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Aliases for SCN5A Gene

Aliases for SCN5A Gene

  • Sodium Voltage-Gated Channel Alpha Subunit 5 2 3 5
  • Sodium Channel, Voltage-Gated, Type V, Alpha Subunit 2 3
  • Sodium Channel Protein Cardiac Muscle Subunit Alpha 3 4
  • Voltage-Gated Sodium Channel Subunit Alpha Nav1.5 3 4
  • HH1 3 4
  • Cardiac Tetrodotoxin-Insensitive Voltage-Dependent Sodium Channel Alpha Subunit 3
  • Sodium Channel, Voltage-Gated, Type V, Alpha (Long QT Syndrome 3) 2
  • Sodium Channel, Voltage Gated, Type V Alpha Subunit 2
  • Sodium Channel Protein Type 5 Subunit Alpha 3
  • Sodium Channel Protein Type V Subunit Alpha 4
  • Long QT Syndrome 3 2
  • Nav1.5 3
  • PFHB1 3
  • CDCD2 3
  • CMPD2 3
  • CMD1E 3
  • HBBD 3
  • ICCD 3
  • LQT3 3
  • SSS1 3
  • HB1 3
  • HB2 3
  • IVF 3
  • VF1 3

External Ids for SCN5A Gene

Previous HGNC Symbols for SCN5A Gene

  • CMD1E

Previous GeneCards Identifiers for SCN5A Gene

  • GC03U990070
  • GC03M038402
  • GC03M038550
  • GC03M038565
  • GC03M038589

Summaries for SCN5A Gene

Entrez Gene Summary for SCN5A Gene

  • 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]

GeneCards Summary for SCN5A Gene

SCN5A (Sodium Voltage-Gated Channel Alpha Subunit 5) is a Protein Coding gene. Diseases associated with SCN5A include Long Qt Syndrome-3 and Brugada Syndrome 1. Among its related pathways are Neuropathic Pain-Signaling in Dorsal Horn Neurons and Developmental Biology. GO annotations related to this gene include protein kinase binding and ubiquitin protein ligase binding. An important paralog of this gene is SCN2A.

UniProtKB/Swiss-Prot for SCN5A Gene

  • This protein mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient. It is a tetrodotoxin-resistant Na(+) channel isoform. This channel is responsible for the initial upstroke of the action potential. Channel inactivation is regulated by intracellular calcium levels.

Tocris Summary for SCN5A Gene

  • Voltage-gated sodium channels (NaV) are responsible for action potential initiation and propagation in excitable cells, including nerve, muscle, and neuroendocrine cell types. They are also expressed at low levels in non-excitable cells, where their physiological role is unclear.

Gene Wiki entry for SCN5A Gene

PharmGKB "VIP" Summary for SCN5A Gene

No data available for CIViC summary , fRNAdb sequence ontologies and piRNA Summary for SCN5A Gene

Genomics for SCN5A Gene

Regulatory Elements for SCN5A Gene

Enhancers for SCN5A Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G038552 0.4 dbSUPER 4.4 +96.3 96314 2.7 ZNF26 GORASP1 SNORA62 SCN5A GC03M038560 PIR55116
GH03G038649 1.1 ENCODE dbSUPER 0.7 -0.1 -132 0.1 TBP ATF1 CBX3 SIN3A GLIS2 EGR1 EGR2 ZNF398 SMARCA4 GLIS1 SCN5A SCN10A
GH03G038651 0.9 ENCODE 0.7 -1.7 -1712 0.2 HDAC1 CBX3 RB1 SIN3A RAD21 GLIS2 ZNF143 KLF13 CREM EGR2 SCN5A SCN10A
GH03G038633 1.1 FANTOM5 ENCODE dbSUPER 0.4 +15.4 15392 1.1 JUND NFIA BHLHE40 SCRT2 GABPA RNU6-1227P SCN5A GC03M038560
GH03G038578 1.5 VISTA Ensembl ENCODE 0.2 +69.7 69744 3.1 CTCF TFAP4 ZIC2 RELA GLIS2 EED RELB IKZF2 MTA2 NFIA GC03M038560 SCN5A
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SCN5A on UCSC Golden Path with GeneCards custom track

