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SCN3A sodium voltage-gated channel alpha subunit 3 [ Homo sapiens (human) ]

Gene ID: 6328, updated on 16-Apr-2024

Summary

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Official Symbol
SCN3Aprovided by HGNC
Official Full Name
sodium voltage-gated channel alpha subunit 3provided by HGNC
Primary source
HGNC:HGNC:10590
See related
Ensembl:ENSG00000153253 MIM:182391; AllianceGenome:HGNC:10590
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
NAC3; DEE62; EIEE62; FFEVF4; Nav1.3
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, and is found in a cluster of five alpha subunit genes on chromosome 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Biased expression in brain (RPKM 5.7), adrenal (RPKM 1.1) and 11 other tissues See more
Orthologs
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Genomic context

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Location:
2q24.3
Exon count:
32
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (165087526..165204050, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (165544858..165661382, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (165944036..166060560, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 110 Neighboring gene NANOG hESC enhancer GRCh37_chr2:165769454-165769970 Neighboring gene RNA, 5S ribosomal pseudogene 111 Neighboring gene solute carrier family 38 member 11 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:165840567-165840754 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:165851409-165851909 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:165926349-165926850 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:165926851-165927350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12066 Neighboring gene Sharpr-MPRA regulatory region 13511 Neighboring gene sodium voltage-gated channel alpha subunit 2 Neighboring gene MAPRE1 pseudogene 3 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:166279515-166280129 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:166283004-166283939 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:166317128-166318327 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:166385525-166386157 Neighboring gene cysteine and serine rich nuclear protein 3 Neighboring gene MPRA-validated peak3912 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr2:166436961-166437478 Neighboring gene NANOG hESC enhancer GRCh37_chr2:166437479-166437996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16726 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16727 Neighboring gene uncharacterized LOC124906085 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:166490986-166491565 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:166491566-166492144

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. SCN3A-Related Neurodevelopmental Disorder. Adam MP, et al. , 1993. PMID 34081427
  2. SCN3A-Related Neurodevelopmental Disorder: A Spectrum of Epilepsy and Brain Malformation. Zaman T, et al. Ann Neurol, 2020 Aug. PMID 32515017, Free PMC Article
  3. Sodium Channel SCN3A (Na(V)1.3) Regulation of Human Cerebral Cortical Folding and Oral Motor Development. Smith RS, et al. Neuron, 2018 Sep 5. PMID 30146301, Free PMC Article
  4. Mutations in SCN3A cause early infantile epileptic encephalopathy. Zaman T, et al. Ann Neurol, 2018 Apr. PMID 29466837, Free PMC Article
  5. Novel SCN3A variants associated with focal epilepsy in children. Vanoye CG, et al. Neurobiol Dis, 2014 Feb. PMID 24157691, Free PMC Article

See all (45) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Targeted blockade of aberrant sodium current in a stem cell-derived neuron model of SCN3A encephalopathy.
    Title: Targeted blockade of aberrant sodium current in a stem cell-derived neuron model of SCN3A encephalopathy.
  2. Association of sodium voltage-gated channel genes polymorphisms with epilepsy risk and prognosis in the Saudi population.
    Title: Association of sodium voltage-gated channel genes polymorphisms with epilepsy risk and prognosis in the Saudi population.
  3. Mutations in the sodium channel genes SCN1A, SCN3A, and SCN9A in children with epilepsy with febrile seizures plus(EFS+).
    Title: Mutations in the sodium channel genes SCN1A, SCN3A, and SCN9A in children with epilepsy with febrile seizures plus(EFS+).
  4. SCN3A-Related Neurodevelopmental Disorder: A Spectrum of Epilepsy and Brain Malformation.
    Title: SCN3A-Related Neurodevelopmental Disorder: A Spectrum of Epilepsy and Brain Malformation.
  5. Long noncoding RNA HOXA-AS2 regulates the expression of SCN3A by sponging miR-106a in breast cancer.
    Title: Long noncoding RNA HOXA-AS2 regulates the expression of SCN3A by sponging miR-106a in breast cancer.
  6. SCN3A expression is involved in the prenatal development of human cortical language areas.
    Title: Sodium Channel SCN3A (Na(V)1.3) Regulation of Human Cerebral Cortical Folding and Oral Motor Development.
  7. The findings of this study established SCN3A as a new gene for infantile epileptic encephalopathy and suggest a potential pharmacologic intervention.
    Title: Mutations in SCN3A cause early infantile epileptic encephalopathy.
  8. Study represents the first evidence of the abnormal changes in voltage-gated sodium channels subtypes (including Nav1.3) and CaM/CaMKII pathway in human brain low-grade astrocytoma, providing new potential targets for molecular therapies of this disease.
    Title: Abnormal changes in voltage-gated sodium channels subtypes Na(V)1.1, Na(V)1.2, Na(V)1.3, Na(V)1.6 and CaM/CaMKII pathway in low-grade astrocytoma.
  9. SCN3A is involved in development of the human brain and oral motor development. When SCN3A is mutated, patients present with polymicrogyria and speech deficits.
    Title: Sodium Channel SCN3A (Na(V)1.3) Regulation of Human Cerebral Cortical Folding and Oral Motor Development.
  10. Novel de novo variant SCN3A-L247P was demonstrated to cause a defect in trafficking, which would be predicted to functionally reduce SCN3A activity. Consistent with the clinical observations, Scn3a+/Hyp mice display increased seizure susceptibility, hypoactivity, and impaired motor learning.
    Title: SCN3A deficiency associated with increased seizure susceptibility.
Submit: New GeneRIF Correction See all GeneRIFs (25)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Vif vif HIV-1 Vif downregulates the expression of sodium channel, voltage-gated, type III, alpha subunit (SCN3A) in Vif-expression T cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1356

