SCN9A Gene (Protein Coding)

Sodium Voltage-Gated Channel Alpha Subunit 9

GC02M166195
GIFtS:
48
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] See more...

Aliases for SCN9A Gene

Aliases for SCN9A Gene

  • Sodium Voltage-Gated Channel Alpha Subunit 9 2 3 5
  • NENA 2 3 4
  • PN1 2 3 4
  • 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
  • Sodium Channel Protein Type 9 Subunit Alpha 3 4
  • Neuroendocrine Sodium Channel 3 4
  • Peripheral Sodium Channel 1 3 4
  • Nav1.7 2 3
  • HNE-Na 3 4
  • NE-NA 2 3
  • ETHA 2 3
  • Sodium Channel, Voltage Gated, Type IX Alpha Subunit 2
  • Voltage-Gated Sodium Channel Alpha Subunit Nav1.7 3
  • GEFSP7 3
  • HSAN2D 3
  • FEB3B 3
  • SCN9A 5
  • 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 Voltage-Gated Channel Alpha Subunit 9) is a Protein Coding gene. Diseases associated with SCN9A include Paroxysmal Extreme Pain Disorder and Indifference To Pain, Congenital, Autosomal Recessive. Among its related pathways are Cardiac conduction and Neuropathic Pain-Signaling in Dorsal Horn Neurons. Gene Ontology (GO) annotations related to this gene include ion channel activity and sodium ion binding. An important paralog of this gene is SCN2A.

UniProtKB/Swiss-Prot Summary 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 (PubMed:7720699, PubMed:17167479, PubMed:25240195, PubMed:26680203, PubMed:15385606, PubMed:16988069, PubMed:17145499, PubMed:19369487, PubMed:24311784). It is a tetrodotoxin-sensitive Na(+) channel isoform (PubMed:7720699). Plays a role in pain mechanisms, especially in the development of inflammatory pain (PubMed:17167479, PubMed:17145499, PubMed:19369487, PubMed:24311784).

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

Additional gene information for SCN9A Gene

No data available for CIViC Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCN9A Gene

Genomics for SCN9A Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SCN9A Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH02J166371 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 272.9 +1.8 1798 6 ZNF600 NCOR1 MYC IKZF1 JUND ZMYM3 CEBPA ZNF10 POLR2A ZIC2 SCN9A piR-35674-293 SCN1A SCN1A-AS1
GH02J166360 Enhancer 0.8 Ensembl 15.4 +14.6 14630 1.7 ZNF654 JUND ZNF592 YY1 REST KLF11 HOMEZ CTCF ARNT KMT2B piR-35674-293 SCN9A SCN1A SCN1A-AS1
GH02J166493 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE CraniofacialAtlas 6.2 -117.4 -117389 3.2 ZNF341 NFE2 ZBTB48 EGR1 ZNF547 ZNF398 MCM2 SMARCE1 EGR2 CBFA2T2 SCN7A SCN9A HSALNG0020170 piR-60995
GH02J166344 Enhancer 0.9 Ensembl ENCODE 10.6 +31.6 31600 2 CEBPA FOXA2 SAP130 PRDM6 BCL6 SOX5 HMG20A EGR1 GLIS1 GATA2 SCN9A SNODB391 lnc-SCN7A-2 SCN1A SCN1A-AS1
GH02J166410 Enhancer 1.2 FANTOM5 Ensembl ENCODE 6.9 -36.1 -36137 3.7 MYC JUND ZNF592 CEBPA CEBPB FEZF1 MNT EP300 MAFF ZNF316 piR-31292-098 TTC21B ENSG00000232411 SCN9A lnc-SCN9A-2 SCN7A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCN9A on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCN9A

Top Transcription factor binding sites by QIAGEN in the SCN9A gene promoter:
  • aMEF-2
  • MEF-2A
  • Oct-B1
  • oct-B3
  • POU2F1
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • Sox5

Genomic Locations for SCN9A Gene

Latest Assembly
chr2:166,195,185-166,376,001
(GRCh38/hg38)
Size:
180,817 bases
Orientation:
Minus strand

