SCN3A Gene (Protein Coding)

Sodium Voltage-Gated Channel Alpha Subunit 3

GC02M165087
GIFtS:
48
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... See more...

Aliases for SCN3A Gene

Aliases for SCN3A Gene

  • Sodium Voltage-Gated Channel Alpha Subunit 3 2 3 5
  • Sodium Channel, Voltage-Gated, Type III, Alpha Polypeptide 2 3
  • Sodium Channel, Voltage Gated, Type III Alpha Subunit 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
  • Sodium Channel Protein Type 3 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
  • EIEE62 3
  • FFEVF4 3
  • 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 Epilepsy, Familial Focal, With Variable Foci 4 and Epileptic Encephalopathy, Early Infantile, 62. Among its related pathways are Neuropathic Pain-Signaling in Dorsal Horn Neurons and Interaction between L1 and Ankyrins. Gene Ontology (GO) annotations related to this gene include ion channel activity and voltage-gated sodium channel activity. An important paralog of this gene is SCN2A.

UniProtKB/Swiss-Prot Summary 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, forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient (PubMed:24157691, PubMed:28235671, PubMed:29466837). May contribute to the regulation of serotonin/5-hydroxytryptamine release by enterochromaffin cells (By similarity). In pancreatic endocrine cells, required for both glucagon and glucose-induced insulin secretion (By similarity).

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

Additional gene information for SCN3A Gene

No data available for CIViC Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCN3A Gene

Genomics for SCN3A Gene

GeneHancer (GH) Regulatory Elements for SCN3A Gene

Promoters and enhancers for SCN3A Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH02J165203 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 500.7 +0.9 887 2 EP300 CTCF RAD21 TRIM22 MXI1 SMC3 ZNF384 ZNF654 RCOR1 KDM1A SCN3A lnc-SCN3A-1 SCN2A piR-57461-122 ENSG00000236283
GH02J165196 Promoter 0.3 EPDnew 500.4 +7.5 7534 0.1 SCN3A SCN2A piR-57461-122 ENSG00000236283
GH02J165067 Enhancer 1.2 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 9.6 +135.8 135797 1.6 EP300 RFX1 POLR2A SMC3 ZBTB17 MXI1 ZNF335 IKZF3 SMARCA4 ZNF366 SCN3A CSRNP3 SCN2A lnc-SCN2A-5 ENSG00000236283
GH02J165239 Promoter/Enhancer 1 VISTA EPDnew 10.8 -36.3 -36314 2.2 EP300 CTCF REST RAD21 TRIM22 SMC3 MXI1 USF1 PKNOX1 ZNF654 SCN2A SCN3A RF00994-530 lnc-SCN3A-1
GH02J165016 Enhancer 0.8 Ensembl CraniofacialAtlas 11.4 +186.5 186487 2.8 EP300 CTCF RFX1 RAD21 MXI1 SMC3 YY1 ZNF654 ZSCAN16 TEAD3 SLC38A11 SCN3A SCN2A lnc-SCN2A-5 piR-58297-268 ENSG00000236283
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCN3A on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCN3A

Top Transcription factor binding sites by QIAGEN in the SCN3A gene promoter:
  • AREB6
  • E47
  • GR
  • GR-alpha
  • GR-beta
  • NRF-2
  • POU2F1
  • POU2F1a
  • Sox5
  • Sox9

Genomic Locations for SCN3A Gene

Genomic Locations for SCN3A Gene
chr2:165,087,520-165,204,088
(GRCh38/hg38)
Size:
116,569 bases
Orientation:
Minus strand
chr2:165,944,030-166,060,577
(GRCh37/hg19)
Size:
116,548 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 Structure • Gene Density

RefSeq DNA sequence for SCN3A Gene

Proteins for SCN3A Gene

Products:

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  • 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:
    • Heterooligomer of a large alpha subunit and 2-3 smaller beta subunits. Heterooligomer with SCN2B or SCN4B; disulfide-linked. Interacts with NEDD4L (PubMed:15548568). Interacts with the conotoxin GVIIJ (PubMed:24497506).

