251482
      Ion_trans; Ion transport protein
      pfam06512
      Location:9971203
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:514630
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17981853
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p7 Primary Assembly

      Range
      165208056..165392310
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004656.1XP_016860145.1  sodium channel protein type 2 subunit alpha isoform X1

      UniProtKB/Swiss-Prot
      Q99250
      Conserved Domains (5) summary
      cd13433
      Location:14741526
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12251482
      Ion_trans; Ion transport protein
      pfam06512
      Location:9971203
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:514630
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17981853
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    2. XM_005246753.3XP_005246810.1  sodium channel protein type 2 subunit alpha isoform X2

      See identical proteins and their annotated locations for XP_005246810.1

      UniProtKB/Swiss-Prot
      Q99250
      Related
      ENSP00000486885, OTTHUMP00000041050, ENST00000631182, OTTHUMT00000102660
      Conserved Domains (5) summary
      cd13433
      Location:14741526
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12251482
      Ion_trans; Ion transport protein
      pfam06512
      Location:9971203
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:514630
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17981853
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    3. XM_017004658.1XP_016860147.1  sodium channel protein type 2 subunit alpha isoform X3

      Conserved Domains (6) summary
      cd13433
      Location:12231275
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:9741231
      Ion_trans; Ion transport protein
      pfam06512
      Location:746952
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:263379
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:15471602
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
      cl16916
      Location:14621497
      ChtBD1; Hevein or type 1 chitin binding domain
    4. XM_017004655.1XP_016860144.1  sodium channel protein type 2 subunit alpha isoform X1

      UniProtKB/Swiss-Prot
      Q99250
      Related
      ENSP00000490866, OTTHUMP00000282561, ENST00000637266, OTTHUMT00000490197
      Conserved Domains (5) summary
      cd13433
      Location:14741526
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12251482
      Ion_trans; Ion transport protein
      pfam06512
      Location:9971203
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:514630
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17981853
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    5. XM_017004657.1XP_016860146.1  sodium channel protein type 2 subunit alpha isoform X2

      UniProtKB/Swiss-Prot
      Q99250
      Conserved Domains (5) summary
      cd13433
      Location:14741526
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12251482
      Ion_trans; Ion transport protein
      pfam06512
      Location:9971203
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:514630
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17981853
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    6. XM_005246755.4XP_005246812.1  sodium channel protein type 2 subunit alpha isoform X3

      Conserved Domains (6) summary
      cd13433
      Location:12231275
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:9741231
      Ion_trans; Ion transport protein
      pfam06512
      Location:746952
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:263379
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:15471602
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
      cl16916
      Location:14621497
      ChtBD1; Hevein or type 1 chitin binding domain
    7. XM_017004659.1XP_016860148.1  sodium channel protein type 2 subunit alpha isoform X4

    Alternate CHM1_1.1

    Genomic

    1. NC_018913.2 Alternate CHM1_1.1

      Range
      166101845..166254789
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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