Human Gene SCN3B (ENST00000392770.6) from GENCODE V44
  Description: Homo sapiens sodium voltage-gated channel beta subunit 3 (SCN3B), transcript variant 1, mRNA. (from RefSeq NM_018400)
RefSeq Summary (NM_018400): Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel beta subunit gene family, and influences the inactivation kinetics of the sodium channel. Two alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000392770.6
Gencode Gene: ENSG00000166257.10
Transcript (Including UTRs)
   Position: hg38 chr11:123,629,189-123,654,604 Size: 25,416 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg38 chr11:123,634,143-123,653,801 Size: 19,659 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr11:123,629,189-123,654,604)mRNA (may differ from genome)Protein (215 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Sodium channel subunit beta-3; Flags: Precursor;
FUNCTION: Modulates channel gating kinetics. Causes unique persistent sodium currents. Inactivates the sodium channel opening more slowly than the subunit beta-1. Its association with neurofascin may target the sodium channels to the nodes of Ranvier of developing axons and retain these channels at the nodes in mature myelinated axons (By similarity).
SUBUNIT: The voltage-sensitive sodium channel consists of an ion conducting pore forming alpha-subunit regulated by one or more beta-1, beta-2 and/or beta-3 subunits. Beta-1 and beta-3 are non- covalently associated with alpha, while beta-2 is covalently linked by disulfide bonds. Beta-1 or beta-3 subunits associate with neurofascin. Associates with SCN10A (By similarity).
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
DISEASE: Defects in SCN3B are the cause of Brugada syndrome type 7 (BRGDA7) [MIM:613120]. A tachyarrhythmia characterized by right bundle branch block and ST segment elevation on an electrocardiogram (ECG). It can cause the ventricles to beat so fast that the blood is prevented from circulating efficiently in the body. When this situation occurs (called ventricular fibrillation), the individual will faint and may die in a few minutes if the heart is not reset.
SIMILARITY: Belongs to the sodium channel auxiliary subunit SCN3B (TC 8.A.17) family.
SIMILARITY: Contains 1 Ig-like C2-type (immunoglobulin-like) domain.
SEQUENCE CAUTION: Sequence=BAA86472.1; Type=Erroneous initiation;

-  Primer design for this transcript

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Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: SCN3B
Diseases sorted by gene-association score: brugada syndrome 7* (1319), scn3b-related familial atrial fibrillation* (500), brugada syndrome* (146), familial atrial fibrillation* (88), atrial fibrillation (14), right bundle branch block (8), short qt syndrome (5), sudden infant death syndrome (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 34.65 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 250.32 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -408.10803-0.508 Picture PostScript Text
3' UTR -1324.704610-0.287 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub
IPR013106 - Ig_V-set

Pfam Domains:
PF07686 - Immunoglobulin V-set domain

ModBase Predicted Comparative 3D Structure on Q9NY72
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005244 voltage-gated ion channel activity
GO:0005248 voltage-gated sodium channel activity
GO:0005272 sodium channel activity
GO:0017080 sodium channel regulator activity
GO:0044325 ion channel binding
GO:0086006 voltage-gated sodium channel activity involved in cardiac muscle cell action potential

Biological Process:
GO:0006811 ion transport
GO:0006814 sodium ion transport
GO:0007399 nervous system development
GO:0010460 positive regulation of heart rate
GO:0010765 positive regulation of sodium ion transport
GO:0019233 sensory perception of pain
GO:0034765 regulation of ion transmembrane transport
GO:0035725 sodium ion transmembrane transport
GO:0051899 membrane depolarization
GO:0060048 cardiac muscle contraction
GO:0060371 regulation of atrial cardiac muscle cell membrane depolarization
GO:0060373 regulation of ventricular cardiac muscle cell membrane depolarization
GO:0061337 cardiac conduction
GO:0072659 protein localization to plasma membrane
GO:0086002 cardiac muscle cell action potential involved in contraction
GO:0086005 ventricular cardiac muscle cell action potential
GO:0086010 membrane depolarization during action potential
GO:0086012 membrane depolarization during cardiac muscle cell action potential
GO:0086014 atrial cardiac muscle cell action potential
GO:0086015 SA node cell action potential
GO:0086091 regulation of heart rate by cardiac conduction
GO:2000649 regulation of sodium ion transmembrane transporter activity

Cellular Component:
GO:0001518 voltage-gated sodium channel complex
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030018 Z disc

