Scn5a sodium channel, voltage-gated, type V, alpha [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Scn5aprovided by MGI
Official Full Name: sodium channel, voltage-gated, type V, alphaprovided by MGI
Primary source: MGI:MGI:98251
See related: Ensembl:ENSMUSG00000032511 AllianceGenome:MGI:98251
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: mH1; SkM1; SkM2; Nav1.5; Nav1.5c
Summary: Enables scaffold protein binding activity; ubiquitin protein ligase binding activity; and voltage-gated sodium channel activity involved in SA node cell action potential. Involved in sodium ion transmembrane transport. Acts upstream of or within cardiac ventricle development; regulation of heart contraction; and response to organic cyclic compound. Located in several cellular components, including T-tubule; intercalated disc; and lateral plasma membrane. Part of sodium channel complex. Is expressed in several structures, including central nervous system; gut; heart; sensory organ; and skeleton. Used to study Brugada syndrome 1; dilated cardiomyopathy 1E; long QT syndrome 3; progressive familial heart block type IA; and sick sinus syndrome. Human ortholog(s) of this gene implicated in heart conduction disease (multiple); intrinsic cardiomyopathy (multiple); and sudden infant death syndrome. Orthologous to human SCN5A (sodium voltage-gated channel alpha subunit 5). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in heart adult (RPKM 37.1) and lung adult (RPKM 3.7) See more
Orthologs: human all
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Genomic context

Location:: 9 F3; 9 71.33 cM

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (119312470..119408096, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (119483404..119579030, complement)

Chromosome 9 - NC_000075.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

In Vivo Base Editing of Scn5a Rescues Type 3 Long QT Syndrome in Mice.
Title: In Vivo Base Editing of Scn5a Rescues Type 3 Long QT Syndrome in Mice.
MYT1L haploinsufficiency in human neurons and mice causes autism-associated phenotypes that can be reversed by genetic and pharmacologic intervention.
Title: MYT1L haploinsufficiency in human neurons and mice causes autism-associated phenotypes that can be reversed by genetic and pharmacologic intervention.
SUMOylation of the cardiac sodium channel NaV1.5 modifies inward current and cardiac excitability.
Title: SUMOylation of the cardiac sodium channel Na(V)1.5 modifies inward current and cardiac excitability.
Enhanced sodium channel inactivation by temperature and FHF2 deficiency blocks heat nociception.
Title: Enhanced sodium channel inactivation by temperature and FHF2 deficiency blocks heat nociception.
Familial atrial fibrillation mutation M1875T-SCN5A increases early sodium current and dampens the effect of flecainide.
Title: Familial atrial fibrillation mutation M1875T-SCN5A increases early sodium current and dampens the effect of flecainide.
Association between SCN5A R225Q variant and dilated cardiomyopathy: potential role of intracellular pH and WNT/beta-catenin pathway.
Title: Association between SCN5A R225Q variant and dilated cardiomyopathy: potential role of intracellular pH and WNT/β-catenin pathway.
Transmembrane protein 168 mutation reduces cardiomyocyte cell surface expression of Nav1.5 through alphaB-crystallin intracellular dynamics.
Title: Transmembrane protein 168 mutation reduces cardiomyocyte cell surface expression of Nav1.5 through αB-crystallin intracellular dynamics.
Phospho-ablation of cardiac sodium channel Nav1.5 mitigates susceptibility to atrial fibrillation and improves glucose homeostasis under conditions of diet-induced obesity.
Title: Phospho-ablation of cardiac sodium channel Na(v)1.5 mitigates susceptibility to atrial fibrillation and improves glucose homeostasis under conditions of diet-induced obesity.
Targeting the Microtubule EB1-CLASP2 Complex Modulates NaV1.5 at Intercalated Discs.
Title: Targeting the Microtubule EB1-CLASP2 Complex Modulates Na(V)1.5 at Intercalated Discs.
Structural and Functional Characterization of a Nav1.5-Mitochondrial Couplon.
Title: Structural and Functional Characterization of a Na(v)1.5-Mitochondrial Couplon.

