Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with four repeat domains, each of which is composed of six membrane-spanning segments, and one or more regulatory beta subunits. Voltage-gated sodium channels function in the generation and propagation of action potentials in neurons and muscle. This gene encodes one member ... See more...

Aliases for SCN2A Gene

Aliases for SCN2A Gene

  • Sodium Voltage-Gated Channel Alpha Subunit 2 2 3 5
  • Sodium Channel, Voltage-Gated, Type II, Alpha 1 Polypeptide 2 3
  • Sodium Channel, Voltage-Gated, Type II, Alpha 2 Polypeptide 2 3
  • Sodium Channel, Voltage-Gated, Type II, Alpha Subunit 2 3
  • Voltage-Gated Sodium Channel Subunit Alpha Nav1.2 3 4
  • Sodium Channel Protein Brain II Subunit Alpha 3 4
  • Sodium Channel Protein Type II Subunit Alpha 3 4
  • Sodium Channel Protein Type 2 Subunit Alpha 3 4
  • SCN2A1 3 4
  • SCN2A2 3 4
  • NAC2 3 4
  • Sodium Channel, Voltage Gated, Type II Alpha Subunit 2
  • Sodium Channel Protein, Brain Type 2 Alpha Subunit 3
  • Voltage-Gated Sodium Channel Type II Alpha Subunit 3
  • Voltage-Gated Sodium Channel Subtype II 3
  • Na(V)1.2 3
  • HBSC II 4
  • EIEE11 3
  • HBSCII 3
  • Nav1.2 3
  • BFIC3 3
  • BFIS3 3
  • BFNIS 3
  • HBSCI 3
  • HBA 3

External Ids for SCN2A Gene

Previous HGNC Symbols for SCN2A Gene

  • SCN2A1
  • SCN2A2

Previous GeneCards Identifiers for SCN2A Gene

  • GC02P165805
  • GC02P166095
  • GC02P157978

Summaries for SCN2A Gene

Entrez Gene Summary for SCN2A Gene

  • Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with four repeat domains, each of which is composed of six membrane-spanning segments, and one or more regulatory beta subunits. Voltage-gated sodium channels function in the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family. Allelic variants of this gene are associated with seizure disorders and autism spectrum disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]

GeneCards Summary for SCN2A Gene

SCN2A (Sodium Voltage-Gated Channel Alpha Subunit 2) is a Protein Coding gene. Diseases associated with SCN2A include Seizures, Benign Familial Infantile, 3 and Epileptic Encephalopathy, Early Infantile, 11. 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 SCN1A.

UniProtKB/Swiss-Prot Summary for SCN2A 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 (PubMed:1325650, PubMed:17021166, PubMed:28256214, PubMed:29844171). Implicated in the regulation of hippocampal replay occurring within sharp wave ripples (SPW-R) important for memory (By similarity).

Tocris Summary for SCN2A 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 SCN2A Gene

Additional gene information for SCN2A Gene

No data available for CIViC Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCN2A Gene

Genomics for SCN2A Gene

GeneHancer (GH) Regulatory Elements for SCN2A Gene

Promoters and enhancers for SCN2A 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
GH02J165293 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 505.1 +164.2 164152 1.4 ZBTB40 ZNF217 CTCF GABPA KLF4 RAD21 TRIM22 TEAD1 MXI1 HCFC1 SCN2A MAPRE1P3 lnc-CSRNP3-8 lnc-CSRNP3-7
GH02J165239 Promoter/Enhancer 1 VISTA EPDnew 500.1 +110.3 110253 2.2 EP300 CTCF REST RAD21 TRIM22 SMC3 MXI1 USF1 PKNOX1 ZNF654 SCN2A SCN3A RF00994-530 lnc-SCN3A-1
GH02J165003 Promoter 0.4 EPDnew 500.1 -126.2 -126174 0.1 NRF1 SCN2A piR-58297-268 lnc-SCN2A-5 ENSG00000236283
GH02J165203 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 10 +73.1 73052 2 EP300 CTCF RAD21 TRIM22 MXI1 SMC3 ZNF384 ZNF654 RCOR1 KDM1A SCN3A lnc-SCN3A-1 SCN2A piR-57461-122 ENSG00000236283
GH02J165016 Enhancer 0.8 Ensembl CraniofacialAtlas 10.7 -112.5 -112548 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 SCN2A on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCN2A