    Alternative splice isoforms for SCN3A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCN3A Gene

Protein Expression for SCN3A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

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 Asn211, Asn290, Asn296, Asn302, Asn307, Asn339, Asn1366, and Asn1380
  • Modification sites at PhosphoSitePlus

Other Protein References for SCN3A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SCN3A Gene

Domains & Families for SCN3A Gene

Gene Families for SCN3A Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • FDA approved drug targets
  • Plasma proteins
  • Predicted membrane proteins
  • Voltage-gated ion channels

Protein Domains for SCN3A Gene

Blocks:
  • IQ calmodulin-binding region
  • Voltage-gated Na+ channel alpha subunit signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SCN3A Gene

GenScript: Design optimal peptide antigens:
  • Voltage-gated sodium channel alpha subunit splice variant SCN3A-s (Q9C007_HUMAN)
  • Voltage-gated sodium channel (Q9GZM4_HUMAN)
  • Voltage-gated sodium channel subunit alpha Nav1.3 (SCN3A_HUMAN)

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.
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

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Molecular function for SCN3A Gene

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, forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient (PubMed:24157691, PubMed:28235671, PubMed:29466837). May contribute to the regulation of serotonin/5-hydroxytryptamine release by enterochromaffin cells (By similarity). In pancreatic endocrine cells, required for both glucagon and glucose-induced insulin secretion (By similarity).
GENATLAS Biochemistry:
sodium voltage-gated channel,type III,alpha polypeptide,expressed in brain,encoding two isoforms (neonatal and adult)

Phenotypes From GWAS Catalog for SCN3A Gene

Gene Ontology (GO) - Molecular Function for SCN3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity IEA --
GO:0005244 voltage-gated ion channel activity IEA --
GO:0005248 voltage-gated sodium channel activity NAS 9589372
GO:0005272 sodium channel activity IEA --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with SCN3A: view
genes like me logo Genes that share phenotypes with SCN3A: view

Human Phenotype Ontology for SCN3A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SCN3A Gene

MGI Knock Outs for SCN3A:

Animal Model Products

  • Taconic Biosciences Mouse Models for SCN3A

CRISPR Products

miRNA for SCN3A Gene

miRTarBase miRNAs that target SCN3A

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCN3A

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SCN3A Gene

Localization for SCN3A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCN3A Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCN3A gene
Compartment Confidence
plasma membrane 4
extracellular 2
cytoskeleton 2
nucleus 2
mitochondrion 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SCN3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001518 voltage-gated sodium channel complex IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SCN3A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SCN3A Gene

Pathways & Interactions for SCN3A Gene

PathCards logo

SuperPathways for SCN3A Gene

SuperPathway Contained pathways
1 Activation of cAMP-Dependent PKA
Activation of cAMP-Dependent PKA
.77
cAMP Pathway
.77
PKA Signaling
.56
2 Neuropathic Pain-Signaling in Dorsal Horn Neurons
Aldosterone Signaling in Epithelial Cells
.47
Neuropathic Pain-Signaling in Dorsal Horn Neurons
.47
Cholera Infection
.40
3 Developmental Biology
Axon guidance
.51
Developmental Biology
.51
4 Cardiac conduction
Cardiac conduction
.70
Muscle contraction
.70
5 Taste transduction
Taste transduction
.35
genes like me logo Genes that share pathways with SCN3A: view

Pathways by source for SCN3A Gene

1 KEGG pathway for SCN3A Gene
7 Qiagen pathways for SCN3A Gene
  • Activation of cAMP-Dependent PKA
  • Aldosterone Signaling in Epithelial Cells
  • cAMP Pathway
  • Cholera Infection
  • GHRH Signaling

