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

Gene ID: 6323, updated on 25-Oct-2020

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
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; 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

Genomic context

See SCN1A in Genome Data Viewer
Location:
2q24.3
Exon count:
31
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (165984641..166149161, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (166845670..167005642, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100506124 Neighboring gene tetratricopeptide repeat domain 21B Neighboring gene TTC21B antisense RNA 1 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

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

Associated conditions

Description Tests
Common variants associated with general and MMR vaccine-related febrile seizures.
GeneReviews: Not available
Epilepsy, hippocampal sclerosis and febrile seizures linked by common genetic variation around SCN1A.
GeneReviews: Not available
Familial hemiplegic migraine type 3
MedGen: C1864987 OMIM: 609634 GeneReviews: Familial Hemiplegic Migraine
Compare labs
Generalized epilepsy with febrile seizures plus, type 2 Compare labs
Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies.
GeneReviews: Not available
Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32
GeneReviews: Not available
Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
GeneReviews: Not available
Severe myoclonic epilepsy in infancy not available

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

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
    P35498
    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/Swiss-Prot
    P35498
    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
    P35498
    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
    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
    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
    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
    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
    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
    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
    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
    Related
    ENSP00000386312.1, ENST00000409050.1
    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
    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
    Conserved Domains (5) summary
    cd13433
    Location:14551507
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11881463
    Ion_trans; Ion transport protein
    pfam06512
    Location:9771184
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:509676
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17711834
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  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/Swiss-Prot
    P35498
    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: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

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

RNA

  1. XR_001738884.1 RNA Sequence

    Related
    ENST00000636194.1
  2. XR_001738883.1 RNA Sequence

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