Top Transcription factor binding sites by QIAGEN in the SCN2A gene promoter:
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-5
  • HOXA5

Genomic Locations for SCN2A Gene

Genomic Locations for SCN2A Gene
chr2:165,130,149-165,392,310
(GRCh38/hg38)
Size:
262,162 bases
Orientation:
Plus strand
chr2:166,095,912-166,248,820
(GRCh37/hg19)
Size:
152,909 bases
Orientation:
Plus strand

Genomic View for SCN2A Gene

Genes around SCN2A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCN2A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCN2A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCN2A Gene

Proteins for SCN2A Gene

  • Protein details for SCN2A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q99250-SCN2A_HUMAN
    Recommended name:
    Sodium channel protein type 2 subunit alpha
    Protein Accession:
    Q99250
    Secondary Accessions:
    • A6NC14
    • A6NIQ5
    • Q14472
    • Q53T77
    • Q9BZC9
    • Q9BZD0

    Protein attributes for SCN2A Gene

    Size:
    2005 amino acids
    Molecular mass:
    227975 Da
    Quaternary structure:
    • Heterooligomer of a large alpha subunit and a smaller beta subunit. Heterooligomer with SCN2B or SCN4B; disulfide-linked. Heterooligomer with SCN1B or SCN3B; non-covalently linked. Interacts with NEDD4L. Interacts with CALM. Interacts with the conotoxin GVIIJ (PubMed:24497506). Interacts with the spider beta/delta-theraphotoxin-Pre1a (PubMed:28428547). Interacts with the conotoxin KIIIA (PubMed:30765605). Interacts with the spider protoxin-II (PubMed:26894959).
    SequenceCaution:
    • Sequence=CAA46438.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=CAA46438.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Sequence of unknown origin in the C-terminal part.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SCN2A Gene

    Alternative splice isoforms for SCN2A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCN2A Gene

Post-translational modifications for SCN2A Gene

  • May be ubiquitinated by NEDD4L; which would promote its endocytosis.
  • Phosphorylation at Ser-1506 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents.
  • Sumoylated at Lys-38. Sumoylation is induced by hypoxia, increases voltage-gated sodium current and mediates the early response to acute hypoxia in neurons. Sumoylated SCN2A is located at the cell membrane.
  • Glycosylation at Asn212, Asn285, Asn291, Asn297, Asn303, Asn308, Asn340, Asn1368, Asn1382, and Asn1393
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SCN2A Gene

Domains & Families for SCN2A Gene

Gene Families for SCN2A Gene

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

Protein Domains for SCN2A Gene

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

Suggested Antigen Peptide Sequences for SCN2A Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ75537, highly similar to Homo sapiens sodium channel, voltage-gated, type II, alpha 2 (SCN2A2), mRNA (A8K0U1_HUMAN)
  • Sodium channel, voltage-gated, type II, alpha 2, isoform CRA_a (D3DPB6_HUMAN)
  • Voltage-gated sodium channel subunit alpha Nav1.2 (SCN2A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q99250

UniProtKB/Swiss-Prot:

SCN2A_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. Nav1.2/SCN2A 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. Nav1.2/SCN2A subfamily.
genes like me logo Genes that share domains with SCN2A: view

Function for SCN2A Gene

Molecular function for SCN2A 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, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient (PubMed:1325650, PubMed:17021166, PubMed:28256214, PubMed:29844171). Implicated in the regulation of hippocampal replay occurring within sharp wave ripples (SPW-R) important for memory (By similarity).