Promoters for SCN5A Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000151030 -27 601 HDGF CBX3 ZNF133 GLIS2 EGR1 EGR2 ZBTB2 ZNF398 ZNF645 SMARCA4

Genomic Location for SCN5A Gene

Chromosome:
3
Start:
38,548,057 bp from pter
End:
38,649,673 bp from pter
Size:
101,617 bases
Orientation:
Minus strand

Genomic View for SCN5A Gene

Genes around SCN5A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCN5A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCN5A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCN5A Gene

Proteins for SCN5A Gene

  • Protein details for SCN5A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q14524-SCN5A_HUMAN
    Recommended name:
    Sodium channel protein type 5 subunit alpha
    Protein Accession:
    Q14524
    Secondary Accessions:
    • A5H1P8
    • A6N922
    • A6N923
    • B2RTU0
    • E7ET19
    • E9PEF3
    • E9PEK2
    • E9PFW7
    • Q59H93
    • Q75RX9
    • Q75RY0
    • Q86UR3
    • Q8IZC9
    • Q96J69

    Protein attributes for SCN5A Gene

    Size:
    2016 amino acids
    Molecular mass:
    226940 Da
    Quaternary structure:
    • Interacts with the PDZ domain of the syntrophin SNTA1, SNTB1 and SNTB2 (By similarity). Interacts with NEDD4, NEDD4L, WWP2 and GPD1L (PubMed:15217910, PubMed:15548568, PubMed:19666841). Interacts with CALM (PubMed:21167176, PubMed:22705208). Interacts with FGF13; the interaction is direct and FGF13 may regulate SNC5A density at membranes and function (PubMed:21817159, PubMed:22705208, PubMed:26392562). May also interact with FGF12 and FGF14 (PubMed:26392562).
    Miscellaneous:
    • Na(+) channels in mammalian cardiac membrane have functional properties quite distinct from Na(+) channels in nerve and skeletal muscle.

    Three dimensional structures from OCA and Proteopedia for SCN5A Gene

    Alternative splice isoforms for SCN5A Gene

neXtProt entry for SCN5A Gene

Post-translational modifications for SCN5A Gene

  • Lacks the cysteine which covalently binds the conotoxin GVIIJ. This cysteine (position 868) is speculated in other sodium channel subunits alpha to be implied in covalent binding with the sodium channel subunit beta-2 or beta-4.
  • Phosphorylation at Ser-1503 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents (Probable). Regulated through phosphorylation by CaMK2D (By similarity).
  • Ubiquitinated by NEDD4L; which promotes its endocytosis. Does not seem to be ubiquitinated by NEDD4 or WWP2.
  • Glycosylation at isoforms=2, 3, 4, 5, 6214, Asn283, isoforms=2, 3, 4, 5, 6288, isoforms=2, 3, 4, 5, 6291, isoforms=2, 3, 4, 5, 6318, Asn328, Asn740, isoforms=2, 3, 4, 5, 6803, Asn864, isoforms=2, 3, 4, 5, 61365, Asn1374, isoforms=2, 3, 4, 5, 61380, Asn1388, and Asn1736
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for SCN5A Gene

Domains & Families for SCN5A Gene

Gene Families for SCN5A Gene

Graphical View of Domain Structure for InterPro Entry

Q14524

UniProtKB/Swiss-Prot:

SCN5A_HUMAN :
  • The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1,S2,S3,S5,S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position.
  • Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.5/SCN5A subfamily.
Domain:
  • The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1,S2,S3,S5,S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position.
  • The IQ domain mediates association with calmodulin.
Family:
  • Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.5/SCN5A subfamily.
genes like me logo Genes that share domains with SCN5A: view

Function for SCN5A Gene

Molecular function for SCN5A Gene

GENATLAS Biochemistry:
sodium voltage-gated channel,type V,alpha polypeptide,tetradotoxin-resistant,heart
UniProtKB/Swiss-Prot Function:
This protein mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient. It is a tetrodotoxin-resistant Na(+) channel isoform. This channel is responsible for the initial upstroke of the action potential. Channel inactivation is regulated by intracellular calcium levels.