SIGNOR curated interactions for SCN3A Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for SCN3A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006814 sodium ion transport NAS 9589372
GO:0019228 neuronal action potential IBA 21873635
GO:0034220 ion transmembrane transport IEA --
GO:0034765 regulation of ion transmembrane transport IEA --
genes like me logo Genes that share ontologies with SCN3A: view

Drugs & Compounds for SCN3A Gene

Products:

  1. Drug

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Carbamazepine Approved, Investigational Pharma Target, inhibitor Inhibitor of neuronal voltage-gated Na+ channels; anticonvulsant 103
Zonisamide Approved, Investigational Pharma blocker, Target, inhibitor Antiepileptic with anticonvulsant and mechanistic effect 73
Oxcarbazepine Approved Pharma Target, inhibitor BTX inhibitor 62
Phenytoin Approved, Vet_approved Pharma Pore Blocker, Target 87
Amylocaine Approved, Withdrawn Pharma Target, blocker 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Na(+)
  • Na+
  • SODIUM ion
 7440-23-5
Amiloride hydrochloride
2016-88-8

(3) Tocris Compounds for SCN3A Gene

Compound Action Cas Number
Amiloride hydrochloride Na+ channel blocker; also I2 imidazoline ligand 2016-88-8
Carbamazepine Inhibitor of neuronal voltage-gated Na+ channels; anticonvulsant 298-46-4
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

Drug Products

Transcripts for SCN3A Gene

Products:

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mRNA/cDNA for SCN3A Gene

3 REFSEQ mRNAs :
19 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCN3A

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

Expression for SCN3A Gene

Products:

  1. Primer
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCN3A Gene

mRNA expression in normal human tissues for SCN3A Gene
mRNA expression by GTEx for SCN3A GenemRNA expression by BioGPS 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 and MOPED for SCN3A Gene



Protein tissue co-expression partners for SCN3A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCN3A

SOURCE GeneReport for Unigene cluster for SCN3A Gene:

Hs.435274

mRNA Expression by UniProt/SwissProt for SCN3A Gene:

Q9NY46-SCN3A_HUMAN
Tissue specificity: Expressed in enterochromaffin cells in both colon and small bowel (at protein level).

Evidence on tissue expression from TISSUES for SCN3A Gene

  • Nervous system(4.6)
  • Kidney(4.2)
genes like me logo Genes that share expression patterns with SCN3A: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer 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
chimpanzee
(Pan troglodytes)
 Mammalia SCN3A 31 30
  • 99.78 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia SCN3A 31 30
  • 93.68 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia SCN3A 31 30
  • 93.61 (n)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia SCN3A 31
  • 93 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Scn3a 17 31 30
  • 89.57 (n)
rat
(Rattus norvegicus)
 Mammalia Scn3a 30
  • 89.34 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia SCN3A 31
  • 88 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves SCN3A 31 30
  • 83.02 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia SCN3A 31
  • 87 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia LOC100488621 30
  • 77.26 (n)
zebrafish
(Danio rerio)
 Actinopterygii scn1lab 31
  • 78 (a)
 OneToMany
fruit fly
(Drosophila melanogaster)
 Insecta NaCP60E 32
  • 63 (a)
para 32
  • 50 (a)
Species where no ortholog for SCN3A was found in the sources mined by GeneCards:
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for SCN3A: view image

Paralogs for SCN3A Gene

Paralogs for SCN3A Gene

(23) SIMAP similar genes for SCN3A Gene using alignment to 7 proteins:

  • SCN3A_HUMAN
  • C9JBM7_HUMAN
  • E7EUE6_HUMAN
  • F5H4V8_HUMAN
  • L8E9G6_HUMAN
  • Q9C007_HUMAN
  • Q9GZM4_HUMAN
genes like me logo Genes that share paralogs with SCN3A: view