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables voltage-gated sodium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables voltage-gated sodium channel activity NAS
Non-traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in behavioral response to pain IEA
Inferred from Electronic Annotation
more info
  
involved_in cardiac muscle cell action potential involved in contraction IBA
Inferred from Biological aspect of Ancestor
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 sarcoplasm IEA
Inferred from Electronic Annotation
more info
  
part_of voltage-gated sodium channel complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
sodium channel protein type 3 subunit alpha
Names
brain III voltage-gated sodium channel
sodium channel protein brain III subunit alpha
sodium channel protein type III subunit alpha
sodium channel, voltage gated, type III alpha subunit
sodium channel, voltage-gated, type III, alpha polypeptide
voltage-gated sodium channel subtype III
voltage-gated sodium channel subunit alpha Nav1.3

NCBI Reference Sequences (RefSeq)

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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_042289.1 RefSeqGene

    Range
    5039..121563
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001081676.2 → NP_001075145.1  sodium channel protein type 3 subunit alpha isoform 2

    See identical proteins and their annotated locations for NP_001075145.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as 12v1, SCN3A-s, or the adult form, uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in a shorter protein (isoform 2).
    Source sequence(s)
    AC013463, AF035686, AF225986, AJ251507, AL079365, BM681920, DA796981
    UniProtKB/TrEMBL
    Q9C007
    Conserved Domains (6) summary
    cd13433
    Location:1420 → 1472
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:1174 → 1428
    Ion_trans; Ion transport protein
    pfam06512
    Location:949 → 1151
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510 → 648
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:1744 → 1799
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:1659 → 1694
    ChtBD1; Hevein or type 1 chitin binding domain

  2. NM_001081677.2 → NP_001075146.1  sodium channel protein type 3 subunit alpha isoform 3

    See identical proteins and their annotated locations for NP_001075146.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), also known as the neonatal form, uses an alternate in-frame splice site in the central coding region and an alternate form of an exon in the 5' coding region, compared to variant 1. The resulting isoform (3) is shorter than isoform 1, and contains one amino acid substitution relative to isoform 2.
    Source sequence(s)
    AC013463, AF035686, AJ251507, AL079365, BM681920, DA772987
    Consensus CDS
    CCDS46440.1
    UniProtKB/TrEMBL
    Q9C007
    Related
    ENSP00000386726.3, ENST00000409101.7
    Conserved Domains (6) summary
    cd13433
    Location:1420 → 1472
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:1174 → 1428
    Ion_trans; Ion transport protein
    pfam06512
    Location:949 → 1151
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510 → 648
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:1744 → 1799
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:1659 → 1694
    ChtBD1; Hevein or type 1 chitin binding domain

  3. NM_006922.4 → NP_008853.3  sodium channel protein type 3 subunit alpha isoform 1

    See identical proteins and their annotated locations for NP_008853.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as 12v4, represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC013463, AF035686, AF225987, AJ251507, AL079365, BM681920, DA796981
    Consensus CDS
    CCDS33312.1
    UniProtKB/TrEMBL
    A0A1W2PRD1
    Related
    ENSP00000283254.7, ENST00000283254.12
    Conserved Domains (6) summary
    cd13433
    Location:1469 → 1521
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:1223 → 1477
    Ion_trans; Ion transport protein
    pfam06512
    Location:998 → 1200
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510 → 629
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:1793 → 1848
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:1708 → 1743
    ChtBD1; Hevein or type 1 chitin binding domain

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    165087526..165204050 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017004662.3 → XP_016860151.1  sodium channel protein type 3 subunit alpha isoform X5

    UniProtKB/TrEMBL
    Q9C007

  2. XM_017004661.3 → XP_016860150.1  sodium channel protein type 3 subunit alpha isoform X3

    UniProtKB/TrEMBL
    A0A1W2PRD1
    Related
    ENSP00000492251.1, ENST00000639244.1
    Conserved Domains (6) summary
    cd13433
    Location:1452 → 1504
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:1206 → 1460
    Ion_trans; Ion transport protein
    pfam06512
    Location:981 → 1183
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510 → 629
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:1776 → 1831
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:1691 → 1726
    ChtBD1; Hevein or type 1 chitin binding domain

