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Aliases for SCN9A Gene

Aliases for SCN9A Gene

  • Sodium Channel, Voltage Gated, Type IX Alpha Subunit 2 3
  • Sodium Channel, Voltage-Gated, Type IX, Alpha Polypeptide 2 3
  • Sodium Channel, Voltage-Gated, Type IX, Alpha Subunit 2 3
  • Voltage-Gated Sodium Channel Subunit Alpha Nav1.7 3 4
  • Sodium Channel Protein Type IX Subunit Alpha 3 4
  • Neuroendocrine Sodium Channel 3 4
  • Peripheral Sodium Channel 1 3 4
  • HNE-Na 3 4
  • NENA 3 4
  • PN1 3 4
  • Voltage-Gated Sodium Channel Alpha Subunit Nav1.7 3
  • GEFSP7 3
  • HSAN2D 3
  • Nav1.7 3
  • FEB3B 3
  • NE-NA 3
  • ETHA 3
  • SFNP 3

External Ids for SCN9A Gene

Previous GeneCards Identifiers for SCN9A Gene

  • GC02M165109
  • GC02M165596
  • GC02M167018
  • GC02M167257
  • GC02M166880
  • GC02M166763
  • GC02M167051
  • GC02M158932

Summaries for SCN9A Gene

Entrez Gene Summary for SCN9A Gene

  • This gene encodes a voltage-gated sodium channel which plays a significant role in nociception signaling. Mutations in this gene have been associated with primary erythermalgia, channelopathy-associated insensitivity to pain, and paroxysmal extreme pain disorder. [provided by RefSeq, Aug 2009]

GeneCards Summary for SCN9A Gene

SCN9A (Sodium Channel, Voltage Gated, Type IX Alpha Subunit) is a Protein Coding gene. Diseases associated with SCN9A include erythromelalgia and paroxysmal extreme pain disorder. Among its related pathways are Developmental Biology and Activation of cAMP-Dependent PKA. GO annotations related to this gene include ion channel activity and sodium ion binding. An important paralog of this gene is CACNA1D.

UniProtKB/Swiss-Prot for SCN9A Gene

  • 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-sensitive Na(+) channel isoform. Plays a role in pain mechanisms, especially in the development of inflammatory pain (By similarity).

Tocris Summary for SCN9A 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 SCN9A Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCN9A Gene

Genomics for SCN9A Gene

Regulatory Elements for SCN9A Gene

Genomic Location for SCN9A Gene

Chromosome:
2
Start:
166,195,185 bp from pter
End:
166,375,993 bp from pter
Size:
180,809 bases
Orientation:
Minus strand

Genomic View for SCN9A Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SCN9A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCN9A Gene

Proteins for SCN9A Gene

  • Protein details for SCN9A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15858-SCN9A_HUMAN
    Recommended name:
    Sodium channel protein type 9 subunit alpha
    Protein Accession:
    Q15858
    Secondary Accessions:
    • A1BUH5
    • Q6B4R9
    • Q6B4S0
    • Q6B4S1
    • Q70HX1
    • Q70HX2
    • Q8WTU1
    • Q8WWN4

    Protein attributes for SCN9A Gene

    Size:
    1988 amino acids
    Molecular mass:
    226372 Da
    Quaternary structure:
    • The sodium channel consists of a large polypeptide and 2-3 smaller ones. This sequence represents a large polypeptide. Interacts with NEDD4 and NEDD4L (By similarity).

    Alternative splice isoforms for SCN9A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCN9A Gene

Proteomics data for SCN9A Gene at MOPED

Post-translational modifications for SCN9A Gene

  • Phosphorylation at Ser-1490 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents.
  • Ubiquitinated by NEDD4L; which may promote its endocytosis. Does not seem to be ubiquitinated by NEDD4 (By similarity).
  • Glycosylation at Asn 209, Asn 283, Asn 1352, Asn 1366, and Asn 1375
  • Modification sites at PhosphoSitePlus

Other Protein References for SCN9A Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SCN9A (SCN9A)