Variants for SCN3A Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCN3A Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
586501 Benign: not provided 165,139,597(-) T/A SYNONYMOUS_VARIANT
586502 Uncertain Significance: not provided 165,176,351(-) C/T MISSENSE_VARIANT
586503 Uncertain Significance: not provided 165,090,953(-) C/G MISSENSE_VARIANT
586504 Benign: not provided 165,164,383(-) G/A INTRON_VARIANT
594198 Uncertain Significance: not provided 165,139,507(-) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for SCN3A Gene

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

Variant ID Type Subtype PubMed ID
dgv2081n106 CNV deletion 24896259
dgv7153n54 CNV loss 21841781
dgv7154n54 CNV loss 21841781
dgv7155n54 CNV loss 21841781
esv2554394 CNV deletion 19546169
esv2585640 CNV deletion 19546169
esv25924 CNV loss 19812545
esv2666303 CNV deletion 23128226
esv2667791 CNV deletion 23128226
esv2673049 CNV deletion 23128226
esv2721067 CNV deletion 23290073
esv3335133 CNV insertion 20981092
esv3560470 CNV deletion 23714750
esv3593232 CNV loss 21293372
esv3593233 CNV loss 21293372
esv7053 CNV loss 19470904
esv8404 CNV gain 19470904
esv992100 CNV gain 20482838
nsv213574 CNV deletion 16902084
nsv435715 CNV deletion 17901297
nsv511183 CNV gain 21212237
nsv583561 CNV loss 21841781
nsv583564 CNV loss 21841781
nsv583578 CNV loss 21841781
nsv583582 CNV loss 21841781
nsv821783 CNV loss 20364138
nsv961524 CNV duplication 23825009
nsv963742 CNV duplication 23825009

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)

Additional Variant Information for SCN3A Gene

Human Gene Mutation Database (HGMD)
SCN3A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCN3A

SNP Genotyping and Copy Number Assay Products

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

Disorders for SCN3A Gene

MalaCards: The human disease database

(33) MalaCards diseases for SCN3A Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

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UniProtKB/Swiss-Prot

SCN3A_HUMAN
  • Epilepsy, familial focal, with variable foci 4 (FFEVF4) [MIM:617935]: An autosomal dominant form of epilepsy characterized by focal seizures arising from different cortical regions, including the temporal, frontal, parietal, and occipital lobes. Seizure types commonly include temporal lobe epilepsy, frontal lobe epilepsy, and nocturnal frontal lobe epilepsy. Some patients may have intellectual disability or autism spectrum disorders. Seizure onset usually occurs in the first or second decades, although later onset has been reported, and there is phenotypic variability within families. A subset of patients have structural brain abnormalities. Penetrance of the disorder is incomplete. FFEVF4 is characterized by onset of focal seizures in the first years of life. {ECO:0000269 PubMed:24157691, ECO:0000269 PubMed:28235671}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Epileptic encephalopathy, early infantile, 62 (EIEE62) [MIM:617938]: A form of epileptic encephalopathy, a heterogeneous group of severe childhood onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. EIEE62 is characterized by onset of seizures in the first year of life. {ECO:0000269 PubMed:29466837}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SCN3A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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No data available for 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 CM … Brown GB (Journal of molecular neuroscience : MN 1998) 2 3 4 54
  2. Targeted gene walking by low stringency polymerase chain reaction: assignment of a putative human brain sodium channel gene (SCN3A) to chromosome 2q24-31. (PMID: 8159690) Malo MS … Ingram VM (Proceedings of the National Academy of Sciences of the United States of America 1994) 3 4 23 54
  3. Mutations in SCN3A cause early infantile epileptic encephalopathy. (PMID: 29466837) Zaman T … Goldberg EM (Annals of neurology 2018) 3 4 54
  4. SCN3A deficiency associated with increased seizure susceptibility. (PMID: 28235671) Lamar T … Kearney JA (Neurobiology of disease 2017) 3 4 54
  5. Novel SCN3A variants associated with focal epilepsy in children. (PMID: 24157691) Vanoye CG … Kearney JA (Neurobiology of disease 2014) 3 4 54

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