SCN1B (sodium voltage-gated channel beta subunit 1)

Gene

• Entrez ID: 6324
• Gene name: Sodium voltage-gated channel beta subunit 1
• Gene symbol: SCN1B
• Synonyms: ATFB13, BRGDA5, DEE52, EIEE52, GEFSP1
• Chromosome: 19
• Chromosome location: 19q13.11
• Summary: Voltage-gated sodium channels are heteromeric proteins that function in the generation and propagation of action potentials in muscle and neuronal cells. They are composed of one alpha and two beta subunits, where the alpha subunit provides channel activity and the beta-1 subunit modulates the kinetics of channel inactivation. This gene encodes a sodium channel beta-1 subunit. Mutations in this gene result in generalized epilepsy with febrile seizures plus, Brugada syndrome 5, and defects in cardiac conduction. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs16969925	G>A	Pathogenic	Coding sequence variant, missense variant
rs66876876	G>A	Benign-likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant, coding sequence variant, missense variant
rs72552027	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity, benign-likely-benign	Coding sequence variant, genic upstream transcript variant, missense variant, upstream transcript variant
rs72558026	G>A	Benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant, coding sequence variant, missense variant
rs72558028	G>A,C	Likely-benign, benign, benign-likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant, coding sequence variant, missense variant
rs104894718	C>A,G,T	Pathogenic-likely-pathogenic, pathogenic, likely-pathogenic	Synonymous variant, coding sequence variant, missense variant, stop gained
rs121434627	G>A,C,T	Pathogenic	Stop gained, coding sequence variant, missense variant
rs193922728	G>A	Likely-pathogenic, uncertain-significance	Missense variant, coding sequence variant, intron variant
rs267607028	G>A	Pathogenic, uncertain-significance	Coding sequence variant, stop gained, intron variant
rs267607029	G>A	Pathogenic	Coding sequence variant, stop gained, intron variant
rs369032304	G>A,T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, intron variant
rs724159982	A>C	Pathogenic	Splice acceptor variant
rs786205830	C>T	Conflicting-interpretations-of-pathogenicity, likely-pathogenic	Missense variant, coding sequence variant
rs786205837	G>A	Pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant
rs794727487	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs931949929	A>G,T	Pathogenic	Missense variant, coding sequence variant
rs1057519457	A>T	Pathogenic	Coding sequence variant, missense variant
rs1064794589	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1135401736	C>T	Pathogenic	Coding sequence variant, missense variant
rs1600364712	T>G	Pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT016821	hsa-miR-335-5p	Microarray	18185580
MIRT038411	hsa-miR-296-3p	CLASH	23622248
MIRT047007	hsa-miR-210-3p	CLASH	23622248
MIRT531880	hsa-miR-4755-3p	PAR-CLIP	22012620
MIRT531881	hsa-miR-4632-3p	PAR-CLIP	22012620
MIRT531882	hsa-miR-6846-3p	PAR-CLIP	22012620
MIRT531883	hsa-miR-6752-3p	PAR-CLIP	22012620
MIRT531884	hsa-miR-6810-3p	PAR-CLIP	22012620
MIRT531885	hsa-miR-6801-3p	PAR-CLIP	22012620
MIRT531886	hsa-miR-6785-3p	PAR-CLIP	22012620
MIRT531887	hsa-miR-136-3p	PAR-CLIP	22012620