No data available for DME Specific Peptides for SCN9A Gene

Domains & Families for SCN9A Gene

Gene Families for SCN9A Gene

Graphical View of Domain Structure for InterPro Entry

Q15858

UniProtKB/Swiss-Prot:

SCN9A_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. Nav1.7/SCN9A 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
  • Contains 1 IQ domain.
Family:
  • Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.7/SCN9A subfamily.
genes like me logo Genes that share domains with SCN9A: view

Function for SCN9A Gene

Molecular function for SCN9A Gene

GENATLAS Biochemistry:
sodium channel voltage-gated,type IX,alpha polypeptide,tetradotoxin sensitive,solely expressed in neuroendocrine cells
UniProtKB/Swiss-Prot Function:
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-sensitive Na(+) channel isoform. Plays a role in pain mechanisms, especially in the development of inflammatory pain (By similarity).

Gene Ontology (GO) - Molecular Function for SCN9A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005216 ion channel activity --
GO:0005248 voltage-gated sodium channel activity IEA --
GO:0005515 protein binding --
GO:0031402 sodium ion binding IEA --
genes like me logo Genes that share ontologies with SCN9A: view
genes like me logo Genes that share phenotypes with SCN9A: view

Animal Models for SCN9A Gene

MGI Knock Outs for SCN9A:

Animal Model Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SCN9A

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SCN9A Gene

Localization for SCN9A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCN9A Gene

Membrane; Multi-pass membrane protein. Note=In neurite terminals. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SCN9A Gene COMPARTMENTS Subcellular localization image for SCN9A gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for SCN9A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001518 voltage-gated sodium channel complex IEA --
GO:0005886 plasma membrane IBA --
GO:0016020 membrane --
genes like me logo Genes that share ontologies with SCN9A: view

Pathways & Interactions for SCN9A Gene

genes like me logo Genes that share pathways with SCN9A: view

Pathways by source for SCN9A Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for SCN9A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport --
GO:0006814 sodium ion transport TAS 7720699
GO:0006954 inflammatory response IEA --
GO:0009636 response to toxic substance IEA --
GO:0009791 post-embryonic development IEA --
genes like me logo Genes that share ontologies with SCN9A: view

No data available for SIGNOR curated interactions for SCN9A Gene

Drugs & Compounds for SCN9A Gene

(42) Drugs for SCN9A Gene - From: IUPHAR, DGIdb, ApexBio, DrugBank, Tocris, NovoSeek, ClinicalTrials, and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Lacosamide Approved Pharma Target Checkpoint kinase inhibitor,ATP competitive, Checkpoint kinase (Chk) inhibitor 79
Lidocaine Approved Pharma Antagonist, Pore Blocker, blocker, Target, inhibitor Anasthetic and class Ib antiarrhythmic agent 991
Ranolazine Approved, Investigational Pharma blocker, Target, inhibitor 74
Zonisamide Approved, Investigational Pharma blocker, Target, inhibitor Antiepileptic with anticonvulsant and mechanistic effect 63
Carbamazepine Approved, Investigational Pharma Inhibitor of neuronal voltage-gated Na+ channels; anticonvulsant 115

(4) Additional Compounds for SCN9A Gene - From: NovoSeek, HMDB, and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Sodium
  • Sodium ion
7440-23-5
QX 222
5369-00-6
QX 314 bromide
24003-58-5
carrageenan
genes like me logo Genes that share compounds with SCN9A: view

Transcripts for SCN9A Gene

Unigene Clusters for SCN9A Gene

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

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SCN9A

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCN9A Gene

No ASD Table

Relevant External Links for SCN9A Gene

GeneLoc Exon Structure for
SCN9A
ECgene alternative splicing isoforms for
SCN9A

Expression for SCN9A Gene

mRNA expression in normal human tissues for SCN9A Gene

mRNA differential expression in normal tissues according to GTEx for SCN9A Gene

This gene is overexpressed in Brain - Hypothalamus (x6.7).