Gene Ontology (GO) - Molecular Function for SCN5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity IEA --
GO:0005244 voltage-gated ion channel activity IEA --
GO:0005248 voltage-gated sodium channel activity IEA,IMP 23085483
GO:0005272 sodium channel activity IEA --
GO:0005515 protein binding IPI 16728661
genes like me logo Genes that share ontologies with SCN5A: view
genes like me logo Genes that share phenotypes with SCN5A: view

Human Phenotype Ontology for SCN5A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SCN5A Gene

MGI Knock Outs for SCN5A:

Animal Model Products

  • Taconic Biosciences Mouse Models for SCN5A

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for SCN5A Gene

Localization for SCN5A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCN5A Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCN5A gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 5
cytosol 2
extracellular 1
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for SCN5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001518 voltage-gated sodium channel complex IDA 19808477
GO:0005622 intracellular IDA 19943616
GO:0005783 endoplasmic reticulum IDA 22529811
GO:0005886 plasma membrane IEA,TAS --
GO:0005901 colocalizes_with caveola TAS 17060380
genes like me logo Genes that share ontologies with SCN5A: view

Pathways & Interactions for SCN5A Gene

genes like me logo Genes that share pathways with SCN5A: view

Pathways by source for SCN5A Gene

SIGNOR curated interactions for SCN5A Gene

Is inactivated by:

Gene Ontology (GO) - Biological Process for SCN5A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002027 regulation of heart rate IMP 10471492
GO:0003231 cardiac ventricle development ISS --
GO:0003360 brainstem development ISS --
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
genes like me logo Genes that share ontologies with SCN5A: view

Drugs & Compounds for SCN5A Gene

(97) Drugs for SCN5A Gene - From: DrugBank, ClinicalTrials, ApexBio, DGIdb, FDA Approved Drugs, IUPHAR, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Lidocaine Approved, Vet_approved Pharma Antagonist, Pore Blocker, blocker, Target, inhibitor Anasthetic and class Ib antiarrhythmic agent 1317
Carbamazepine Approved, Investigational Pharma blocker, Target, inhibitor 132
Oxcarbazepine Approved Pharma blocker, Target, inhibitor BTX inhibitor 56
Riluzole Approved, Investigational Pharma Activator, blocker, Target, inhibitor Sodium channel protein inhibitor 65
Flecainide Approved, Withdrawn Pharma Pore Blocker, blocker, Target, inhibitor 43

(7) Additional Compounds for SCN5A Gene - From: HMDB, Novoseek, and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Sodium
  • Sodium ion
7440-23-5
3',4'-Dihydrodiol
O-Desmethylverapamil (D-702)
Tetrodotoxin citrate
18660-81-6

(5) Tocris Compounds for SCN5A Gene

Compound Action Cas Number
QX 314 bromide Na+ channel blocker 24003-58-5
QX 314 chloride Na+ channel blocker 5369-03-9
Tetrodotoxin Na+ channel blocker 4368-28-9
Tetrodotoxin citrate Na+ channel blocker; citrate salt of tetrodotoxin (Cat. No. 1078) 18660-81-6
Veratridine Voltage-gated Na+ channel opener 71-62-5

