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    SCN8A sodium voltage-gated channel alpha subunit 8 [ Homo sapiens (human) ]

    Gene ID: 6334, updated on 17-Jun-2024

    Summary

    Official Symbol
    SCN8Aprovided by HGNC
    Official Full Name
    sodium voltage-gated channel alpha subunit 8provided by HGNC
    Primary source
    HGNC:HGNC:10596
    See related
    Ensembl:ENSG00000196876 MIM:600702; AllianceGenome:HGNC:10596
    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
    MED; PN4; CIAT; BFIS5; DEE13; NaCh6; CERIII; EIEE13; MYOCL2; Nav1.6
    Summary
    This gene encodes a member of the sodium channel alpha subunit gene family. The encoded protein forms the ion pore region of the voltage-gated sodium channel. This protein is essential for the rapid membrane depolarization that occurs during the formation of the action potential in excitable neurons. Mutations in this gene are associated with cognitive disability, pancerebellar atrophy and ataxia. Alternate splicing results in multiple transcript variants.[provided by RefSeq, May 2010]
    Expression
    Biased expression in brain (RPKM 8.0), testis (RPKM 1.0) and 2 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SCN8A in Genome Data Viewer
    Location:
    12q13.13
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (51591233..51812864)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (51554795..51776384)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (51985017..52206648)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6379 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr12:51765098-51765664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51773037-51773538 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51773539-51774038 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51781791-51782290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6380 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51784367-51784952 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51784953-51785537 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6381 Neighboring gene NANOG hESC enhancer GRCh37_chr12:51813535-51814036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4468 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6382 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:51826488-51826988 Neighboring gene solute carrier family 4 member 8 Neighboring gene SLC4A8 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4470 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51895635-51896136 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:51896137-51896636 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6383 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6384 Neighboring gene NANOG hESC enhancer GRCh37_chr12:51938922-51939423 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4471 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4472 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52039206-52040092 Neighboring gene SCN8A eExon liver enhancer Neighboring gene heterogeneous nuclear ribonucleoprotein A3 pseudogene 10 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:52208409-52208908 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4473 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4474 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52220360-52220860 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52221534-52222085 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52223188-52223737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52229864-52230815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:52241735-52242726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52238698-52239408 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:52239409-52240117 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:52240828-52241536 Neighboring gene fidgetin like 2 Neighboring gene transmembrane and death domain 1 Neighboring gene FIGNL2 divergent transcript

    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?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ33996

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sodium ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables voltage-gated sodium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables voltage-gated sodium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables voltage-gated sodium channel activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables voltage-gated sodium channel activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cardiac muscle cell action potential involved in contraction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in myelination ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in nervous system development TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in neuronal action potential IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in optic nerve development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in peripheral nervous system development ISS
    Inferred from Sequence or Structural Similarity
    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 Z disc ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in axon initial segment ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell junction IDA
    Inferred from Direct Assay
    more info
     
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane TAS
    Traceable Author Statement
    more info
    PubMed 
    located_in node of Ranvier ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in parallel fiber to Purkinje cell synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in presynaptic active zone membrane IEA
    Inferred from Electronic Annotation
    more info
     
    part_of voltage-gated sodium channel complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of voltage-gated sodium channel complex IC
    Inferred by Curator
    more info
    PubMed 
    part_of voltage-gated sodium channel complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    sodium channel protein type 8 subunit alpha
    Names
    hNa6/Scn8a voltage-gated sodium channel
    sodium channel, voltage gated, type VIII, alpha subunit
    voltage-gated sodium channel subunit alpha Nav1.6
    voltage-gated sodium channel type VIII alpha protein

    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_021180.3 RefSeqGene

      Range
      6276..227907
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1389

    mRNA and Protein(s)

    1. NM_001177984.3NP_001171455.1  sodium channel protein type 8 subunit alpha isoform 2

      See identical proteins and their annotated locations for NP_001171455.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1. Isoforms 2 and 4 are the same length but differ in their sequence.
      Source sequence(s)
      AB027567, AC013421, AC025097, AC068987, BX112779
      Consensus CDS
      CCDS53794.1
      UniProtKB/Swiss-Prot
      Q9UQD0
      Related
      ENSP00000440360.1, ENST00000545061.5
      Conserved Domains (6) summary
      smart00015
      Location:18531874
      IQ; Calmodulin-binding motif
      cd13433
      Location:14241476
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:14811735
      Ion_trans; Ion transport protein
      pfam06512
      Location:9911192
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:502688
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17391802
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    2. NM_001330260.2NP_001317189.1  sodium channel protein type 8 subunit alpha isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate in-frame exon in the 5' coding region, compared to variant 1. Isoforms 1 and 3 are the same length but differ in their sequence.
      Source sequence(s)
      AC013421, AC025097, AC068987, AC140060
      Consensus CDS
      CCDS81692.1
      UniProtKB/Swiss-Prot
      Q9UQD0
      UniProtKB/TrEMBL
      Q6B4S4
      Related
      ENSP00000487583.2, ENST00000627620.5
      Conserved Domains (6) summary
      smart00015
      Location:18941915
      IQ; Calmodulin-binding motif
      cd13433
      Location:14651517
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11971473
      Ion_trans; Ion transport protein
      pfam06512
      Location:9911192
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:504702
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17881835
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    3. NM_001369788.1NP_001356717.1  sodium channel protein type 8 subunit alpha isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: Isoforms 2 and 4 are the same length but differ in their sequence.
      Source sequence(s)
      AC013421, AC025097, AC068987, AC140060
      Consensus CDS
      CCDS91697.1
      UniProtKB/TrEMBL
      A0A590UK43
      Related
      ENSP00000499691.1, ENST00000668547.1
      Conserved Domains (6) summary
      smart00015
      Location:18531874
      IQ; Calmodulin-binding motif
      cd13433
      Location:14241476
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:14811735
      Ion_trans; Ion transport protein
      pfam06512
      Location:9911192
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:502692
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17391802
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    4. NM_014191.4NP_055006.1  sodium channel protein type 8 subunit alpha isoform 1

      See identical proteins and their annotated locations for NP_055006.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longest isoform (1). Isoforms 1 and 3 are the same length but differ in their sequence.
      Source sequence(s)
      AB027567, AC013421, AC025097, AC068987
      Consensus CDS
      CCDS44891.1
      UniProtKB/Swiss-Prot
      B9VWG8, O95788, Q9NYX2, Q9UPB2, Q9UQD0
      Related
      ENSP00000346534.4, ENST00000354534.11
      Conserved Domains (6) summary
      smart00015
      Location:18941915
      IQ; Calmodulin-binding motif
      cd13433
      Location:14651517
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11971473
      Ion_trans; Ion transport protein
      pfam06512
      Location:9911192
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:502688
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17801843
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      51591233..51812864
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      51554795..51776384
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_175894.2: Suppressed sequence

      Description
      NM_175894.2: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.