Previous Assembly
chr2:167,051,695-167,232,497
(GRCh37/hg19 by Entrez Gene)
Size:
180,803 bases
Orientation:
Minus strand

chr2:167,051,695-167,232,503
(GRCh37/hg19 by Ensembl)
Size:
180,809 bases
Orientation:
Minus strand

Genomic View for SCN9A Gene

Genes around SCN9A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCN9A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCN9A Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SCN9A Gene

Proteins for SCN9A Gene

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  • 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 complex consists of a large, channel-forming alpha subunit (SCN9A) regulated by one or more beta subunits (SCN1B, SCN2B, SCN3B and SCN4B) (PubMed:7720699, PubMed:17167479, PubMed:25240195). SCN1B and SCN3B are non-covalently associated with SCN2A. SCN2B and SCN4B are disulfide-linked to SCN2A. Interacts with NEDD4 and NEDD4L (By similarity). Interacts with the scorpion alpha-toxin CvIV4 (PubMed:21887265). Interacts with the conotoxin GVIIJ (PubMed:24497506). Interacts with the spider huwentoxin-IV (through the extracellular loop S3-S4 of repeat II) (PubMed:20855463, PubMed:21659528, PubMed:30661758, PubMed:30765606). Interacts with the spider protoxin-II (through the extracellular loop S3-S4 of repeats II and IV) (PubMed:20855463, PubMed:21659528, PubMed:30661758, PubMed:30765606). Interacts with the spider beta/delta-theraphotoxin-Pre1a (PubMed:28428547).

    Three dimensional structures from OCA and Proteopedia for SCN9A Gene

    Alternative splice isoforms for SCN9A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SCN9A Gene

Protein Expression for SCN9A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SCN9A Gene

  • Phosphorylation at Ser-1490 by PKC in a highly conserved cytoplasmic loop increases peak sodium currents.
  • Ubiquitinated by NEDD4L; which may promote its endocytosis. Does not seem to be ubiquitinated by NEDD4.
  • Glycosylation at Asn209, Asn283, Asn1352, Asn1366, and Asn1375
  • Modification sites at PhosphoSitePlus

Other Protein References for SCN9A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SCN9A Gene

Domains & Families for SCN9A Gene

Gene Families for SCN9A Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Disease related genes
  • FDA approved drug targets
  • Predicted membrane proteins
  • Transporters
  • Voltage-gated ion channels

Protein Domains for SCN9A Gene

InterPro:
Blocks:
  • IQ calmodulin-binding region
  • Voltage-gated Na+ channel alpha subunit signature

Suggested Antigen Peptide Sequences for SCN9A Gene

GenScript: Design optimal peptide antigens:
  • Sodium channel, voltage-gated, type IX, alpha, isoform CRA_a (D3DPB7_HUMAN)
  • Voltage-gated sodium channel subunit alpha NaV1.7 (F5C0A4_HUMAN)
  • Voltage-gated sodium channel subunit alpha Nav1.7 (SCN9A_HUMAN)

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.
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

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Molecular function for SCN9A Gene

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 (PubMed:7720699, PubMed:17167479, PubMed:25240195, PubMed:26680203, PubMed:15385606, PubMed:16988069, PubMed:17145499, PubMed:19369487, PubMed:24311784). It is a tetrodotoxin-sensitive Na(+) channel isoform (PubMed:7720699). Plays a role in pain mechanisms, especially in the development of inflammatory pain (PubMed:17167479, PubMed:17145499, PubMed:19369487, PubMed:24311784).
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by tetrodotoxin (PubMed:23077250). Weakly inhibited by saxitoxin (PubMed:23077250).
GENATLAS Biochemistry:
sodium channel voltage-gated,type IX,alpha polypeptide,tetradotoxin sensitive,solely expressed in neuroendocrine cells

Phenotypes From GWAS Catalog for SCN9A Gene

Gene Ontology (GO) - Molecular Function for SCN9A 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,IDA 17145499
GO:0005261 cation channel activity IEA --
GO:0005272 sodium channel activity IEA --
genes like me logo Genes that share ontologies with SCN9A: view
genes like me logo Genes that share phenotypes with SCN9A: view

Human Phenotype Ontology for SCN9A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SCN9A Gene

MGI Knock Outs for SCN9A:

Animal Models for research

  • Taconic Biosciences Mouse Models for SCN9A

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCN9A

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

Cell membrane. Multi-pass membrane protein. Cell projection, neuron projection. Note=In neurite terminals. {ECO:0000250 UniProtKB:O08562}.