(41) ApexBio Compounds for SCN5A Gene

Compound Action Cas Number
Ambroxol HCl TTX-resistant Na+ currents inhibitor 23828-92-4
Amiloride HCl dihydrate 17440-83-4
Bupivacaine HCl Anaesthetic drug 18010-40-7
Carbamazepine 298-46-4
Co 102862 181144-66-1
Dibucaine (Cinchocaine) HCl 1961-12-1
Flecainide acetate Antiarrhythmic drug 54143-56-5
GS967 inhibitor of cardiac late sodium current 1262618-39-2
GSK1014802(CNV1014802) Novel sodium channel blocker 934240-30-9
Huwentoxin IV 526224-73-7
Ibutilide Fumarate Class III antiarrhythmic agent 122647-32-9
ICA 121431 313254-51-2
Jingzhaotoxin III 925463-91-8
KC 12291 hydrochloride 181936-98-1
Licarbazepine 29331-92-8
M2 ion channel blocker M2 ion channel blocker 1190215-03-2
Nav1.7 inhibitor 1355631-24-1
Ouabain 630-60-4
Oxcarbazepine BTX inhibitor 28721-07-5
PF 04885614
Phenytoin 57-41-0
Phenytoin sodium Sodium channel stabilizer 630-93-3
Phrixotoxin 3 880886-00-0
Procainamide HCl 614-39-1
Procaine HCl 1951-05-8
Propafenone HCl 34183-22-7
Proparacaine HCl 5875-06-9
ProTx II 484598-36-9
QX 222 5369-00-6
QX 314 bromide 24003-58-5
QX 314 chloride 5369-03-9
Ralfinamide mesylate 202825-45-4
Ranolazine 2HCl Partial fatty acid oxidation inhibitor 95635-56-6
Riluzole Sodium channel protein inhibitor 1744-22-5
Rostafuroxin (PST 2238) Selective antagonist of endogenous ouabain, antihypertensive agent 156722-18-8
Sipatrigine 130800-90-7
Sodium Channel inhibitor 1 Voltage-gated sodium channel for pain treatment 1198117-23-5
TC-N 1752 1211866-85-1
Triamterene 396-01-0
Veratridine 71-62-5
β-Pompilidotoxin Slows Na+ channel inactivation 216064-36-7
genes like me logo Genes that share compounds with SCN5A: view

Drug Products

Transcripts for SCN5A Gene

Unigene Clusters for SCN5A Gene

Sodium channel, voltage-gated, type V, alpha subunit:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SCN5A Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8
SP1: -
SP2: - -
SP3: - - -
SP4: - - -
SP5:

Relevant External Links for SCN5A Gene

GeneLoc Exon Structure for
SCN5A
ECgene alternative splicing isoforms for
SCN5A

Expression for SCN5A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCN5A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCN5A Gene

This gene is overexpressed in Heart - Left Ventricle (x27.1) and Heart - Atrial Appendage (x15.9).

Protein differential expression in normal tissues from HIPED for SCN5A Gene

This gene is overexpressed in Plasma (46.9) and Pancreatic juice (16.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SCN5A Gene



Protein tissue co-expression partners for SCN5A Gene

NURSA nuclear receptor signaling pathways regulating expression of SCN5A Gene:

SCN5A

SOURCE GeneReport for Unigene cluster for SCN5A Gene:

Hs.517898

mRNA Expression by UniProt/SwissProt for SCN5A Gene:

Q14524-SCN5A_HUMAN
Tissue specificity: Found in jejunal circular smooth muscle cells (at protein level). Expressed in human atrial and ventricular cardiac muscle but not in adult skeletal muscle, brain, myometrium, liver, or spleen. Isoform 4 is expressed in brain.

Evidence on tissue expression from TISSUES for SCN5A Gene

  • Heart(4.7)
  • Nervous system(4.4)
  • Intestine(4.2)
  • Muscle(3.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SCN5A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • head
  • sinus
  • skull
Thorax:
  • heart
  • heart valve
  • lung
Limb:
  • lower limb
  • upper limb
General:
  • blood
  • blood vessel
  • coagulation system
  • peripheral nervous system
  • red blood cell
  • spinal cord
genes like me logo Genes that share expression patterns with SCN5A: view

Primer Products

Orthologs for SCN5A Gene

This gene was present in the common ancestor of animals.

