Scn2a sodium channel, voltage-gated, type II, alpha [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Scn2aprovided by MGI
Official Full Name: sodium channel, voltage-gated, type II, alphaprovided by MGI
Primary source: MGI:MGI:98248
See related: Ensembl:ENSMUSG00000075318 AllianceGenome:MGI:98248
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Nav1.2; Scn2a1; 6430408L10; A230052E19Rik
Summary: 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 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. In humans, variants of this gene are associated with seizure disorders and autism spectrum disorder. Mice homozygous for a knockout mutation die with severe hypoxia and extensive neuronal cell death, while gain of function mutations result in progressive seizure disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2016]
Expression: Biased expression in cerebellum adult (RPKM 21.0), cortex adult (RPKM 18.1) and 4 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 C1.3; 2 38.61 cM

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (65451108..65597791)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (65620764..65767447)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Physical and functional convergence of the autism risk genes Scn2a and Ank2 in neocortical pyramidal cell dendrites.
Title: Physical and functional convergence of the autism risk genes Scn2a and Ank2 in neocortical pyramidal cell dendrites.
Experimental and computational evidence that Calpain-10 binds to the carboxy terminus of NaV1.2 and NaV1.6.
Title: Experimental and computational evidence that Calpain-10 binds to the carboxy terminus of Na(V)1.2 and Na(V)1.6.
Inversed Effects of Nav1.2 Deficiency at Medial Prefrontal Cortex and Ventral Tegmental Area for Prepulse Inhibition in Acoustic Startle Response.
Title: Inversed Effects of Nav1.2 Deficiency at Medial Prefrontal Cortex and Ventral Tegmental Area for Prepulse Inhibition in Acoustic Startle Response.
Dynamic Foraging Behavior Performance Is Not Affected by Scn2a Haploinsufficiency.
Title: Dynamic Foraging Behavior Performance Is Not Affected by Scn2a Haploinsufficiency.
Deficiency of autism-related Scn2a gene in mice disrupts sleep patterns and circadian rhythms.
Title: Deficiency of autism-related Scn2a gene in mice disrupts sleep patterns and circadian rhythms.
SCN2A contributes to oligodendroglia excitability and development in the mammalian brain.
Title: SCN2A contributes to oligodendroglia excitability and development in the mammalian brain.
Generation and basic characterization of a gene-trap knockout mouse model of Scn2a with a substantial reduction of voltage-gated sodium channel Nav 1.2 expression.
Title: Generation and basic characterization of a gene-trap knockout mouse model of Scn2a with a substantial reduction of voltage-gated sodium channel Na(v) 1.2 expression.
Paradoxical hyperexcitability from NaV1.2 sodium channel loss in neocortical pyramidal cells.
Title: Paradoxical hyperexcitability from Na(V)1.2 sodium channel loss in neocortical pyramidal cells.
Severe deficiency of the voltage-gated sodium channel NaV1.2 elevates neuronal excitability in adult mice.
Title: Severe deficiency of the voltage-gated sodium channel Na(V)1.2 elevates neuronal excitability in adult mice.
Antisense oligonucleotide therapy reduces seizures and extends life span in an SCN2A gain-of-function epilepsy model.
Title: Antisense oligonucleotide therapy reduces seizures and extends life span in an SCN2A gain-of-function epilepsy model.

Submit: New GeneRIF Correction See all GeneRIFs (34)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (6) 1 citation
Targeted (11) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Scn1a (e-PCR), detects polymorphism
- UniSTS:516634