Phenotypes From GWAS Catalog for SCN2A Gene

Gene Ontology (GO) - Molecular Function for SCN2A 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 ISS,TAS --
GO:0005272 sodium channel activity IEA --
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with SCN2A: view
genes like me logo Genes that share phenotypes with SCN2A: view

Human Phenotype Ontology for SCN2A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SCN2A Gene

MGI Knock Outs for SCN2A:

Animal Model Products

  • Taconic Biosciences Mouse Models for SCN2A

CRISPR Products

miRNA for SCN2A Gene

miRTarBase miRNAs that target SCN2A

Clone Products

  • Addgene plasmids for SCN2A

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SCN2A Gene

Localization for SCN2A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCN2A 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 SCN2A gene
Compartment Confidence
plasma membrane 5
cytosol 3
extracellular 2
cytoskeleton 2
mitochondrion 2
nucleus 2
endoplasmic reticulum 2
peroxisome 1
endosome 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for SCN2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001518 voltage-gated sodium channel complex IBA 21873635
GO:0005886 plasma membrane IBA,ISS --
GO:0005887 integral component of plasma membrane TAS 1325650
GO:0014704 intercalated disc IEA --
GO:0016020 membrane ISS --
genes like me logo Genes that share ontologies with SCN2A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SCN2A Gene

Pathways & Interactions for SCN2A Gene

PathCards logo

SuperPathways for SCN2A Gene

SuperPathway Contained pathways
1 Activation of cAMP-Dependent PKA
.77
.77
.56
2 Neuropathic Pain-Signaling in Dorsal Horn Neurons
.47
.47
.40
3 Developmental Biology
4 Cardiac conduction
5 Neuroscience
genes like me logo Genes that share pathways with SCN2A: view

Pathways by source for SCN2A Gene

7 Qiagen pathways for SCN2A Gene
  • Activation of cAMP-Dependent PKA
  • Aldosterone Signaling in Epithelial Cells
  • cAMP Pathway
  • Cholera Infection
  • GHRH Signaling
1 Cell Signaling Technology pathway for SCN2A Gene

SIGNOR curated interactions for SCN2A Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for SCN2A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006814 sodium ion transport TAS,ISS --
GO:0007399 nervous system development ISS --
GO:0007613 memory ISS --
GO:0008627 intrinsic apoptotic signaling pathway in response to osmotic stress ISS --
genes like me logo Genes that share ontologies with SCN2A: view

Drugs & Compounds for SCN2A Gene

(35) Drugs for SCN2A Gene - From: DrugBank, PharmGKB, DGIdb, IUPHAR, HMDB, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Lamotrigine Approved, Investigational Pharma blocker, Target, inhibitor 5-HT inhibitor 199
Phenytoin Approved, Vet_approved Pharma Pore Blocker, blocker, Target, inhibitor 87
Zonisamide Approved, Investigational Pharma blocker, Target, inhibitor Antiepileptic with anticonvulsant and mechanistic effect 73
Carbamazepine Approved, Investigational Pharma Target, inhibitor Inhibitor of neuronal voltage-gated Na+ channels; anticonvulsant 103
Oxcarbazepine Approved Pharma Target, inhibitor BTX inhibitor 62

(3) Additional Compounds for SCN2A Gene - From: HMDB, Novoseek, and Tocris

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

(3) Tocris Compounds for SCN2A 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
genes like me logo Genes that share compounds with SCN2A: view

Transcripts for SCN2A Gene

mRNA/cDNA for SCN2A Gene

5 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
18 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids for SCN2A

Alternative Splicing Database (ASD) splice patterns (SP) for SCN2A Gene

No ASD Table

Relevant External Links for SCN2A Gene

GeneLoc Exon Structure for
SCN2A

Expression for SCN2A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCN2A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCN2A Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x11.2), Brain - Cerebellum (x10.3), Brain - Frontal Cortex (BA9) (x5.3), and Brain - Anterior cingulate cortex (BA24) (x4.5).