Protein differential expression in normal tissues from HIPED for SCN9A Gene

This gene is overexpressed in Heart (53.6) and Salivary gland (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SCN9A Gene



SOURCE GeneReport for Unigene cluster for SCN9A Gene Hs.439145

mRNA Expression by UniProt/SwissProt for SCN9A Gene

Q15858-SCN9A_HUMAN
Tissue specificity: Expressed strongly in dorsal root ganglion, with only minor levels elsewhere in the body, smooth muscle cells, MTC cell line and C-cell carcinoma. Isoform 1 is expressed preferentially in the central and peripheral nervous system. Isoform 2 is expressed preferentially in the dorsal root ganglion.
genes like me logo Genes that share expression patterns with SCN9A: view

Protein tissue co-expression partners for SCN9A Gene

Primer Products

In Situ Assay Products

Orthologs for SCN9A Gene

This gene was present in the common ancestor of animals.

Orthologs for SCN9A Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SCN9A 35
  • 91.27 (n)
  • 94.6 (a)
SCN9A 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SCN9A 35
  • 91.09 (n)
  • 94.33 (a)
SCN9A 36
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Scn9a 35
  • 86.37 (n)
  • 92.04 (a)
Scn9a 16
Scn9a 36
  • 92 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SCN9A 35
  • 99.43 (n)
  • 99.7 (a)
SCN9A 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Scn9a 35
  • 86.72 (n)
  • 92.9 (a)
oppossum
(Monodelphis domestica)
Mammalia SCN9A 36
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SCN9A 36
  • 83 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCN9A 35
  • 75.3 (n)
  • 76.2 (a)
SCN9A 36
  • 75 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SCN9A 36
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia scn2a 35
  • 71.83 (n)
  • 72.88 (a)
zebrafish
(Danio rerio)
Actinopterygii scn1lab 36
  • 73 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta NaCP37B 37
  • 57 (a)
NaCP60E 37
  • 64 (a)
para 37
  • 49 (a)
Species with no ortholog for SCN9A:
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 SCN9A Gene

ENSEMBL:
Gene Tree for SCN9A (if available)
TreeFam:
Gene Tree for SCN9A (if available)

Paralogs for SCN9A Gene

Pseudogenes.org Pseudogenes for SCN9A Gene

genes like me logo Genes that share paralogs with SCN9A: view

Variants for SCN9A Gene

Sequence variations from dbSNP and Humsavar for SCN9A Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs951510 -- 166,338,943(-) TTTTT(C/T)CTATA intron-variant
rs952462 -- 166,353,494(-) AAATA(A/G)GGAAA intron-variant
rs952463 -- 166,353,525(-) CGTAG(A/T)ATAAT intron-variant
rs1011778 -- 166,366,235(-) GGCAG(A/G)TAAGA intron-variant
rs1358532 -- 166,346,072(+) CTGCT(C/T)CTCTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SCN9A Gene

Variant ID Type Subtype PubMed ID
dgv4355n71 CNV Gain 21882294
nsv459937 CNV Loss 19166990
esv2721082 CNV Deletion 23290073
esv2127014 CNV Deletion 18987734
esv2721083 CNV Deletion 23290073
esv1764654 CNV Deletion 17803354
esv2666983 CNV Deletion 23128226
esv23265 CNV Loss 19812545
esv2658860 CNV Deletion 23128226
nsv834448 CNV Loss 17160897
nsv507046 CNV Insertion 20534489

Variation tolerance for SCN9A Gene

Residual Variation Intolerance Score: 63.31% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.23; 90.50% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SCN9A Gene

HapMap Linkage Disequilibrium report
SCN9A
Human Gene Mutation Database (HGMD)
SCN9A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCN9A Gene

Disorders for SCN9A Gene

MalaCards: The human disease database

(20) MalaCards diseases for SCN9A Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, NovoSeek, and GeneCards

