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

Gene ID: 6326, updated on 7-Oct-2018

Summary

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]
Expression
Biased expression in brain (RPKM 20.5) and kidney (RPKM 1.1) See more
Orthologs

Genomic context

See SCN2A in Genome Data Viewer
Location:
2q24.3
Exon count:
31
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

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

Pathways from BioSystems

  • 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...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
voltage-gated ion channel activity IEA
Inferred from Electronic Annotation
more info
 
voltage-gated sodium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
voltage-gated sodium channel activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
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
PubMed 
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
PubMed 
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
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon TAS
Traceable Author Statement
more info
PubMed 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
integral component of presynaptic membrane IEA
Inferred from Electronic Annotation
more info
 
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
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sodium channel complex ISS
Inferred from Sequence or Structural Similarity
more info
 
voltage-gated sodium channel complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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
    ENSP00000364586.2, ENST00000375437.6
    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
    ENSP00000364576.2, ENST00000375427.4
    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
    ENSP00000283256.6, OTTHUMP00000041049, ENST00000283256.10, 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 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 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
    Related
    ENSP00000490866.1, ENST00000637266.2
    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
    ENSP00000486885.1, OTTHUMP00000041050, ENST00000631182.2, 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_024453037.1XP_024308805.1  sodium channel protein type 2 subunit alpha isoform X3

    Conserved Domains (5) summary
    cd13433
    Location:12231275
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:9561231
    Ion_trans; Ion transport protein
    pfam06512
    Location:746952
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:263445
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:15391602
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  4. XM_017004658.1XP_016860147.1  sodium channel protein type 2 subunit alpha isoform X3

    Conserved Domains (5) summary
    cd13433
    Location:12231275
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:9561231
    Ion_trans; Ion transport protein
    pfam06512
    Location:746952
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:263445
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:15391602
    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_017004659.1XP_016860148.1  sodium channel protein type 2 subunit alpha isoform X4

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