Orthologs for SCN5A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCN5A 34 35
  • 98.79 (n)
dog
(Canis familiaris)
Mammalia SCN5A 34 35
  • 91.02 (n)
cow
(Bos Taurus)
Mammalia SCN5A 34 35
  • 90.64 (n)
rat
(Rattus norvegicus)
Mammalia Scn5a 34
  • 89.61 (n)
mouse
(Mus musculus)
Mammalia Scn5a 34 16 35
  • 89.1 (n)
oppossum
(Monodelphis domestica)
Mammalia SCN5A 35
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SCN5A 35
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCN5A 34 35
  • 72.41 (n)
lizard
(Anolis carolinensis)
Reptilia SCN5A 35
  • 68 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia scn5a 34
  • 69.23 (n)
zebrafish
(Danio rerio)
Actinopterygii scn12aa 34
  • 67.12 (n)
CABZ01063402.1 35
  • 61 (a)
ManyToMany
scn1a 35
  • 59 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta NaCP60E 36
  • 63 (a)
para 36
  • 49 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.9565 34
Species where no ortholog for SCN5A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCN5A Gene

ENSEMBL:
Gene Tree for SCN5A (if available)
TreeFam:
Gene Tree for SCN5A (if available)

Paralogs for SCN5A Gene

Variants for SCN5A Gene

Sequence variations from dbSNP and Humsavar for SCN5A Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs12720452 Pathogenic, Brugada syndrome 1 (BRGDA1) [MIM:601144], Long QT syndrome 3 (LQT3) [MIM:603830] 38,603,758(-) CCCAG(A/G)AAGCC reference, missense
rs137854600 Pathogenic, Brugada syndrome 1 (BRGDA1) [MIM:601144], Long QT syndrome 3 (LQT3) [MIM:603830], Long QT syndrome 3 (LQT3) [MIM:603830] 38,551,504(-) CTTCC(A/G/T)AGTCA reference, missense
rs137854601 Pathogenic, Brugada syndrome 1 (BRGDA1) [MIM:601144], Long QT syndrome 3 (LQT3) [MIM:603830] 38,551,022(-) GCACC(A/G)AGCCC reference, missense
rs137854602 Likely pathogenic, Brugada syndrome 1 (BRGDA1) [MIM:601144] 38,555,664(-) TCCCA(C/T)GGCCC reference, missense
rs137854603 Pathogenic, Brugada syndrome 1 (BRGDA1) [MIM:601144] 38,550,602(-) AGCAT(A/G)CCTCC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for SCN5A Gene

Variant ID Type Subtype PubMed ID
esv2725164 CNV deletion 23290073
nsv3770 CNV insertion 18451855
nsv508912 CNV insertion 20534489
nsv517802 CNV loss 19592680
nsv819980 CNV loss 19587683

Variation tolerance for SCN5A Gene

Residual Variation Intolerance Score: 79.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.41; 77.13% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SCN5A Gene

Human Gene Mutation Database (HGMD)
SCN5A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCN5A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCN5A Gene