Protein differential expression in normal tissues from HIPED for SCN2A Gene

This gene is overexpressed in Frontal cortex (55.6) and Brain (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SCN2A Gene



Protein tissue co-expression partners for SCN2A Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCN2A

SOURCE GeneReport for Unigene cluster for SCN2A Gene:

Hs.93485

Evidence on tissue expression from TISSUES for SCN2A Gene

  • Nervous system(4.9)
  • Blood(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SCN2A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • eye
  • face
  • forehead
  • head
  • lip
  • mouth
  • nose
  • pharynx
  • skull
Thorax:
  • chest wall
  • diaphragm
  • esophagus
  • lung
  • rib
  • rib cage
Abdomen:
  • abdominal wall
  • intestine
  • large intestine
  • stomach
Pelvis:
  • pelvis
  • rectum
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • upper limb
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with SCN2A: view

No data available for mRNA Expression by UniProt/SwissProt for SCN2A Gene

Orthologs for SCN2A Gene

This gene was present in the common ancestor of animals.

Orthologs for SCN2A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCN2A 31 30
  • 99.77 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SCN2A 31
  • 95 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SCN2A 31
  • 95 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SCN2A 31 30
  • 93.63 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SCN2A 31 30
  • 93.15 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Scn2a1 31 30
  • 89.46 (n)
OneToOne
Scn2a 17
rat
(Rattus norvegicus)
Mammalia Scn2a1 30
  • 88.74 (n)
chicken
(Gallus gallus)
Aves SCN2A 31 30
  • 83.59 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SCN2A 31
  • 91 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia scn3a 30
  • 75.66 (n)
African clawed frog
(Xenopus laevis)
Amphibia scn2a2-A 30
zebrafish
(Danio rerio)
Actinopterygii scn1lab 31 30
  • 71.88 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004707 30
  • 55.66 (n)
fruit fly
(Drosophila melanogaster)
Insecta para 30
  • 54.47 (n)
Species where no ortholog for SCN2A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 SCN2A Gene

ENSEMBL:
Gene Tree for SCN2A (if available)
TreeFam:
Gene Tree for SCN2A (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCN2A: view image

Paralogs for SCN2A Gene

(11) SIMAP similar genes for SCN2A Gene using alignment to 2 proteins:

  • SCN2A_HUMAN
  • A8K0U1_HUMAN

Pseudogenes.org Pseudogenes for SCN2A Gene

genes like me logo Genes that share paralogs with SCN2A: view

Variants for SCN2A Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCN2A Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
207086 Uncertain Significance: History of neurodevelopmental disorder 165,315,613(+) A/G MISSENSE_VARIANT
566988 Uncertain Significance: Benign familial neonatal-infantile seizures; Early infantile epileptic encephalopathy 11 165,354,449(+) A/G MISSENSE_VARIANT
567909 Uncertain Significance: Benign familial neonatal-infantile seizures; Early infantile epileptic encephalopathy 11 165,295,957(+) A/T MISSENSE_VARIANT
568298 Uncertain Significance: Benign familial neonatal-infantile seizures; Early infantile epileptic encephalopathy 11 165,308,788(+) C/G MISSENSE_VARIANT
574402 Uncertain Significance: Benign familial neonatal-infantile seizures; History of neurodevelopmental disorder; Early infantile epileptic encephalopathy 11 165,388,832(+) A/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for SCN2A Gene

Structural Variations from Database of Genomic Variants (DGV) for SCN2A Gene

Variant ID Type Subtype PubMed ID
dgv1179e212 CNV loss 25503493
esv5728 CNV gain 19470904
nsv526967 CNV loss 19592680
nsv528928 CNV loss 19592680
nsv963743 CNV duplication 23825009
nsv979143 CNV duplication 23825009

Variation tolerance for SCN2A Gene

Residual Variation Intolerance Score: 1.05% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.25; 70.16% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCN2A Gene

Human Gene Mutation Database (HGMD)
SCN2A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCN2A

