Human Gene SCN5A (uc021wvq.1)
  Description: Homo sapiens sodium channel, voltage-gated, type V, alpha subunit (SCN5A), transcript variant 2, mRNA.
RefSeq Summary (NM_000335): The protein encoded by this gene is an integral membrane protein and tetrodotoxin-resistant voltage-gated sodium channel subunit. This protein is found primarily in cardiac muscle and is responsible for the initial upstroke of the action potential in an electrocardiogram. Defects in this gene are a cause of long QT syndrome type 3 (LQT3), an autosomal dominant cardiac disease. Alternative splicing results in several transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr3:38,589,553-38,691,164 Size: 101,612 Total Exon Count: 28 Strand: -
Coding Region
   Position: hg19 chr3:38,597,227-38,674,798 Size: 77,572 Coding Exon Count: 25 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesGeneReviewsModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:38,589,553-38,691,164)mRNA (may differ from genome)Protein (2015 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHuman Cortex Gene ExpressionLynxMalacards
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SCN5A
CDC HuGE Published Literature: SCN5A
Positive Disease Associations: atrial fibrillation , Brugada syndrome , cardiac arrhythmias and sudden death , cardiac conduction disturbances and degenerative changes , Drug-induced long-QT syndrome , early onset of sudden infant death. , Electrocardiographic conduction measures , Electrocardiography , Heart Function Tests , inherited cardiac arrhythmia long QT syndrome , QT interval , SIDS/sudden infant death syndrome
Related Studies:
  1. atrial fibrillation
    Chen, L. Y. et al. 2007, A Common Polymorphism in SCN5A is Associated with Lone Atrial Fibrillation, Clin Pharmacol Ther 2007 81(1) 35-41. [PubMed 17185997]
  2. Brugada syndrome
    Shin, D. J. et al. 2004, Genetic analysis of the cardiac sodium channel gene SCN5A in Koreans with Brugada syndrome, Journal of human genetics. 2004 ;49(10):573-8. [PubMed 15338453]
    This mutation was not found in 150 unrelated normal individuals. This finding is the first report of a novel mutation in SCN5A associated with Brugada syndrome in Koreans.
  3. Brugada syndrome
    Rook MB et al. 1999, Human SCN5A gene mutations alter cardiac sodium channel kinetics and are associated with the Brugada syndrome., Cardiovascular research. 1999 Dec;44(3):507-17. [PubMed 10690282]
    Two SCN5A mutations associated with the Brugada syndrome, significantly affect cardiac sodium channel characteristics. The alterations seem to be associated with an increase in inward sodium current during the action potential upstroke.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SCN5A
Diseases sorted by gene-association score: long qt syndrome-3* (1376), brugada syndrome 1* (1363), heart block, progressive, type ia* (1320), atrial fibrillation, familial, 10* (1231), sick sinus syndrome 1* (1230), sudden infant death syndrome* (944), brugada syndrome* (941), ventricular fibrillation, familial, 1* (820), familial sick sinus syndrome* (794), cardiomyopathy, dilated, 1e* (712), long qt syndrome* (514), scn5a-associated dilated cardiomyopathy* (500), scn5a-related dilated cardiomyopathy* (500), scn5a-related familial atrial fibrillation* (500), sick sinus syndrome 1, autosomal recessive* (500), sick sinus syndrome* (483), atrial standstill* (389), familial progressive cardiac conduction defect* (375), idiopathic ventricular fibrillation, non brugada type* (375), atrial fibrillation* (321), brugada syndrome 5* (283), paroxysmal ventricular fibrillation* (265), familial isolated dilated cardiomyopathy* (247), familial long qt syndrome* (242), long qt syndrome 1* (233), myh7-related dilated cardiomyopathy* (231), arrhythmogenic right ventricular cardiomyopathy* (207), familial atrial fibrillation* (191), dilated cardiomyopathy* (117), scn5a-related disorders* (100), scn5a-related brugada syndrome* (100), scn5a-related romano ward syndrome* (100), atrial standstill, digenic* (90), progressive familial heart block (66), right bundle branch block (48), atrioventricular block (33), sudden cardiac death (28), heart disease (15), syncope (14), brugada syndrome 2 (13), cardiac arrest (12), heart conduction disease (11), cardiac conduction disease with or without dilated cardiomyopathy (11), first-degree atrioventricular block (11), cardiac conduction defect (11), sinoatrial node disease (10), ventricular tachycardia, catecholaminergic polymorphic, 1 (10), intrinsic cardiomyopathy (10), familial hemiplegic migraine (9), peripartum cardiomyopathy (9), keshan disease (9), long qt syndrome 2 (8), long qt syndrome 13 (8), long qt syndrome 6 (8), long qt syndrome 5 (7), hemiplegic migraine (7), jervell and lange-nielsen syndrome (6), long qt syndrome 12 (6), long qt syndrome 9 (6), arrhythmogenic right ventricular dysplasia 5 (6), third-degree atrioventricular block (6), critical illness polyneuropathy (5), left ventricular noncompaction (5), short qt syndrome (5), cardiomyopathy (5), andersen syndrome (4), catecholaminergic polymorphic ventricular tachycardia (4)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 24.98 RPKM in Heart - Left Ventricle
Total median expression: 58.49 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 -89.70195-0.460 Picture PostScript Text
3' UTR -1504.613848-0.391 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
  Pfam Domains:
PF00520 - Ion transport protein
PF00612 - IQ calmodulin-binding motif
PF06512 - Sodium ion transport-associated
PF08016 - Polycystin cation channel
PF11933 - Cytoplasmic domain of voltage-gated Na+ ion channel

