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Aliases for SCN3A Gene

Aliases for SCN3A Gene

  • Sodium Voltage-Gated Channel Alpha Subunit 3 2 3
  • Sodium Channel, Voltage Gated, Type III Alpha Subunit 2 3 5
  • Sodium Channel, Voltage-Gated, Type III, Alpha Polypeptide 2 3
  • Voltage-Gated Sodium Channel Subunit Alpha Nav1.3 3 4
  • Sodium Channel Protein Brain III Subunit Alpha 3 4
  • Sodium Channel Protein Type III Subunit Alpha 3 4
  • Voltage-Gated Sodium Channel Subtype III 3 4
  • NAC3 3 4
  • Sodium Channel, Voltage-Gated, Type III, Alpha Subunit 2
  • Brain III Voltage-Gated Sodium Channel 3
  • KIAA1356 4
  • Nav1.3 3

External Ids for SCN3A Gene

Previous GeneCards Identifiers for SCN3A Gene

  • GC02M163999
  • GC02M164485
  • GC02M165908
  • GC02M166146
  • GC02M165769
  • GC02M165652
  • GC02M157826

Summaries for SCN3A Gene

Entrez Gene Summary for SCN3A Gene

  • 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]

GeneCards Summary for SCN3A Gene

SCN3A (Sodium Voltage-Gated Channel Alpha Subunit 3) is a Protein Coding gene. Diseases associated with SCN3A include Trigeminal Neuralgia and Dravet Syndrome. Among its related pathways are Neuropathic Pain-Signaling in Dorsal Horn Neurons and Activation of cAMP-Dependent PKA. GO annotations related to this gene include ion channel activity and voltage-gated sodium channel activity. An important paralog of this gene is CACNA1G.

UniProtKB/Swiss-Prot for SCN3A Gene

  • Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient.

Tocris Summary for SCN3A Gene

  • Voltage-gated sodium channels (NaV) are responsible for action potential initiation and propagation in excitable cells, including nerve, muscle, and neuroendocrine cell types. They are also expressed at low levels in non-excitable cells, where their physiological role is unclear.

Gene Wiki entry for SCN3A Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCN3A Gene

Genomics for SCN3A Gene

Regulatory Elements for SCN3A Gene

Enhancers for SCN3A Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SCN3A on UCSC Golden Path with GeneCards custom track

Promoters for SCN3A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SCN3A on UCSC Golden Path with GeneCards custom track

Genomic Location for SCN3A Gene

Chromosome:
2
Start:
165,087,520 bp from pter
End:
165,204,088 bp from pter
Size:
116,569 bases
Orientation:
Minus strand

Genomic View for SCN3A Gene

Genes around SCN3A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCN3A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCN3A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCN3A Gene

Proteins for SCN3A Gene

  • Protein details for SCN3A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NY46-SCN3A_HUMAN
    Recommended name:
    Sodium channel protein type 3 subunit alpha
    Protein Accession:
    Q9NY46
    Secondary Accessions:
    • Q16142
    • Q53SX0
    • Q9BZB3
    • Q9C006
    • Q9NYK2
    • Q9P2J1
    • Q9UPD1
    • Q9Y6P4

    Protein attributes for SCN3A Gene

    Size:
    2000 amino acids
    Molecular mass:
    226294 Da
    Quaternary structure:
    • The sodium channel consists of a large polypeptide and 2-3 smaller ones. This sequence represents a large polypeptide. Interacts with NEDD4L.

    Alternative splice isoforms for SCN3A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCN3A Gene

Proteomics data for SCN3A Gene at MOPED

Post-translational modifications for SCN3A Gene

  • May be ubiquitinated by NEDD4L; which would promote its endocytosis.
  • Phosphorylation at Ser-1501 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents.
  • Glycosylation at Asn 211, Asn 290, Asn 296, Asn 302, Asn 307, Asn 339, Asn 1366, and Asn 1380
  • Modification sites at PhosphoSitePlus

Other Protein References for SCN3A Gene

No data available for DME Specific Peptides for SCN3A Gene

Domains & Families for SCN3A Gene

Gene Families for SCN3A Gene

Graphical View of Domain Structure for InterPro Entry

Q9NY46

UniProtKB/Swiss-Prot:

SCN3A_HUMAN :
  • The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1,S2,S3,S5,S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position.
  • Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.3/SCN3A subfamily.
Domain:
  • The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1,S2,S3,S5,S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position.
  • Contains 1 IQ domain.
Family:
  • Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.3/SCN3A subfamily.
genes like me logo Genes that share domains with SCN3A: view

Function for SCN3A Gene

Molecular function for SCN3A Gene

GENATLAS Biochemistry:
sodium voltage-gated channel,type III,alpha polypeptide,expressed in brain,encoding two isoforms (neonatal and adult)
UniProtKB/Swiss-Prot Function:
Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient.
genes like me logo Genes that share phenotypes with SCN3A: view

