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SCN2A sodium channel, voltage-gated, type II, alpha subunit [ Homo sapiens (human) ]

Gene ID: 6326, updated on 13-Jul-2014
Official Symbol
SCN2Aprovided by HGNC
Official Full Name
sodium channel, voltage-gated, type II, alpha subunitprovided by HGNC
Primary source
HGNC:10588
See related
Ensembl:ENSG00000136531; HPRD:03133; 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 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family. It is heterogeneously expressed in the brain, and mutations in this gene have been linked to several seizure disorders. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, Jul 2008]
See SCN2A in Epigenomics, MapViewer
Location:
2q24.3
Exon count:
33
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 2 NC_000002.12 (165130149..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 uncharacterized LOC101929633 Neighboring gene solute carrier family 38, member 11 Neighboring gene uncharacterized LOC101929658 Neighboring gene sodium channel, voltage-gated, type III, alpha subunit Neighboring gene MAPRE1 pseudogene 3 Neighboring gene cysteine-serine-rich nuclear protein 3 Neighboring gene uncharacterized LOC102724230 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 3

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)

ISCA Genome Curation Page
Haploinsufficency

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

ISCA Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
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...
  • 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...
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
 
sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
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
 
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
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
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
sodium channel protein type 2 subunit alpha
HBSC II
voltage-gated sodium channel subtype II
sodium channel protein type II subunit alpha
sodium channel protein brain II subunit alpha
voltage-gated sodium channel subunit alpha Nav1.2
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

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 

    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 proteins identical to 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 (4) summary
    cd13433
    Location:14741526
    Blast Score: 298
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12441472
    Blast Score: 462
    Ion_trans; Ion transport protein
    pfam06512
    Location:9971218
    Blast Score: 815
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:516710
    Blast Score: 592
    DUF3451; Domain of unknown function (DUF3451)
  2. NM_001040143.1NP_001035233.1  sodium channel protein type 2 subunit alpha isoform 2

    See proteins identical to 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, AH010232, BP311214, BU729783, DA232976, M94055
    Consensus CDS
    CCDS33313.1
    UniProtKB/Swiss-Prot
    Q99250
    Conserved Domains (4) summary
    cd13433
    Location:14741526
    Blast Score: 298
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12441472
    Blast Score: 461
    Ion_trans; Ion transport protein
    pfam06512
    Location:9971218
    Blast Score: 815
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:516710
    Blast Score: 592
    DUF3451; Domain of unknown function (DUF3451)
  3. NM_021007.2NP_066287.2  sodium channel protein type 2 subunit alpha isoform 1

    See proteins identical to 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 (4) summary
    cd13433
    Location:14741526
    Blast Score: 298
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12441472
    Blast Score: 462
    Ion_trans; Ion transport protein
    pfam06512
    Location:9971218
    Blast Score: 815
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:516710
    Blast Score: 592
    DUF3451; Domain of unknown function (DUF3451)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000002.12 

    Range
    165130149..165392310
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005246750.2XP_005246807.1  

    See proteins identical to XP_005246807.1

    UniProtKB/Swiss-Prot
    Q99250
    Conserved Domains (4) summary
    cd13433
    Location:14741526
    Blast Score: 298
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12441472
    Blast Score: 462
    Ion_trans; Ion transport protein
    pfam06512
    Location:9971218
    Blast Score: 815
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:516710
    Blast Score: 592
    DUF3451; Domain of unknown function (DUF3451)
  2. XM_005246753.1XP_005246810.1  

    See proteins identical to XP_005246810.1

    UniProtKB/Swiss-Prot
    Q99250
    Related
    ENSP00000349973, ENST00000357398
    Conserved Domains (4) summary
    cd13433
    Location:14741526
    Blast Score: 298
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12441472
    Blast Score: 461
    Ion_trans; Ion transport protein
    pfam06512
    Location:9971218
    Blast Score: 815
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:516710
    Blast Score: 592
    DUF3451; Domain of unknown function (DUF3451)
  3. XM_005246754.2XP_005246811.1  

    Conserved Domains (4) summary
    cd13433
    Location:14641516
    Blast Score: 298
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12341462
    Blast Score: 459
    Ion_trans; Ion transport protein
    pfam06512
    Location:9871208
    Blast Score: 815
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:506700
    Blast Score: 592
    DUF3451; Domain of unknown function (DUF3451)
  4. XM_005246751.2XP_005246808.1  

    See proteins identical to XP_005246808.1

    UniProtKB/Swiss-Prot
    Q99250
    Conserved Domains (4) summary
    cd13433
    Location:14741526
    Blast Score: 298
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12441472
    Blast Score: 462
    Ion_trans; Ion transport protein
    pfam06512
    Location:9971218
    Blast Score: 815
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:516710
    Blast Score: 592
    DUF3451; Domain of unknown function (DUF3451)
  5. XM_005246755.2XP_005246812.1  

    Conserved Domains (5) summary
    cd13433
    Location:12231275
    Blast Score: 299
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:9931221
    Blast Score: 461
    Ion_trans; Ion transport protein
    pfam06512
    Location:746967
    Blast Score: 813
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:265459
    Blast Score: 592
    DUF3451; Domain of unknown function (DUF3451)
    cl16916
    Location:14621497
    Blast Score: 84
    ChtBD1; Hevein or type 1 chitin binding domain
  6. XM_005246756.2XP_005246813.1  

    Conserved Domains (4) summary
    cd13433
    Location:740792
    Blast Score: 296
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:510738
    Blast Score: 441
    Ion_trans; Ion transport protein
    pfam06512
    Location:263484
    Blast Score: 812
    Na_trans_assoc; Sodium ion transport-associated
    cl16916
    Location:9791014
    Blast Score: 84
    ChtBD1; Hevein or type 1 chitin binding domain

Alternate HuRef

Genomic

  1. AC_000134.1 

    Range
    157978323..158131089
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018913.2 

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