Scn1a (e-PCR), detects polymorphism
- UniSTS:516635

Scn2a1 (e-PCR), detects polymorphism
- UniSTS:516638

Scn2a1 (e-PCR), detects polymorphism
- UniSTS:516639

Scn3a (e-PCR), detects polymorphism
- UniSTS:516640

Scn1a (e-PCR), detects polymorphism
- UniSTS:463470

Scn1a (e-PCR), detects polymorphism
- UniSTS:463471

D3Wox9 (e-PCR)
- UniSTS:142318

D2Kyo1 (e-PCR), detects polymorphism
- UniSTS:142318

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables calmodulin binding	IEA Inferred from Electronic Annotation more info
enables calmodulin binding	ISO Inferred from Sequence Orthology more info
enables leucine zipper domain binding	ISO Inferred from Sequence Orthology more info
enables sodium channel activity	TAS Traceable Author Statement more info
enables sodium ion binding	ISO Inferred from Sequence Orthology more info
enables voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	ISO Inferred from Sequence Orthology more info
enables voltage-gated sodium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables voltage-gated sodium channel activity	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated sodium channel activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables voltage-gated sodium channel activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to hypoxia	ISO Inferred from Sequence Orthology more info
involved_in cellular response to hypoxia	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within dentate gyrus development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within determination of adult lifespan	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to osmotic stress	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in membrane depolarization during action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in memory	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nerve development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within nerve development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuronal action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuronal action potential	IEA Inferred from Electronic Annotation more info
involved_in neuronal action potential	ISO Inferred from Sequence Orthology more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in sodium ion transmembrane transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sodium ion transmembrane transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sodium ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in sodium ion transport	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in T-tubule	IDA Inferred from Direct Assay more info	PubMed
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in axon	ISO Inferred from Sequence Orthology more info
located_in axon initial segment	ISO Inferred from Sequence Orthology more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in intercalated disc	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in node of Ranvier	ISO Inferred from Sequence Orthology more info
located_in paranode region of axon	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	TAS Traceable Author Statement more info
is_active_in presynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
part_of voltage-gated sodium channel complex	IBA Inferred from Biological aspect of Ancestor more info
part_of voltage-gated sodium channel complex	ISO Inferred from Sequence Orthology more info
part_of voltage-gated sodium channel complex	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: sodium channel protein type 2 subunit alpha

Names: sodium channel, voltage-gated, type II, alpha 1; sodium channel, voltage-gated, type II, alpha polypeptide 1; voltage-gated sodium channel subunit alpha Nav1.2

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.

mRNA and Protein(s)

NM_001099298.3 → NP_001092768.1 sodium channel protein type 2 subunit alpha

See identical proteins and their annotated locations for NP_001092768.1

Status: REVIEWED

Source sequence(s)

AL772235, BX284648

Consensus CDS

CCDS38130.1

UniProtKB/Swiss-Prot

A0A0J9YTW6, B1AWN6

UniProtKB/TrEMBL

A0A0R5RP29

Related

ENSMUSP00000097645.4, ENSMUST00000100067.7

Conserved Domains (5) summary

cd13433
Location:1475 → 1527

Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits

pfam00520
Location:1208 → 1483

Ion_trans; Ion transport protein

pfam06512
Location:998 → 1204

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:516 → 700

Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel

pfam16905
Location:1791 → 1854

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
NM_001346679.2 → NP_001333608.1 sodium channel protein type 2 subunit alpha

Status: REVIEWED

Source sequence(s)

AL772235, BX284648

Consensus CDS

CCDS84529.1

UniProtKB/TrEMBL

A0A0R5RP29, A0A5H1ZRM8
NM_001346680.1 → NP_001333609.1 sodium channel protein type 2 subunit alpha

Status: REVIEWED

Source sequence(s)

AL772235, BX284648

Consensus CDS

CCDS84529.1

UniProtKB/TrEMBL

A0A0R5RP29, A0A5H1ZRM8

Related

ENSMUSP00000143882.2, ENSMUST00000200829.4

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

65451108..65597791

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017314945.1 → XP_017170434.1 sodium channel protein type 2 subunit alpha isoform X1

UniProtKB/TrEMBL

A0A0R5RP29

Conserved Domains (5) summary

cd13433
Location:1403 → 1455

Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits

pfam00520
Location:1136 → 1411

Ion_trans; Ion transport protein

pfam06512
Location:926 → 1132

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:444 → 638

Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel

pfam16905
Location:1727 → 1774

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_006498583.5 → XP_006498646.1 sodium channel protein type 2 subunit alpha isoform X2

UniProtKB/TrEMBL

A0A0R5RP29

Conserved Domains (5) summary

cd13433
Location:1224 → 1276

Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits

pfam00520
Location:957 → 1232

Ion_trans; Ion transport protein

pfam06512
Location:747 → 953

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:265 → 459

Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel

pfam16905
Location:1548 → 1595

GPHH; Voltage-dependent L-type calcium channel, IQ-associated