SCOP Domains:
81324 - Voltage-gated potassium channels

ModBase Predicted Comparative 3D Structure on Q14524-2
FrontTopSide
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
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AY038064 - Homo sapiens voltage-gated sodium channel type V alpha subunit jejunal variant (SCN5A) mRNA, complete cds.
M77235 - Human cardiac tetrodotoxin-insensitive voltage-dependent sodium channel alpha subunit (HH1) mRNA, complete cds.
BC140813 - Homo sapiens sodium channel, voltage-gated, type V, alpha subunit, mRNA (cDNA clone MGC:176490 IMAGE:9021681), complete cds.
BC144621 - Homo sapiens sodium channel, voltage-gated, type V, alpha subunit, mRNA (cDNA clone MGC:178169 IMAGE:9053152), complete cds.
AB158469 - Homo sapiens Nav1.5 mRNA for TTX-resistant sodium channel, complete cds.
AB158470 - Homo sapiens Nav1.5 mRNA for TTX-resistant sodium channel splicing variant, complete cds.
AY148488 - Homo sapiens cardiac sodium channel alpha subunit Nav1.5 mRNA, complete cds.
AF482988 - Homo sapiens cardiac sodium channel alpha subunit (H1B) mRNA, complete cds.
GU014840 - Synthetic construct Homo sapiens clone IMAGE:100068744; MGC:198458 voltage-gated sodium channel type V alpha isoform a (SCN5A) gene, encodes complete protein.
KC858891 - Homo sapiens cell-line THP-1 NaV1.5 variant (SCN5A) mRNA, complete cds, alternatively spliced.
EF629346 - Homo sapiens Nav1.5 Na+ channel mRNA, complete cds, alternatively spliced.
EF629347 - Homo sapiens Nav1.5 Na+ channel mRNA, complete cds, alternatively spliced.
BC051374 - Homo sapiens sodium channel, voltage-gated, type V, alpha subunit, mRNA (cDNA clone IMAGE:6671632), complete cds.
AB208866 - Homo sapiens mRNA for voltage-gated sodium channel type V alpha isoform b variant protein.
EF092293 - Homo sapiens cardiac sodium channel alpha subunit variant (SCN5A) mRNA, partial cds, alternatively spliced.
JD401368 - Sequence 382392 from Patent EP1572962.
JD383402 - Sequence 364426 from Patent EP1572962.
JD179197 - Sequence 160221 from Patent EP1572962.
JD106744 - Sequence 87768 from Patent EP1572962.
JD538580 - Sequence 519604 from Patent EP1572962.
JD406432 - Sequence 387456 from Patent EP1572962.
JD119567 - Sequence 100591 from Patent EP1572962.
JD347578 - Sequence 328602 from Patent EP1572962.
JD290189 - Sequence 271213 from Patent EP1572962.
JD500799 - Sequence 481823 from Patent EP1572962.
JD438771 - Sequence 419795 from Patent EP1572962.
JD099772 - Sequence 80796 from Patent EP1572962.
JD246522 - Sequence 227546 from Patent EP1572962.
JD455035 - Sequence 436059 from Patent EP1572962.
JD122872 - Sequence 103896 from Patent EP1572962.
JD482796 - Sequence 463820 from Patent EP1572962.
JD087510 - Sequence 68534 from Patent EP1572962.
JD551687 - Sequence 532711 from Patent EP1572962.
JD515136 - Sequence 496160 from Patent EP1572962.
JD210967 - Sequence 191991 from Patent EP1572962.
JD470797 - Sequence 451821 from Patent EP1572962.
JD215973 - Sequence 196997 from Patent EP1572962.
JD464715 - Sequence 445739 from Patent EP1572962.
JD477972 - Sequence 458996 from Patent EP1572962.
JD076908 - Sequence 57932 from Patent EP1572962.
JD456005 - Sequence 437029 from Patent EP1572962.
JD539188 - Sequence 520212 from Patent EP1572962.
JD554794 - Sequence 535818 from Patent EP1572962.
JD078642 - Sequence 59666 from Patent EP1572962.
JD050389 - Sequence 31413 from Patent EP1572962.