-  Descriptions from all associated GenBank mRNAs
  AK055033 - Homo sapiens cDNA FLJ30471 fis, clone BRAWH1000045.
AB032984 - Homo sapiens KIAA1158 mRNA for KIAA1158 protein.
BC045704 - Homo sapiens sodium channel, voltage-gated, type III, beta, mRNA (cDNA clone IMAGE:5311260).
AL136589 - Homo sapiens mRNA; cDNA DKFZp761F182 (from clone DKFZp761F182).
JD269002 - Sequence 250026 from Patent EP1572962.
JD410846 - Sequence 391870 from Patent EP1572962.
JD189332 - Sequence 170356 from Patent EP1572962.
JD299951 - Sequence 280975 from Patent EP1572962.
JD347919 - Sequence 328943 from Patent EP1572962.
JD534061 - Sequence 515085 from Patent EP1572962.
JD095761 - Sequence 76785 from Patent EP1572962.
JD356249 - Sequence 337273 from Patent EP1572962.
JD511745 - Sequence 492769 from Patent EP1572962.
JD425882 - Sequence 406906 from Patent EP1572962.
JD441187 - Sequence 422211 from Patent EP1572962.
JD244036 - Sequence 225060 from Patent EP1572962.
JD190980 - Sequence 172004 from Patent EP1572962.
JD335749 - Sequence 316773 from Patent EP1572962.
JD511372 - Sequence 492396 from Patent EP1572962.
JD414549 - Sequence 395573 from Patent EP1572962.
JD524759 - Sequence 505783 from Patent EP1572962.
JD352547 - Sequence 333571 from Patent EP1572962.
JD183641 - Sequence 164665 from Patent EP1572962.
JD564272 - Sequence 545296 from Patent EP1572962.
JD362784 - Sequence 343808 from Patent EP1572962.
JD531328 - Sequence 512352 from Patent EP1572962.
JD048644 - Sequence 29668 from Patent EP1572962.
BC117282 - Homo sapiens sodium channel, voltage-gated, type III, beta, mRNA (cDNA clone MGC:150891 IMAGE:40125833), complete cds.
BC126265 - Homo sapiens sodium channel, voltage-gated, type III, beta, mRNA (cDNA clone MGC:161543 IMAGE:8991981), complete cds.
JD046853 - Sequence 27877 from Patent EP1572962.
JD308991 - Sequence 290015 from Patent EP1572962.
JD147056 - Sequence 128080 from Patent EP1572962.
JD131254 - Sequence 112278 from Patent EP1572962.
JD172838 - Sequence 153862 from Patent EP1572962.
JD420364 - Sequence 401388 from Patent EP1572962.
JD564232 - Sequence 545256 from Patent EP1572962.
JD552271 - Sequence 533295 from Patent EP1572962.
JD322275 - Sequence 303299 from Patent EP1572962.
JD322276 - Sequence 303300 from Patent EP1572962.
JD213141 - Sequence 194165 from Patent EP1572962.
JD407602 - Sequence 388626 from Patent EP1572962.
JD567119 - Sequence 548143 from Patent EP1572962.
JD127161 - Sequence 108185 from Patent EP1572962.
JD348833 - Sequence 329857 from Patent EP1572962.
JD060877 - Sequence 41901 from Patent EP1572962.
JD260965 - Sequence 241989 from Patent EP1572962.
JD231255 - Sequence 212279 from Patent EP1572962.
JD049852 - Sequence 30876 from Patent EP1572962.
JD250876 - Sequence 231900 from Patent EP1572962.
AJ243396 - Homo sapiens mRNA for voltage-gated sodium channel beta-3 subunit (scn3b gene).
JD132958 - Sequence 113982 from Patent EP1572962.
JD421297 - Sequence 402321 from Patent EP1572962.
JD085483 - Sequence 66507 from Patent EP1572962.
JD111384 - Sequence 92408 from Patent EP1572962.
JD190834 - Sequence 171858 from Patent EP1572962.
JD499921 - Sequence 480945 from Patent EP1572962.
JD322477 - Sequence 303501 from Patent EP1572962.
JD264046 - Sequence 245070 from Patent EP1572962.
AK314513 - Homo sapiens cDNA, FLJ95332, Homo sapiens voltage-gated sodium channel beta-3 subunit (scn3b gene) (HSA243396), mRNA.
AB384126 - Synthetic construct DNA, clone: pF1KSDA1158, Homo sapiens SCN3B gene for sodium channel subunit beta-3 precursor, complete cds, without stop codon, in Flexi system.
HQ258123 - Synthetic construct Homo sapiens clone IMAGE:100072432 sodium channel, voltage-gated, type III, beta (SCN3B), transcript variant 2 (SCN3B) gene, encodes complete protein.
KJ894262 - Synthetic construct Homo sapiens clone ccsbBroadEn_03656 SCN3B gene, encodes complete protein.
AM393297 - Synthetic construct Homo sapiens clone IMAGE:100001723 for hypothetical protein (SCN3B gene).
JD559887 - Sequence 540911 from Patent EP1572962.
JD464970 - Sequence 445994 from Patent EP1572962.
JD347952 - Sequence 328976 from Patent EP1572962.
JD394926 - Sequence 375950 from Patent EP1572962.
JD457928 - Sequence 438952 from Patent EP1572962.
JD322567 - Sequence 303591 from Patent EP1572962.
JD507281 - Sequence 488305 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9NY72 (Reactome details) participates in the following event(s):

R-HSA-373739 Ankyrins link voltage-gated sodium and potassium channels to spectrin and L1
R-HSA-5576895 SCNAs:SNCBs transport Na+ from extracellular region to cytosol
R-HSA-445095 Interaction between L1 and Ankyrins
R-HSA-5576892 Phase 0 - rapid depolarisation
R-HSA-373760 L1CAM interactions
R-HSA-5576891 Cardiac conduction
R-HSA-422475 Axon guidance
R-HSA-397014 Muscle contraction
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: A5H1I5, ENST00000392770.1, ENST00000392770.2, ENST00000392770.3, ENST00000392770.4, ENST00000392770.5, KIAA1158, NM_018400, Q17RL3, Q9NY72, Q9ULR2, SCN3B_HUMAN, uc001pzb.1, uc001pzb.2
UCSC ID: ENST00000392770.6
RefSeq Accession: NM_018400
Protein: Q9NY72 (aka SCN3B_HUMAN or CIB3_HUMAN)
CCDS: CCDS8442.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SCN3B:
brugada (Brugada Syndrome)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.