Submit: New GeneRIF Correction See all GeneRIFs (80)

Variation

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Alleles

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

Endonuclease-mediated (4) 1 citation
Targeted (19) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

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

Scn4a (e-PCR), detects polymorphism
- UniSTS:516642

Scn5a (e-PCR), detects polymorphism
- UniSTS:516644

Scn5a (e-PCR), detects polymorphism
- UniSTS:516645

PMC122928P1 (e-PCR)
- UniSTS:270417

D9Dcr134 (e-PCR), detects polymorphism
- UniSTS:499036

D9Mit82 (e-PCR), detects polymorphism
- UniSTS:116365

RH94513 (e-PCR)
- UniSTS:119761

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ankyrin binding	ISO Inferred from Sequence Orthology more info
enables calmodulin binding	IEA Inferred from Electronic Annotation more info
enables calmodulin binding	ISO Inferred from Sequence Orthology more info
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables fibroblast growth factor binding	ISO Inferred from Sequence Orthology more info
enables nitric-oxide synthase binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables scaffold protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables scaffold protein binding	ISO Inferred from Sequence Orthology more info
enables transmembrane transporter binding	ISO Inferred from Sequence Orthology more info
enables ubiquitin protein ligase binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase binding	ISO Inferred from Sequence Orthology more info
enables voltage-gated sodium channel activity	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated sodium channel activity	ISO Inferred from Sequence Orthology more info
enables voltage-gated sodium channel activity involved in AV node cell action potential	ISO Inferred from Sequence Orthology more info
enables voltage-gated sodium channel activity involved in Purkinje myocyte action potential	ISO Inferred from Sequence Orthology more info
enables voltage-gated sodium channel activity involved in SA node cell action potential	IMP Inferred from Mutant Phenotype more info	PubMed
enables voltage-gated sodium channel activity involved in SA node cell action potential	ISO Inferred from Sequence Orthology more info
enables voltage-gated sodium channel activity involved in bundle of His cell action potential	ISO Inferred from Sequence Orthology more info
enables voltage-gated sodium channel activity involved in cardiac muscle cell action potential	IBA Inferred from Biological aspect of Ancestor more info
enables voltage-gated sodium channel activity involved in cardiac muscle cell action potential	IMP Inferred from Mutant Phenotype more info	PubMed
enables voltage-gated sodium channel activity involved in cardiac muscle cell action potential	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in AV node cell action potential	ISO Inferred from Sequence Orthology more info
involved_in AV node cell to bundle of His cell communication	ISO Inferred from Sequence Orthology more info
involved_in SA node cell action potential	ISO Inferred from Sequence Orthology more info
involved_in atrial cardiac muscle cell action potential	ISO Inferred from Sequence Orthology more info
involved_in bundle of His cell action potential	ISO Inferred from Sequence Orthology more info
involved_in cardiac muscle cell action potential involved in contraction	ISO Inferred from Sequence Orthology more info
involved_in cardiac muscle contraction	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cardiac ventricle development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to calcium ion	ISO Inferred from Sequence Orthology more info
involved_in cellular response to calcium ion	ISS Inferred from Sequence or Structural Similarity more info
involved_in membrane depolarization	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during AV node cell action potential	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during Purkinje myocyte cell action potential	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during SA node cell action potential	IEA Inferred from Electronic Annotation more info
involved_in membrane depolarization during SA node cell action potential	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in membrane depolarization during action potential	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during atrial cardiac muscle cell action potential	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during bundle of His cell action potential	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during cardiac muscle cell action potential	IEA Inferred from Electronic Annotation more info
involved_in membrane depolarization during cardiac muscle cell action potential	ISO Inferred from Sequence Orthology more info
involved_in neuronal action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of action potential	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of heart rate	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of sodium ion transport	ISO Inferred from Sequence Orthology more info
involved_in regulation of atrial cardiac muscle cell membrane depolarization	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of atrial cardiac muscle cell membrane depolarization	ISO Inferred from Sequence Orthology more info
involved_in regulation of atrial cardiac muscle cell membrane repolarization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cardiac muscle cell contraction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cardiac muscle cell contraction	ISO Inferred from Sequence Orthology more info
involved_in regulation of heart rate	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of heart rate	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of heart rate by cardiac conduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of heart rate by cardiac conduction	ISO Inferred from Sequence Orthology more info
involved_in regulation of sodium ion transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in regulation of ventricular cardiac muscle cell membrane depolarization	ISO Inferred from Sequence Orthology more info
involved_in regulation of ventricular cardiac muscle cell membrane repolarization	ISO Inferred from Sequence Orthology more info
involved_in response to denervation involved in regulation of muscle adaptation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to organic cyclic compound	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sodium ion import across plasma membrane	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	IDA Inferred from Direct Assay more info	PubMed
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
involved_in sodium ion transport	ISO Inferred from Sequence Orthology more info
involved_in ventricular cardiac muscle cell action potential	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in T-tubule	IDA Inferred from Direct Assay more info	PubMed
located_in T-tubule	ISO Inferred from Sequence Orthology more info
located_in Z disc	ISO Inferred from Sequence Orthology more info
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in caveola	ISO Inferred from Sequence Orthology more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum	ISO Inferred from Sequence Orthology more info
located_in intercalated disc	IDA Inferred from Direct Assay more info	PubMed
located_in intercalated disc	ISO Inferred from Sequence Orthology more info
located_in lateral plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in sarcolemma	ISO Inferred from Sequence Orthology more info
part_of sodium channel complex	IPI Inferred from Physical Interaction 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	IC Inferred by Curator more info	PubMed
part_of voltage-gated sodium channel complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: sodium channel protein type 5 subunit alpha