JD354751 - Sequence 335775 from Patent EP1572962.
JD126988 - Sequence 108012 from Patent EP1572962.
JD037752 - Sequence 18776 from Patent EP1572962.
JD494153 - Sequence 475177 from Patent EP1572962.
JD317512 - Sequence 298536 from Patent EP1572962.
JD406960 - Sequence 387984 from Patent EP1572962.
JD040911 - Sequence 21935 from Patent EP1572962.
JD401354 - Sequence 382378 from Patent EP1572962.
EF092294 - Homo sapiens cardiac sodium channel alpha subunit variant (SCN5A) mRNA, partial cds, alternatively spliced.
EF092292 - Homo sapiens cardiac sodium channel alpha subunit variant (SCN5A) mRNA, partial cds, alternatively spliced.
AJ310896 - Homo sapiens partial mRNA for voltage-gated sodium Nav1.5 (SCN5A gene) (SCN5A gene), cell line MDA-MB-231.
AJ310886 - Homo sapiens partial mRNA for voltage gated sodium channel Nav1.5 (SCN5A gene), D1 neonatal splice variant, cell line MDA-MB-231.
AJ310887 - Homo sapiens partial mRNA for voltage-gated sodium channel Nav1.5 (SCN5A gene) D1 neonatal splice variant, cell line MCF-7.
AJ310888 - Homo sapiens partial mRNA for voltage-gated sodium channel Nav1.5 (SCN5A gene), D1 neonatal splice variant, biopsy sample 2.
AJ310889 - Homo sapiens partial mRNA for voltage-gated sodium channel Nav1.5 (SCN5A gene), D1 neonatal splice variant, biopsy sample 3.
AJ310890 - Homo sapiens partial mRNA for voltage-gated sodium channel Nav1.5 (SCN5A gene) D1 adult splice variant, biopsy sample 1.
AJ310891 - Homo sapiens partial mRNA for voltage gated sodium channel Nav1.5 (SCN5A gene), D1 adult splice variant, biopsy sample 7.
AJ310892 - Homo sapiens partial mRNA for voltage-gated sodium channel Nav1.5 (SCN5A gene), D1 neonatal splice variant, biopsy sample 6.
AJ310893 - Homo sapiens partial mRNA for voltage gated sodium channel Nav1.5 (SCN5A gene), D1 S3 exon-skipped splice variant, biopsy sample 8.
AJ310894 - Homo sapiens partial mRNA for voltage-gated sodium channel Nav1.5 (SCN5A gene), D1 neonatal splice variant, biopsy sample 4.
AJ310895 - Homo sapiens partial mRNA voltage-gated sodium channel Nav1.5 (SCN5A gene), D1 neonatal splice variant, biopsy sample 5.
EF092295 - Homo sapiens cardiac sodium channel alpha subunit (SCN5A) mRNA, partial cds, alternatively spliced.
GU447319 - Homo sapiens sodium channel alpha subunit variant 1 (SCN5A) mRNA, 5' UTR, alternatively spliced.
GU447320 - Homo sapiens sodium channel alpha subunit variant 2 (SCN5A) mRNA, 5' UTR, alternatively spliced.

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

Protein Q14524 (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: NM_000335, NP_000326, Q14524-2
UCSC ID: uc021wvq.1
RefSeq Accession: NM_000335
Protein: Q14524-2, splice isoform of Q14524

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SCN5A:
brugada (Brugada Syndrome)
dcm-ov (Dilated Cardiomyopathy Overview)
rws (Long QT Syndrome Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: yes RNA accession: NM_000335.4
exon count: 28CDS single in 3' UTR: no RNA size: 8501
ORF size: 4455CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 7511.00frame shift in genome: no % Coverage: 99.95
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 1
selenocysteine: no end bleed into intron: 0# strange splices: 1
Click here for a detailed description of the fields of the table above.

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