Animal Models for SCN3A Gene

MGI Knock Outs for SCN3A:

Animal Model Products

  • Taconic Biosciences Mouse Models for SCN3A

miRNA for SCN3A Gene

miRTarBase miRNAs that target SCN3A

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SCN3A Gene

Localization for SCN3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCN3A Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SCN3A Gene COMPARTMENTS Subcellular localization image for SCN3A gene
Compartment Confidence
plasma membrane 4

No data available for Gene Ontology (GO) - Cellular Components for SCN3A Gene

Pathways & Interactions for SCN3A Gene

genes like me logo Genes that share pathways with SCN3A: view

Gene Ontology (GO) - Biological Process for SCN3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007399 nervous system development IEA --
GO:0034220 ion transmembrane transport IEA --
GO:0055085 transmembrane transport IEA --
GO:0071236 cellular response to antibiotic IEA --
genes like me logo Genes that share ontologies with SCN3A: view

No data available for SIGNOR curated interactions for SCN3A Gene

Drugs & Compounds for SCN3A Gene

(38) Drugs for SCN3A Gene - From: DrugBank, ApexBio, DGIdb, IUPHAR, HMDB, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Zonisamide Approved, Investigational Pharma blocker, Target, inhibitor Antiepileptic with anticonvulsant and mechanistic effect 65
Lacosamide Approved Pharma Target Checkpoint kinase inhibitor,ATP competitive, Checkpoint kinase (Chk) inhibitor 76
Valproic Acid Approved, Investigational Pharma Target HDAC1 inhibitor, Histone deacetylase (HDAC)inhibitors 312
Benzocaine Approved Pharma 1733
Carbamazepine Approved, Investigational Pharma 128

(4) Additional Compounds for SCN3A Gene - From: Tocris, Novoseek, and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Sodium
  • Sodium ion
7440-23-5
Amiloride hydrochloride
2016-88-8
Flunarizine dihydrochloride
30484-77-6
Riluzole hydrochloride
850608-87-6

(5) Tocris Compounds for SCN3A Gene

Compound Action Cas Number
Amiloride hydrochloride Na+ channel blocker; also I2 imidazoline ligand 2016-88-8
Flunarizine dihydrochloride Dual Na+/Ca2+ channel (T-type) blocker 30484-77-6
Riluzole hydrochloride Glutamate release inhibitor/GABA uptake inhibitor 850608-87-6
Veratridine Voltage-gated Na+ channel opener 71-62-5
Vinpocetine Na+ channel blocker 42971-09-5

(26) ApexBio Compounds for SCN3A Gene

Compound Action Cas Number
A-803467 NaV1.8 channel blocker,potent and selective 944261-79-4
Ambroxol HCl TTX-resistant Na+ currents inhibitor 23828-92-4
Amiloride HCl 2016-88-8
Amiloride HCl dihydrate 17440-83-4
Benzocaine 1994-09-7
Bupivacaine HCl Anaesthetic drug 18010-40-7
Camostat Mesilate Trypsin-like protease inhibitor 59721-29-8
Carbamazepine 298-46-4
Dibucaine (Cinchocaine) HCl 1961-12-1
Ibutilide Fumarate Class III antiarrhythmic agent 122647-32-9
Lamotrigine 5-HT inhibitor 84057-84-1
Levobupivacaine HCl 27262-48-2
Mexiletine HCl 5370-01-4
Nefopam HCl 23327-57-3
Ouabain 630-60-4
Oxcarbazepine BTX inhibitor 28721-07-5
Phenytoin 57-41-0
Phenytoin sodium Sodium channel stabilizer 630-93-3
Primidone 125-33-7
Procainamide HCl 614-39-1
Procaine HCl 1951-05-8
Propafenone HCl 34183-22-7
Proparacaine HCl 5875-06-9
Riluzole Sodium channel protein inhibitor 1744-22-5
Tolperisone HCl 3644-61-9
Triamterene 396-01-0
genes like me logo Genes that share compounds with SCN3A: view

Transcripts for SCN3A Gene

Unigene Clusters for SCN3A Gene

Sodium channel, voltage-gated, type III, alpha subunit:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SCN3A Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^
SP1: - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8: -
SP9: -

ExUns: 20 ^ 21 ^ 22 ^ 23 ^ 24a · 24b · 24c ^ 25a · 25b ^ 26a · 26b · 26c ^ 27 ^ 28 ^ 29
SP1: -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:

Relevant External Links for SCN3A Gene

GeneLoc Exon Structure for
SCN3A
ECgene alternative splicing isoforms for
SCN3A

Expression for SCN3A Gene

mRNA expression in normal human tissues for SCN3A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCN3A Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x4.9) and Brain - Hypothalamus (x4.7).

