Scn3a sodium channel, voltage-gated, type III, alpha [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Scn3aprovided by MGI
Official Full Name: sodium channel, voltage-gated, type III, alphaprovided by MGI
Primary source: MGI:MGI:98249
See related: Ensembl:ENSMUSG00000057182 AllianceGenome:MGI:98249
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Gm1000; Nav1.3
Summary: Predicted to enable calmodulin binding activity; sodium ion binding activity; and voltage-gated sodium channel activity. Predicted to be involved in several processes, including neuronal action potential; response to pyrethroid; and sodium ion transmembrane transport. Predicted to act upstream of or within regulation of ion transmembrane transport and sodium ion transport. Located in cytoplasm and membrane. Is expressed in cerebral cortex; heart; sciatic nerve; sympathetic ganglion; and telencephalon. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 62 and focal epilepsy. Orthologous to human SCN3A (sodium voltage-gated channel alpha subunit 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in whole brain E14.5 (RPKM 13.5), CNS E18 (RPKM 13.4) and 6 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 2 C1.3; 2 38.55 cM

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (65287462..65397935, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (65457118..65567591, complement)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nav1.3 and FGF14 are primary determinants of the TTX-sensitive sodium current in mouse adrenal chromaffin cells.
Title: Nav1.3 and FGF14 are primary determinants of the TTX-sensitive sodium current in mouse adrenal chromaffin cells.
Nav1.3 is expressed in neutrophils in vivo and regulates attachment, transmigration, and chemotaxis.
Title: Sodium Channel Nav1.3 Is Expressed by Polymorphonuclear Neutrophils during Mouse Heart and Kidney Ischemia In Vivo and Regulates Adhesion, Transmigration, and Chemotaxis of Human and Mouse Neutrophils In Vitro.
enterochromaffin (EC) cells use Scn3a-encoded voltage-gated sodium channel NaV1.3 for electrical excitability and 5-HT release. NaV1.3-dependent electrical excitability and its contribution to 5-HT release is a novel mechanism of EC cell function
Title: Sodium channel Na(V)1.3 is important for enterochromaffin cell excitability and serotonin release.
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.
Scn3a was mapped to the QTL for febrile seizure susceptibility.
Title: Mapping of a FEB3 homologous febrile seizure locus on mouse chromosome 2 containing candidate genes Scn1a and Scn3a.
a huge difference in electrophysiological function between SCN1A and SCN3A mutations in the pore region; this might explain the more common SCN1A mutations detected in patients with epilepsy and the more severe phenotypes associated with these mutations
Title: Electrophysiological Differences between the Same Pore Region Mutation in SCN1A and SCN3A.
these findings suggest that CpG methylation and MBD2 are involved in altering Scn3a expression during postnatal development and seizure condition.
Title: Alteration of Scn3a expression is mediated via CpG methylation and MBD2 in mouse hippocampus during postnatal development and seizure condition.
the time course of declining expression of the murine embryonic sodium channel Nav 1.3 and the rise in expression of the adult sodium channel Nav 1.1 with susceptibility to epileptic seizures and increased incidence of sudden death
Title: Correlations in timing of sodium channel expression, epilepsy, and sudden death in Dravet syndrome.
These results suggest that the GC box and CpG methylation might play important roles in regulating mouse Scn3a gene expression.
Title: Promoter analysis of mouse Scn3a gene and regulation of the promoter activity by GC box and CpG methylation.
SCN2A, SCN3A, and SCN9A are expressed beneath tight junctions in subsets of taste cells. SCN3A and SCN9A are expressed in TRPM5 cells, while SCN2A was expressed in TRPM5 and PKD2L1 cells.
Title: Voltage-gated sodium channels in taste bud cells.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Variation

Go to the top of the page Help

Alleles

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

Gene trapped (1)
Targeted (3) 1 citation
Endonuclease-mediated (2)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

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

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

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

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

Scn3a (e-PCR), detects polymorphism
- UniSTS:516641

RH94597 (e-PCR)
- UniSTS:119845

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

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

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables calmodulin binding	ISO Inferred from Sequence Orthology more info
enables monoatomic cation channel activity	IEA Inferred from Electronic Annotation more info
enables monoatomic ion channel activity	IEA Inferred from Electronic Annotation more info
enables sodium channel activity	IEA Inferred from Electronic Annotation 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 sodium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables voltage-gated sodium channel activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in behavioral response to pain	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to antibiotic	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during action potential	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within monoatomic ion transmembrane transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within monoatomic ion transport	IEA Inferred from Electronic Annotation more info
involved_in monoatomic ion transport	IEA Inferred from Electronic Annotation more info
involved_in neuronal action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuronal action potential	ISO Inferred from Sequence Orthology more info
involved_in response to pyrethroid	ISO Inferred from Sequence Orthology more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within sodium ion transport	IEA Inferred from Electronic Annotation more info
involved_in sodium ion transport	IEA Inferred from Electronic Annotation more info
involved_in transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	ISO Inferred from Sequence Orthology more info
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
part_of monoatomic ion channel complex	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	TAS Traceable Author Statement more info
located_in sarcoplasm	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