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 SCN9A gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytoskeleton 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
mitochondrion 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
  • Focal adhesion sites (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCN9A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001518 voltage-gated sodium channel complex IEA,IBA 21873635
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IMP 17145499
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SCN9A: view

Pathways & Interactions for SCN9A Gene

PathCards logo

SuperPathways for SCN9A Gene

SuperPathway Contained pathways
1 Activation of cAMP-Dependent PKA
Activation of cAMP-Dependent PKA
.77
cAMP Pathway
.77
PKA Signaling
.56
2 Neuropathic Pain-Signaling in Dorsal Horn Neurons
Aldosterone Signaling in Epithelial Cells
.47
Neuropathic Pain-Signaling in Dorsal Horn Neurons
.47
Cholera Infection
.40
3 Developmental Biology
Axon guidance
.51
Developmental Biology
.51
4 Cardiac conduction
Cardiac conduction
.70
Muscle contraction
.70
5 Neuroscience
Neuroscience
-
genes like me logo Genes that share pathways with SCN9A: view

Pathways by source for SCN9A Gene

1 KEGG pathway for SCN9A Gene
7 Qiagen pathways for SCN9A Gene
  • Activation of cAMP-Dependent PKA
  • Aldosterone Signaling in Epithelial Cells
  • cAMP Pathway
  • Cholera Infection
  • GHRH Signaling
1 Cell Signaling Technology pathway for SCN9A Gene

SIGNOR curated interactions for SCN9A Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for SCN9A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006814 sodium ion transport IEA,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

Drugs & Compounds for SCN9A Gene

Products:

  1. Drug products for research

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Lacosamide Approved Pharma Target Checkpoint kinase inhibitor,ATP competitive, Checkpoint kinase (Chk) inhibitor 95
Lidocaine Approved, Vet_approved Pharma Target, inhibitor, blocker Anasthetic and class Ib antiarrhythmic agent 2340
Ranolazine Approved, Investigational Pharma Target, inhibitor, blocker 87
Zonisamide Approved, Investigational Pharma Target, inhibitor, blocker Antiepileptic with anticonvulsant and mechanistic effect 78
Carbamazepine Approved, Investigational Pharma Target, inhibitor Inhibitor of neuronal voltage-gated Na+ channels; anticonvulsant 109

(3) Additional Compounds for SCN9A Gene - From: Novoseek, HMDB, and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Na(+)
  • Na+
  • SODIUM ion
  • Sodium(1+)
 7440-23-5
Amiloride hydrochloride
2016-88-8

(3) Tocris Compounds for SCN9A Gene

Compound Action Cas Number
Amiloride hydrochloride Na+ channel blocker; also I2 imidazoline ligand 2016-88-8
Carbamazepine Inhibitor of neuronal voltage-gated Na+ channels; anticonvulsant 298-46-4
Vinpocetine Na+ channel blocker 42971-09-5