Protein differential expression in normal tissues from HIPED for SCN3A Gene

This gene is overexpressed in Fetal Brain (37.6) and Breast (31.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SCN3A Gene



SOURCE GeneReport for Unigene cluster for SCN3A Gene Hs.435274

genes like me logo Genes that share expression patterns with SCN3A: view

Protein tissue co-expression partners for SCN3A Gene

- Elite partner

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for SCN3A Gene

Orthologs for SCN3A Gene

This gene was present in the common ancestor of animals.

Orthologs for SCN3A Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SCN3A 35
  • 93.61 (n)
  • 97.5 (a)
SCN3A 36
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SCN3A 35
  • 93.68 (n)
  • 97.75 (a)
SCN3A 36
  • 97 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Scn3a 35
  • 89.57 (n)
  • 97.43 (a)
Scn3a 16
Scn3a 36
  • 97 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SCN3A 35
  • 99.78 (n)
  • 99.95 (a)
SCN3A 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Scn3a 35
  • 89.34 (n)
  • 97.23 (a)
oppossum
(Monodelphis domestica)
Mammalia SCN3A 36
  • 93 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SCN3A 36
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCN3A 35
  • 83.02 (n)
  • 89.89 (a)
SCN3A 36
  • 90 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SCN3A 36
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100488621 35
  • 77.26 (n)
  • 84.46 (a)
zebrafish
(Danio rerio)
Actinopterygii scn1lab 36
  • 78 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta NaCP60E 37
  • 63 (a)
para 37
  • 50 (a)
Species with no ortholog for SCN3A:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCN3A Gene

ENSEMBL:
Gene Tree for SCN3A (if available)
TreeFam:
Gene Tree for SCN3A (if available)

Paralogs for SCN3A Gene

genes like me logo Genes that share paralogs with SCN3A: view

Variants for SCN3A Gene

Sequence variations from dbSNP and Humsavar for SCN3A Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
VAR_014275 -
rs12474273 - 165,127,704(+) CTCCA(A/G)CAGCA reference, missense
VAR_029745 -
rs3731762 - 165,090,746(-) ATCCC(A/G)ATGCG reference, missense
rs1550385 -- 165,121,055(+) CTGAA(C/G)CAGCT intron-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for SCN3A Gene

Variant ID Type Subtype PubMed ID
nsv511183 CNV Gain 21212237
esv2666303 CNV Deletion 23128226
nsv435715 CNV Deletion 17901297
esv2554394 CNV Deletion 19546169
esv2721067 CNV Deletion 23290073
esv7053 CNV Loss 19470904
esv25924 CNV Loss 19812545
esv992100 CNV Gain 20482838
esv2667791 CNV Deletion 23128226
nsv213574 CNV Loss 16902084
nsv821783 CNV Loss 20364138
esv2585640 CNV Deletion 19546169
esv2673049 CNV Deletion 23128226

Variation tolerance for SCN3A Gene

Residual Variation Intolerance Score: 0.831% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.79; 66.78% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SCN3A Gene

Human Gene Mutation Database (HGMD)
SCN3A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCN3A Gene

Disorders for SCN3A Gene

MalaCards: The human disease database

(4) MalaCards diseases for SCN3A Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
trigeminal neuralgia
  • trifacial neuralgia
dravet syndrome
  • dravet syndrome, modifier of
focal epilepsy
  • localisation-related epilepsy
generalized epilepsy with febrile seizures plus
  • gefs+
- elite association - COSMIC cancer census association via MalaCards
Search SCN3A in MalaCards View complete list of genes associated with diseases

Relevant External Links for SCN3A

Genetic Association Database (GAD)
SCN3A
Human Genome Epidemiology (HuGE) Navigator
SCN3A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SCN3A
genes like me logo Genes that share disorders with SCN3A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCN3A Gene

Publications for SCN3A Gene

  1. Isolation of a human-brain sodium-channel gene encoding two isoforms of the subtype III alpha-subunit. (PMID: 9589372) Lu C.M. … Brown G.B. (J. Mol. Neurosci. 1998) 2 3 4 67
  2. The antiepileptic drug zonisamide inhibits MAO-B and attenuates MPTP toxicity in mice: clinical relevance. (PMID: 19948168) Sonsalla P.K. … Buckley B. (Exp. Neurol. 2010) 25 26
  3. Zonisamide in the treatment of epilepsy. (PMID: 20001433) Schulze-Bonhage A. (Expert Opin Pharmacother 2010) 25 26
  4. Long-term safety and effectiveness of zonisamide in the treatment of epilepsy: a review of the literature. (PMID: 19557119) Zaccara G. … Specchio L.M. (Neuropsychiatr Dis Treat 2009) 25 26
  5. [Role of zonisamid in treating epilepsy, Parkinson disorders and other neurological diseases]. (PMID: 20025128) Janszky J. (Ideggyogy Sz 2009) 25 26

Products for SCN3A Gene

Sources for SCN3A Gene

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