Disorders for SCN5A Gene

MalaCards: The human disease database

(65) MalaCards diseases for SCN5A Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
long qt syndrome-3
  • long qt syndrome 3
brugada syndrome 1
  • brgda1
sick sinus syndrome 1
  • sick sinus syndrome 1, autosomal recessive
heart block, progressive, type ia
  • heart block, nonprogressive
atrial fibrillation, familial, 10
  • atfb10
- elite association - COSMIC cancer census association via MalaCards
Search SCN5A in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SCN5A_HUMAN
  • Atrial fibrillation, familial, 10 (ATFB10) [MIM:614022]: A familial form of atrial fibrillation, a common sustained cardiac rhythm disturbance. Atrial fibrillation is characterized by disorganized atrial electrical activity and ineffective atrial contraction promoting blood stasis in the atria and reduces ventricular filling. It can result in palpitations, syncope, thromboembolic stroke, and congestive heart failure. {ECO:0000269 PubMed:18088563, ECO:0000269 PubMed:18378609}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Atrial standstill 1 (ATRST1) [MIM:108770]: A rare arrhythmia characterized by the absence of electrical and mechanical activity in the atria. Electrocardiographically, it is characterized by bradycardia, the absence of P waves, and a junctional narrow complex escape rhythm. {ECO:0000269 PubMed:12522116}. Note=The disease may be caused by mutations affecting distinct genetic loci, including the gene represented in this entry. A mutation in SCN5A has been detected in combination with a rare GJA5 genotype in a large family with atrial standstill.
  • Brugada syndrome 1 (BRGDA1) [MIM:601144]: 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, the individual will faint and may die in a few minutes if the heart is not reset. {ECO:0000269 PubMed:10532948, ECO:0000269 PubMed:10618304, ECO:0000269 PubMed:10690282, ECO:0000269 PubMed:11410597, ECO:0000269 PubMed:11748104, ECO:0000269 PubMed:11823453, ECO:0000269 PubMed:11901046, ECO:0000269 PubMed:12051963, ECO:0000269 PubMed:12106943, ECO:0000269 PubMed:15023552, ECO:0000269 PubMed:15338453, ECO:0000269 PubMed:15579534, ECO:0000269 PubMed:15851320, ECO:0000269 PubMed:16266370, ECO:0000269 PubMed:16325048, ECO:0000269 PubMed:16616735, ECO:0000269 PubMed:17075016, ECO:0000269 PubMed:17081365, ECO:0000269 PubMed:17198989, ECO:0000269 PubMed:18252757, ECO:0000269 PubMed:18341814, ECO:0000269 PubMed:18451998, ECO:0000269 PubMed:18456723, ECO:0000269 PubMed:18616619, ECO:0000269 PubMed:19251209, ECO:0000269 PubMed:19272188, ECO:0000269 PubMed:20129283, ECO:0000269 PubMed:23085483, ECO:0000269 PubMed:24167619, ECO:0000269 PubMed:26279430, ECO:0000269 PubMed:26776555, ECO:0000269 PubMed:9521325}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Cardiomyopathy, dilated 1E (CMD1E) [MIM:601154]: A disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Patients are at risk of premature death. {ECO:0000269 PubMed:15466643}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Familial paroxysmal ventricular fibrillation 1 (VF1) [MIM:603829]: A cardiac arrhythmia marked by fibrillary contractions of the ventricular muscle due to rapid repetitive excitation of myocardial fibers without coordinated contraction of the ventricle and by absence of atrial activity. {ECO:0000269 PubMed:10940383}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Long QT syndrome 3 (LQT3) [MIM:603830]: A heart disorder characterized by a prolonged QT interval on the ECG and polymorphic ventricular arrhythmias. They cause syncope and sudden death in response to exercise or emotional stress, and can present with a sentinel event of sudden cardiac death in infancy. {ECO:0000269 PubMed:10377081, ECO:0000269 PubMed:10508990, ECO:0000269 PubMed:10590249, ECO:0000269 PubMed:10627139, ECO:0000269 PubMed:10911008, ECO:0000269 PubMed:10973849, ECO:0000269 PubMed:11304498, ECO:0000269 PubMed:11410597, ECO:0000269 PubMed:11710892, ECO:0000269 PubMed:11889015, ECO:0000269 PubMed:11997281, ECO:0000269 PubMed:12209021, ECO:0000269 PubMed:12454206, ECO:0000269 PubMed:12673799, ECO:0000269 PubMed:15840476, ECO:0000269 PubMed:16414944, ECO:0000269 PubMed:16922724, ECO:0000269 PubMed:18060054, ECO:0000269 PubMed:18451998, ECO:0000269 PubMed:18708744, ECO:0000269 PubMed:18848812, ECO:0000269 PubMed:18929331, ECO:0000269 PubMed:19716085, ECO:0000269 PubMed:26392562, ECO:0000269 PubMed:7651517, ECO:0000269 PubMed:7889574, ECO:0000269 PubMed:8541846, ECO:0000269 PubMed:9506831, ECO:0000269 PubMed:9686753, ECO:0000269 Ref.31}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Progressive familial heart block 1A (PFHB1A) [MIM:113900]: A cardiac bundle branch disorder characterized by progressive alteration of cardiac conduction through the His-Purkinje system, with a pattern of a right bundle-branch block and/or left anterior hemiblock occurring individually or together. It leads to complete atrio-ventricular block causing syncope and sudden death. {ECO:0000269 PubMed:11234013, ECO:0000269 PubMed:11804990, ECO:0000269 PubMed:12569159, ECO:0000269 PubMed:12574143, ECO:0000269 PubMed:19251209}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Sick sinus syndrome 1 (SSS1) [MIM:608567]: The term sick sinus syndrome encompasses a variety of conditions caused by sinus node dysfunction. The most common clinical manifestations are syncope, presyncope, dizziness, and fatigue. Electrocardiogram typically shows sinus bradycardia, sinus arrest, and/or sinoatrial block. Episodes of atrial tachycardias coexisting with sinus bradycardia (tachycardia-bradycardia syndrome) are also common in this disorder. SSS occurs most often in the elderly associated with underlying heart disease or previous cardiac surgery, but can also occur in the fetus, infant, or child without heart disease or other contributing factors. SSS1 onset is in utero, infancy, or early childhood. {ECO:0000269 PubMed:11748104, ECO:0000269 PubMed:14523039, ECO:0000269 PubMed:22795782}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Sudden infant death syndrome (SIDS) [MIM:272120]: SIDS is the sudden death of an infant younger than 1 year that remains unexplained after a thorough case investigation, including performance of a complete autopsy, examination of the death scene, and review of clinical history. Pathophysiologic mechanisms for SIDS may include respiratory dysfunction, cardiac dysrhythmias, cardiorespiratory instability, and inborn errors of metabolism, but definitive pathogenic mechanisms precipitating an infant sudden death remain elusive. {ECO:0000269 PubMed:18596570, ECO:0000269 PubMed:19302788}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Relevant External Links for SCN5A