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001518	Component	Voltage-gated sodium channel complex	IBA	21873635
GO:0001518	Component	Voltage-gated sodium channel complex	IDA	8125980, 19808477, 21051419, 30190309
GO:0005244	Function	Voltage-gated ion channel activity	IEA
GO:0005248	Function	Voltage-gated sodium channel activity	IDA	19808477
GO:0005515	Function	Protein binding	IPI	26900580, 30190309
GO:0005576	Component	Extracellular region	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0005887	Component	Integral component of plasma membrane	IDA	19710327, 30190309
GO:0007155	Process	Cell adhesion	IEA
GO:0007411	Process	Axon guidance	ISS
GO:0010765	Process	Positive regulation of sodium ion transport	IDA	19808477
GO:0010976	Process	Positive regulation of neuron projection development	ISS
GO:0014704	Component	Intercalated disc	ISS
GO:0017080	Function	Sodium channel regulator activity	IDA	8125980, 18464934, 19710327, 19808477
GO:0019227	Process	Neuronal action potential propagation	ISS
GO:0019871	Function	Sodium channel inhibitor activity	IBA	21873635
GO:0019871	Function	Sodium channel inhibitor activity	ISS	17884088
GO:0021966	Process	Corticospinal neuron axon guidance	ISS
GO:0030315	Component	T-tubule	ISS
GO:0033268	Component	Node of Ranvier	ISS
GO:0035725	Process	Sodium ion transmembrane transport	IDA	18464934, 19808477, 21051419
GO:0040011	Process	Locomotion	ISS
GO:0043204	Component	Perikaryon	IEA
GO:0044325	Function	Ion channel binding	IBA	21873635
GO:0046684	Process	Response to pyrethroid	IEA
GO:0051899	Process	Membrane depolarization	IDA	21051419
GO:0060048	Process	Cardiac muscle contraction	IMP	19808477
GO:0060307	Process	Regulation of ventricular cardiac muscle cell membrane repolarization	ISS	17884088
GO:0060371	Process	Regulation of atrial cardiac muscle cell membrane depolarization	IMP	19808477, 22247482
GO:0061337	Process	Cardiac conduction	ISS
GO:0061337	Process	Cardiac conduction	TAS
GO:0086002	Process	Cardiac muscle cell action potential involved in contraction	IBA	21873635
GO:0086002	Process	Cardiac muscle cell action potential involved in contraction	IMP	19808477
GO:0086006	Function	Voltage-gated sodium channel activity involved in cardiac muscle cell action potential	IMP	19808477
GO:0086012	Process	Membrane depolarization during cardiac muscle cell action potential	ISS	17884088
GO:0086047	Process	Membrane depolarization during Purkinje myocyte cell action potential	IMP	18464934
GO:0086062	Function	Voltage-gated sodium channel activity involved in Purkinje myocyte action potential	IMP	18464934
GO:0086091	Process	Regulation of heart rate by cardiac conduction	IBA	21873635
GO:0086091	Process	Regulation of heart rate by cardiac conduction	IMP	19808477
GO:1905150	Process	Regulation of voltage-gated sodium channel activity	IEA
GO:2000649	Process	Regulation of sodium ion transmembrane transporter activity	IBA	21873635
GO:2000649	Process	Regulation of sodium ion transmembrane transporter activity	IDA	19808477

Other IDs

• MIM: 600235
• HGNC: 10586
• e!Ensembl: ENSG00000105711

Protein

• UniProt ID: Q07699
• Protein name: Sodium channel subunit beta-1
• Protein function: Regulatory subunit of multiple voltage-gated sodium channel complexes that play important roles in excitable membranes in brain, heart and skeletal muscle. Enhances the presence of the pore-forming alpha subunit at the cell surface and modulates channel gating characteristics and the rate of channel inactivation. Modulates the activity of multiple pore-forming alpha subunits, such as SCN1A, SCN2A, SCN3A, SCN4A, SCN5A and SCN10A. ; [Isoform 2]: Cell adhesion molecule that plays a critical role in neuronal migration and pathfinding during brain development. Stimulates neurite outgrowth (PubMed:21994374). Has no regulatory function on the SCN2A sodium channel complex (PubMed:14622265).
• PDB: 6AGF, 6J8G, 6J8H, 6J8I, 6J8J
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF07686	V-set	23 → 146	Immunoglobulin V-set domain	Domain

• Sequence:

  MGRLLALVVGAALVSSACGGCVEVDSETEAVYGMTFKILCISCKRRSETNAETFTEWTFR
  QKGTEEFVKILRYENEVLQLEEDERFEGRVVWNGSRGTKDLQDLSIFITNVTYNHSGDYE
  CHVYRLLFFENYEHNTSVVKKIHIEVVDKANRDMASIVSEIMMYVLIVVLTIWLVAEMIY
  CYKKIAAATETAAQENASEYLAITSESKENCTGVQVAE

• Sequence length: 218