Disorder Aliases PubMed IDs
erythromelalgia
  • mitchell disease
paroxysmal extreme pain disorder
  • familial rectal pain
erythermalgia, primary
  • small fiber neuropathy
febrile seizures, familial, 3b
  • epilepsy, generalized, with febrile seizures plus, type 7
channelopathy-associated congenital insensitivity to pain
- elite association
Search SCN9A in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SCN9A_HUMAN
  • Febrile seizures, familial, 3B (FEB3B) [MIM:613863]: Seizures associated with febrile episodes in childhood without any evidence of intracranial infection or defined pathologic or traumatic cause. It is a common condition, affecting 2-5% of children aged 3 months to 5 years. The majority are simple febrile seizures (generally defined as generalized onset, single seizures with a duration of less than 30 minutes). Complex febrile seizures are characterized by focal onset, duration greater than 30 minutes, and/or more than one seizure in a 24 hour period. The likelihood of developing epilepsy following simple febrile seizures is low. Complex febrile seizures are associated with a moderately increased incidence of epilepsy. {ECO:0000269 PubMed:19763161}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Generalized epilepsy with febrile seizures plus 7 (GEFS+7) [MIM:613863]: A rare autosomal dominant, familial condition with incomplete penetrance and large intrafamilial variability. Patients display febrile seizures persisting sometimes beyond the age of 6 years and/or a variety of afebrile seizure types. This disease combines febrile seizures, generalized seizures often precipitated by fever at age 6 years or more, and partial seizures, with a variable degree of severity. {ECO:0000269 PubMed:19763161}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Indifference to pain, congenital, autosomal recessive (CIP) [MIM:243000]: A disorder characterized by congenital inability to perceive any form of pain, in any part of the body. All other sensory modalities are preserved and the peripheral and central nervous systems are apparently intact. Patients perceive the sensations of touch, warm and cold temperature, proprioception, tickle and pressure, but not painful stimuli. There is no evidence of a motor or sensory neuropathy, either axonal or demyelinating. {ECO:0000269 PubMed:20635406}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Paroxysmal extreme pain disorder (PEPD) [MIM:167400]: Autosomal dominant paroxysmal disorder of pain and autonomic dysfunction. The distinctive features are paroxysmal episodes of burning pain in the rectal, ocular, and mandibular areas accompanied by autonomic manifestations such as skin flushing. {ECO:0000269 PubMed:17145499, ECO:0000269 PubMed:18945915, ECO:0000269 PubMed:25285947}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Primary erythermalgia (PERYTHM) [MIM:133020]: Autosomal dominant disease characterized by recurrent episodes of severe pain associated with redness and warmth in the feet or hands. {ECO:0000269 PubMed:14985375, ECO:0000269 PubMed:15955112, ECO:0000269 PubMed:15958509, ECO:0000269 PubMed:16216943, ECO:0000269 PubMed:16392115, ECO:0000269 PubMed:18945915, ECO:0000269 PubMed:19369487, ECO:0000269 PubMed:24311784}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SCN9A

Genetic Association Database (GAD)
SCN9A
Human Genome Epidemiology (HuGE) Navigator
SCN9A
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SCN9A
genes like me logo Genes that share disorders with SCN9A: view

No data available for Genatlas for SCN9A Gene

Publications for SCN9A Gene

  1. A Nav1.7 channel mutation associated with hereditary erythromelalgia contributes to neuronal hyperexcitability and displays reduced lidocaine sensitivity. (PMID: 17430993) Sheets P.L. … Cummins T.R. (J. Physiol. (Lond.) 2007) 25 26 67
  2. Structure and functional expression of a new member of the tetrodotoxin-sensitive voltage-activated sodium channel family from human neuroendocrine cells. (PMID: 7720699) Klugbauer N. … Hofmann F. (EMBO J. 1995) 2 23 67
  3. Linkage analysis and functional evaluation of inherited clinical pain conditions. (PMID: 20336431) Krupp J.J. … Eriksson A.B. (Methods Mol. Biol. 2010) 23 67
  4. Sodium channel gene family: epilepsy mutations, gene interactions and modifier effects. (PMID: 20351042) Meisler M.H. … Sharkey L.M. (J. Physiol. (Lond.) 2010) 23 67
  5. Familial pain syndromes from mutations of the NaV1.7 sodium channel. (PMID: 20146699) Fischer T.Z. … Waxman S.G. (Ann. N. Y. Acad. Sci. 2010) 23 67

Products for SCN9A Gene

Sources for SCN9A Gene

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