  3. XM_047445394.1 → XP_047301350.1  sodium channel protein type 3 subunit alpha isoform X4

    UniProtKB/TrEMBL
    A0A994J5P2
    Related
    ENSP00000516211.1, ENST00000706067.1

  4. XM_017004660.3 → XP_016860149.1  sodium channel protein type 3 subunit alpha isoform X1

    UniProtKB/Swiss-Prot
    Q16142, Q53SX0, Q9BZB3, Q9C006, Q9NY46, Q9NYK2, Q9P2J1, Q9UPD1, Q9Y6P4
    UniProtKB/TrEMBL
    A0A1W2PRD1
    Conserved Domains (6) summary
    cd13433
    Location:1469 → 1521
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:1223 → 1477
    Ion_trans; Ion transport protein
    pfam06512
    Location:998 → 1200
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510 → 629
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:1793 → 1848
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:1708 → 1743
    ChtBD1; Hevein or type 1 chitin binding domain

  5. XM_011511610.4 → XP_011509912.1  sodium channel protein type 3 subunit alpha isoform X2

    See identical proteins and their annotated locations for XP_011509912.1

    UniProtKB/TrEMBL
    A0A1W2PRD1
    Conserved Domains (6) summary
    cd13433
    Location:1469 → 1521
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:1223 → 1477
    Ion_trans; Ion transport protein
    pfam06512
    Location:998 → 1200
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510 → 629
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:1793 → 1848
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:1708 → 1743
    ChtBD1; Hevein or type 1 chitin binding domain

  6. XM_011511613.4 → XP_011509915.1  sodium channel protein type 3 subunit alpha isoform X6

    Conserved Domains (5) summary
    cd13433
    Location:839 → 891
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:593 → 847
    Ion_trans; Ion transport protein
    pfam06512
    Location:368 → 570
    Na_trans_assoc; Sodium ion transport-associated
    pfam16905
    Location:1163 → 1218
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:1078 → 1113
    ChtBD1; Hevein or type 1 chitin binding domain

  7. XM_047445395.1 → XP_047301351.1  sodium channel protein type 3 subunit alpha isoform X7

    Related
    ENSP00000403348.1, ENST00000440431.6

  8. XM_017004666.2 → XP_016860155.1  sodium channel protein type 3 subunit alpha isoform X10

    UniProtKB/TrEMBL
    A0A1W2PSB2

  9. XM_017004665.2 → XP_016860154.1  sodium channel protein type 3 subunit alpha isoform X9

    UniProtKB/TrEMBL
    A0A1W2PSB2, A0A590UJH3
    Related
    ENSP00000499420.1, ENST00000668657.1

  10. XM_017004664.2 → XP_016860153.1  sodium channel protein type 3 subunit alpha isoform X8

    UniProtKB/TrEMBL
    A0A1W2PSB2
    Related
    ENSP00000492807.1, ENST00000640652.1
    Conserved Domains (3) summary
    pfam00520
    Location:143 → 434
    Ion_trans; Ion transport protein
    pfam06512
    Location:998 → 1117
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510 → 629
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    165544858..165661382 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054343307.1 → XP_054199282.1  sodium channel protein type 3 subunit alpha isoform X5

  2. XM_054343305.1 → XP_054199280.1  sodium channel protein type 3 subunit alpha isoform X3

  3. XM_054343306.1 → XP_054199281.1  sodium channel protein type 3 subunit alpha isoform X4

    UniProtKB/TrEMBL
    A0A994J5P2

  4. XM_054343303.1 → XP_054199278.1  sodium channel protein type 3 subunit alpha isoform X1

    UniProtKB/Swiss-Prot
    Q16142, Q53SX0, Q9BZB3, Q9C006, Q9NY46, Q9NYK2, Q9P2J1, Q9UPD1, Q9Y6P4

  5. XM_054343304.1 → XP_054199279.1  sodium channel protein type 3 subunit alpha isoform X2

  6. XM_054343308.1 → XP_054199283.1  sodium channel protein type 3 subunit alpha isoform X6

  7. XM_054343309.1 → XP_054199284.1  sodium channel protein type 3 subunit alpha isoform X7

  8. XM_054343312.1 → XP_054199287.1  sodium channel protein type 3 subunit alpha isoform X10

  9. XM_054343311.1 → XP_054199286.1  sodium channel protein type 3 subunit alpha isoform X9

    UniProtKB/TrEMBL
    A0A590UJH3

  10. XM_054343310.1 → XP_054199285.1  sodium channel protein type 3 subunit alpha isoform X8

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NY46.2 GenPept UniProtKB/Swiss-Prot:Q9NY46

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