Genetic Association Database (GAD)
SCN5A
Human Genome Epidemiology (HuGE) Navigator
SCN5A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SCN5A
genes like me logo Genes that share disorders with SCN5A: view

No data available for Genatlas for SCN5A Gene

Publications for SCN5A Gene

  1. Sodium channel mutation in irritable bowel syndrome: evidence for an ion channelopathy. (PMID: 19056759) Saito Y.A. … Farrugia G. (Am. J. Physiol. 2009) 3 4 22 46 64
  2. Type of SCN5A mutation determines clinical severity and degree of conduction slowing in loss-of-function sodium channelopathies. (PMID: 19251209) Meregalli P.G. … Wilde A.A.M. (Heart Rhythm 2009) 3 4 22 46 64
  3. SCN5A variants in Japanese patients with left ventricular noncompaction and arrhythmia. (PMID: 18368697) Shan L. … Towbin J.A. (Mol. Genet. Metab. 2008) 3 4 22 46 64
  4. Cardiac sodium channel (SCN5A) variants associated with atrial fibrillation. (PMID: 18378609) Darbar D. … Roden D.M. (Circulation 2008) 3 4 22 46 64
  5. Genetic analysis of the cardiac sodium channel gene SCN5A in Koreans with Brugada syndrome. (PMID: 15338453) Shin D.-J. … Yoon S.K. (J. Hum. Genet. 2004) 3 4 22 46 64

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