General protein information

Go to the top of the page Help

Preferred Names: sodium channel protein type 3 subunit alpha

Names: sodium channel protein brain III subunit alpha; sodium channel protein type III subunit alpha; 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)

Go to the top of the page Help

NEW Try the new Transcript table

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_001355166.1 → NP_001342095.1 sodium channel protein type 3 subunit alpha isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AL772235, AL928621

Conserved Domains (5) summary

cd13433
Location:1470 → 1522

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

pfam00520
Location:1206 → 1478

Ion_trans; Ion transport protein

pfam06512
Location:998 → 1201

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 697

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

pfam16905
Location:1786 → 1849

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
NM_001355167.1 → NP_001342096.1 sodium channel protein type 3 subunit alpha isoform 2

Status: VALIDATED

Source sequence(s)

AL772235, AL928621

Conserved Domains (5) summary

cd13433
Location:1453 → 1505

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

pfam00520
Location:1189 → 1461

Ion_trans; Ion transport protein

pfam06512
Location:981 → 1184

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 680

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

pfam16905
Location:1769 → 1832

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
NM_001355168.1 → NP_001342097.1 sodium channel protein type 3 subunit alpha isoform 3

Status: VALIDATED

Source sequence(s)

AL772235, AL928621

Conserved Domains (5) summary

cd13433
Location:1424 → 1476

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

pfam00520
Location:1160 → 1432

Ion_trans; Ion transport protein

pfam06512
Location:952 → 1155

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 651

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

pfam16905
Location:1740 → 1803

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
NM_001355169.1 → NP_001342098.1 sodium channel protein type 3 subunit alpha isoform 4

Status: VALIDATED

Source sequence(s)

AL772235, AL928621

Conserved Domains (5) summary

cd13433
Location:1424 → 1476

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

pfam00520
Location:1160 → 1432

Ion_trans; Ion transport protein

pfam06512
Location:952 → 1155

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 651

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

pfam16905
Location:1740 → 1803

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
NM_001355170.1 → NP_001342099.1 sodium channel protein type 3 subunit alpha isoform 6

Status: VALIDATED

Source sequence(s)

AL772235, AL928621

Conserved Domains (5) summary

cd13433
Location:1421 → 1473

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

pfam00520
Location:1157 → 1429

Ion_trans; Ion transport protein

pfam06512
Location:949 → 1152

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 648

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

pfam16905
Location:1737 → 1800

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
NM_001355171.1 → NP_001342100.1 sodium channel protein type 3 subunit alpha isoform 7

Status: VALIDATED

Source sequence(s)

AL772235, AL928621

Conserved Domains (5) summary

cd13433
Location:835 → 887

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

pfam00520
Location:571 → 843

Ion_trans; Ion transport protein

pfam06512
Location:363 → 566

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:40 → 62

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

pfam16905
Location:1151 → 1214

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
NM_018732.3 → NP_061202.3 sodium channel protein type 3 subunit alpha isoform 5

Status: VALIDATED

Source sequence(s)

AK048407, AK141113, AK148881, AL928621, CD348085, CJ126715, CJ133030, CX562753

Consensus CDS

CCDS50596.1

UniProtKB/Swiss-Prot

A0A0R5RP23, A0A0R5RP41, A2ASI5

Related

ENSMUSP00000097647.3, ENSMUST00000100069.9

Conserved Domains (5) summary

cd13433
Location:1421 → 1473

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

pfam00520
Location:1157 → 1429

Ion_trans; Ion transport protein

pfam06512
Location:949 → 1152

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 648

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

pfam16905
Location:1737 → 1800

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

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

65287462..65397935 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011239391.2 → XP_011237693.1 sodium channel protein type 3 subunit alpha isoform X1

Conserved Domains (5) summary

cd13433
Location:1470 → 1522

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

pfam00520
Location:1206 → 1478

Ion_trans; Ion transport protein

pfam06512
Location:998 → 1201

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:513 → 710

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

pfam16905
Location:1794 → 1841

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_006499031.4 → XP_006499094.1 sodium channel protein type 3 subunit alpha isoform X2

Conserved Domains (3) summary

pfam00520
Location:759 → 972

Ion_trans; Ion transport protein

pfam06512
Location:998 → 1118

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:513 → 710

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