Names: sodium channel protein cardiac muscle subunit alpha; sodium channel protein type V subunit alpha; sodium channel, voltage-gated, type V, alpha polypeptide; voltage-gated sodium channel subunit alpha Nav1.5

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_001253860.1 → NP_001240789.1 sodium channel protein type 5 subunit alpha isoform 2

See identical proteins and their annotated locations for NP_001240789.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) switches an exon in the coding region, compared to variant 1. The resulting protein (isoform 2) is the same length as isoform 1 yet it has a different sequence.

Source sequence(s)

AC121922, AK085822, AK147254

Consensus CDS

CCDS57715.1

UniProtKB/Swiss-Prot

E9Q1D2, Q3UH91, Q9JJV9

UniProtKB/TrEMBL

K3W4N7

Related

ENSMUSP00000066228.7, ENSMUST00000065196.13

Conserved Domains (5) summary

cd13433
Location:1474 → 1526

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

pfam00520
Location:1207 → 1482

Ion_trans; Ion transport protein

pfam06512
Location:955 → 1203

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:485 → 667

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

pfam16905
Location:1797 → 1844

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
NM_021544.4 → NP_067519.2 sodium channel protein type 5 subunit alpha isoform 1

See identical proteins and their annotated locations for NP_067519.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and it encodes the longer protein (isoform 1).

Source sequence(s)

AK085822, AK147254

Consensus CDS

CCDS52965.1

UniProtKB/Swiss-Prot

E9Q1D2, Q3UH91, Q9JJV9

UniProtKB/TrEMBL

A0A0R4J1M7

Related

ENSMUSP00000112838.2, ENSMUST00000117911.8

Conserved Domains (5) summary

cd13433
Location:1474 → 1526

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

pfam00520
Location:1225 → 1482

Ion_trans; Ion transport protein

pfam06512
Location:955 → 1203

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:485 → 577

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

pfam16905
Location:1795 → 1852

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_000075.7 Reference GRCm39 C57BL/6J

Range

119312470..119408096 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006511997.1 → XP_006512060.1 sodium channel protein type 5 subunit alpha isoform X4

See identical proteins and their annotated locations for XP_006512060.1

UniProtKB/Swiss-Prot

E9Q1D2, Q3UH91, Q9JJV9

UniProtKB/TrEMBL

K3W4N7

Related

ENSMUSP00000113272.2, ENSMUST00000120420.2

Conserved Domains (5) summary

cd13433
Location:1474 → 1526

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

pfam00520
Location:1207 → 1482

Ion_trans; Ion transport protein

pfam06512
Location:955 → 1203

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:485 → 667

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

pfam16905
Location:1797 → 1844

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_006511996.1 → XP_006512059.1 sodium channel protein type 5 subunit alpha isoform X3

UniProtKB/TrEMBL

A0A0R5RP31

Conserved Domains (5) summary

cd13433
Location:1485 → 1537

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

pfam00520
Location:1218 → 1493

Ion_trans; Ion transport protein

pfam06512
Location:1020 → 1214

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:550 → 732

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

pfam16905
Location:1808 → 1855

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_006511995.1 → XP_006512058.1 sodium channel protein type 5 subunit alpha isoform X2

UniProtKB/Swiss-Prot

E9Q1D2, Q3UH91, Q9JJV9

Conserved Domains (5) summary

cd13433
Location:1538 → 1590

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

pfam00520
Location:1271 → 1546

Ion_trans; Ion transport protein

pfam06512
Location:1020 → 1267

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:550 → 732

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

pfam16905
Location:1861 → 1908

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_006511993.1 → XP_006512056.1 sodium channel protein type 5 subunit alpha isoform X1

UniProtKB/Swiss-Prot

E9Q1D2, Q3UH91, Q9JJV9

Conserved Domains (5) summary

cd13433
Location:1539 → 1591

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

pfam00520
Location:1272 → 1547

Ion_trans; Ion transport protein

pfam06512
Location:1020 → 1268

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:550 → 732

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

pfam16905
Location:1862 → 1909

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