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCN2A Gene

Disorders for SCN2A Gene

MalaCards: The human disease database

(67) MalaCards diseases for SCN2A Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search SCN2A in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SCN2A_HUMAN
  • Seizures, benign familial infantile, 3 (BFIS3) [MIM:607745]: A form of benign familial infantile epilepsy, a neurologic disorder characterized by afebrile seizures occurring in clusters during the first year of life, without neurologic sequelae. BFIS3 inheritance is autosomal dominant. {ECO:0000269 PubMed:11371648, ECO:0000269 PubMed:12243921, ECO:0000269 PubMed:15048894, ECO:0000269 PubMed:16417554, ECO:0000269 PubMed:17021166, ECO:0000269 PubMed:17386050, ECO:0000269 PubMed:18479388, ECO:0000269 PubMed:20371507, ECO:0000269 PubMed:22612257, ECO:0000269 PubMed:23360469, ECO:0000269 PubMed:23758435, ECO:0000269 PubMed:25982755, ECO:0000269 PubMed:26291284, ECO:0000269 PubMed:29844171, ECO:0000269 PubMed:30144217}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Epileptic encephalopathy, early infantile, 11 (EIEE11) [MIM:613721]: An autosomal dominant seizure disorder characterized by neonatal or infantile onset of refractory seizures with resultant delayed neurologic development and persistent neurologic abnormalities. Patients may progress to West syndrome, which is characterized by tonic spasms with clustering, arrest of psychomotor development, and hypsarrhythmia on EEG. {ECO:0000269 PubMed:19783390, ECO:0000269 PubMed:19786696, ECO:0000269 PubMed:20956790, ECO:0000269 PubMed:22677033, ECO:0000269 PubMed:23033978, ECO:0000269 PubMed:23195492, ECO:0000269 PubMed:23550958, ECO:0000269 PubMed:23662938, ECO:0000269 PubMed:23708187, ECO:0000269 PubMed:23935176, ECO:0000269 PubMed:23988467, ECO:0000269 PubMed:24463883, ECO:0000269 PubMed:24579881, ECO:0000269 PubMed:24659627, ECO:0000269 PubMed:24710820, ECO:0000269 PubMed:25457084, ECO:0000269 PubMed:25459969, ECO:0000269 PubMed:25772804, ECO:0000269 PubMed:25818041, ECO:0000269 PubMed:26138355, ECO:0000269 PubMed:26291284, ECO:0000269 PubMed:26993267, ECO:0000269 PubMed:27864847, ECO:0000269 PubMed:29625812, ECO:0000269 PubMed:29844171, ECO:0000269 PubMed:30144217, ECO:0000269 PubMed:30415926}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=Defects in SCN2A are associated with genetic epilepsy with febrile seizures plus (GEFS+), a familial autosomal dominant epilepsy syndrome, a clinical subset of febrile seizures, characterized by frequent episodes after 6 years of age and various types of subsequent epilepsy. {ECO:0000269 PubMed:29635106}.
  • Note=Defects in SCN2A are associated with autism spectrum disorders (ASD). It seems that mutations resulting in sodium channel gain of function and increased neuron excitability lead to infantile seizures, whereas variants resulting in sodium channel loss of function and decrease neuron excitability are associated with ASD. {ECO:0000269 PubMed:28256214}.

Additional Disease Information for SCN2A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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Publications for SCN2A Gene

  1. A nonsense mutation of the sodium channel gene SCN2A in a patient with intractable epilepsy and mental decline. (PMID: 15028761) Kamiya K … Yamakawa K (The Journal of neuroscience : the official journal of the Society for Neuroscience 2004) 3 4 23 54
  2. The voltage-gated sodium channel gene SCN2A and idiopathic generalized epilepsy. (PMID: 11738931) Haug K … Heils A (Epilepsy research 2001) 3 4 41 54
  3. Differential expression of two sodium channel subtypes in human brain. (PMID: 1317301) Lu CM … Brown GB (FEBS letters 1992) 2 3 4 54
  4. Molecular basis for pore blockade of human Na+ channel Nav1.2 by the μ-conotoxin KIIIA. (PMID: 30765605) Pan X … Yan N (Science (New York, N.Y.) 2019) 3 4 54
  5. Relationship of electrophysiological dysfunction and clinical severity in SCN2A-related epilepsies. (PMID: 30144217) Lauxmann S … Hedrich UBS (Human mutation 2018) 3 4 54

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