(26) ApexBio Compounds for SCN9A Gene

Compound Action Cas Number
A-803467 NaV1.8 channel blocker,potent and selective 944261-79-4
Ambroxol HCl TTX-resistant Na+ currents inhibitor 23828-92-4
Amiloride HCl 2016-88-8
Amiloride HCl dihydrate 17440-83-4
Benzocaine 1994-09-7
Bupivacaine HCl Anaesthetic drug 18010-40-7
Camostat Mesilate Trypsin-like protease inhibitor 59721-29-8
Carbamazepine 298-46-4
Dibucaine (Cinchocaine) HCl 1961-12-1
GX-674 Nav1.7 antagonist
Lamotrigine 5-HT inhibitor 84057-84-1
Levobupivacaine HCl 27262-48-2
Mexiletine HCl 5370-01-4
Nefopam HCl 23327-57-3
Ouabain 630-60-4
Oxcarbazepine BTX inhibitor 28721-07-5
Phenytoin 57-41-0
Phenytoin sodium Sodium channel stabilizer 630-93-3
Primidone 125-33-7
Procainamide HCl 614-39-1
Procaine HCl 1951-05-8
Propafenone HCl 34183-22-7
Proparacaine HCl 5875-06-9
Ranolazine 2HCl Partial fatty acid oxidation inhibitor 95635-56-6
Tolperisone HCl 3644-61-9
Triamterene 396-01-0
genes like me logo Genes that share compounds with SCN9A: view

Drug products for research

Transcripts for SCN9A Gene

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mRNA/cDNA for SCN9A Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
15 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCN9A

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

No ASD Table

Relevant External Links for SCN9A Gene

GeneLoc Exon Structure for
SCN9A

Expression for SCN9A Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCN9A Gene

mRNA expression in normal human tissues for SCN9A Gene
mRNA expression by GTEx for SCN9A GenemRNA expression by BioGPS 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 and MOPED for SCN9A Gene



Protein tissue co-expression partners for SCN9A Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCN9A

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. Also expressed in vagus nerves within the head and neck region (PubMed:31647222). Isoform 1 is expressed preferentially in the central and peripheral nervous system. Isoform 2 is expressed preferentially in the dorsal root ganglion.

Evidence on tissue expression from TISSUES for SCN9A Gene

  • Nervous system(4.6)
  • Thyroid gland(4.2)
  • Muscle(2.4)
  • Heart(2.1)
  • Kidney(2)
  • Lung(2)
  • Pancreas(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SCN9A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • eye
  • head
  • jaw
  • lacrimal apparatus
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • olfactory bulb
  • salivary gland
  • skull
  • tongue
  • tooth
Thorax:
  • chest wall
  • clavicle
  • esophagus
  • heart
  • heart valve
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • intestine
  • large intestine
  • small intestine
  • stomach
Pelvis:
  • pelvis
  • prostate
  • rectum
  • urinary bladder
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood vessel
  • bone marrow
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
genes like me logo Genes that share expression patterns with SCN9A: view

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Orthologs for SCN9A Gene

This gene was present in the common ancestor of animals.

Orthologs for SCN9A Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia SCN9A 29 30
  • 99.43 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia SCN9A 29 30
  • 91.27 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia SCN9A 29 30
  • 91.09 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Scn9a 29
  • 86.72 (n)
Mouse
(Mus musculus)
 Mammalia Scn9a 29 16 30
  • 86.37 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia SCN9A 30
  • 84 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia SCN9A 30
  • 83 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves SCN9A 29 30
  • 75.3 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia SCN9A 30
  • 73 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia scn2a 29
  • 71.83 (n)
Zebrafish
(Danio rerio)
 Actinopterygii scn1lab 30
  • 73 (a)
 OneToMany
Fruit Fly
(Drosophila melanogaster)
 Insecta NaCP60E 31
  • 64 (a)
NaCP37B 31
  • 57 (a)
para 31
  • 49 (a)
Species where no ortholog for SCN9A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for SCN9A: view image
Alliance of Genome Resources:
Additional Orthologs for SCN9A

Paralogs for SCN9A Gene

Paralogs for SCN9A Gene

(15) SIMAP similar genes for SCN9A Gene using alignment to 7 proteins:

  • SCN9A_HUMAN
  • D3DPB7_HUMAN
  • E9PBA5_HUMAN
  • E9PF08_HUMAN
  • F5C0A4_HUMAN
  • H7C064_HUMAN
  • Q53QP0_HUMAN
genes like me logo Genes that share paralogs with SCN9A: view

Variants for SCN9A Gene

Products:

  1. SNP Genotyping and Copy Number Assays for research

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCN9A Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
1000913 Uncertain Significance: Generalized epilepsy with febrile seizures plus, type 7; Hereditary sensory and autonomic neuropathy type IIA 166,272,409(-) T/A
NM_001365536.1(SCN9A):c.3341A>T (p.Tyr1114Phe) 		MISSENSE
1001954 Uncertain Significance: Generalized epilepsy with febrile seizures plus, type 7; Hereditary sensory and autonomic neuropathy type IIA 166,280,357(-) C/T
NM_001365536.1(SCN9A):c.2343G>A (p.Leu781=) 		SYNONYMOUS
1003274 Uncertain Significance: Generalized epilepsy with febrile seizures plus, type 7; Hereditary sensory and autonomic neuropathy type IIA 166,204,154(-) G/C
NM_001365536.1(SCN9A):c.4575C>G (p.Ile1525Met) 		MISSENSE
1003532 Uncertain Significance: Generalized epilepsy with febrile seizures plus, type 7; Hereditary sensory and autonomic neuropathy type IIA 166,278,219(-) C/T
NM_001365536.1(SCN9A):c.2438G>A (p.Ser813Asn) 		MISSENSE
1003716 Uncertain Significance: Generalized epilepsy with febrile seizures plus, type 7; Hereditary sensory and autonomic neuropathy type IIA 166,272,515(-) A/C
NM_001365536.1(SCN9A):c.3235T>G (p.Phe1079Val) 		MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SCN9A Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
esv1764654 CNV deletion 17803354
esv2127014 CNV deletion 18987734
esv23265 CNV loss 19812545
esv2658860 CNV deletion 23128226
esv2666983 CNV deletion 23128226
esv2721082 CNV deletion 23290073
esv2721083 CNV deletion 23290073
esv3593247 CNV loss 21293372
nsv1071633 CNV deletion 25765185
nsv1136433 CNV deletion 24896259
nsv1136434 CNV deletion 24896259
nsv459937 CNV loss 19166990
nsv507046 OTHER sequence alteration 20534489
nsv583585 CNV loss 21841781
nsv834448 CNV loss 17160897
nsv961905 CNV duplication 23825009
nsv961906 CNV duplication 23825009

Variation tolerance for SCN9A Gene

Residual Variation Intolerance Score: 63.3% 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)

Additional Variant Information for SCN9A Gene

Human Gene Mutation Database (HGMD)
SCN9A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCN9A
Leiden Open Variation Database (LOVD)
SCN9A

SNP Genotyping and Copy Number Assays for research

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

Disorders for SCN9A Gene

MalaCards: The human disease database

(62) MalaCards diseases for SCN9A Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards
Search SCN9A in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SCN9A_HUMAN
  • 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:15385606, ECO:0000269 PubMed:15955112, ECO:0000269 PubMed:15958509, ECO:0000269 PubMed:16216943, ECO:0000269 PubMed:16392115, ECO:0000269 PubMed:16702558, ECO:0000269 PubMed:16988069, ECO:0000269 PubMed:18945915, ECO:0000269 PubMed:19369487, ECO:0000269 PubMed:24311784}. Note=The disease is caused by variants 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 variants 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 variants 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 variants affecting the gene represented in this entry.
  • 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 variants affecting the gene represented in this entry.

Additional Disease Information for SCN9A

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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 role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome. (PMID: 19763161) Singh NA … Leppert MF (PLoS genetics 2009) 3 4 22 40 72
  2. An SCN9A channelopathy causes congenital inability to experience pain. (PMID: 17167479) Cox JJ … Woods CG (Nature 2006) 3 4 22 72
  3. Electrophysiological properties of mutant Nav1.7 sodium channels in a painful inherited neuropathy. (PMID: 15385606) Cummins TR … Waxman SG (The Journal of neuroscience : the official journal of the Society for Neuroscience 2004) 3 4 22 72
  4. Mutations in SCN9A, encoding a sodium channel alpha subunit, in patients with primary erythermalgia. (PMID: 14985375) Yang Y … Shen Y (Journal of medical genetics 2004) 3 4 22 72
  5. 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 (The EMBO journal 1995) 2 3 4 22

ExternalLinks

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