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SCN9A Gene(Protein Coding)

Sodium Voltage-Gated Channel Alpha Subunit 9

GCID:
GC02M166195
GIFtS:
55
Genes Participants
UDN Logo

Aliases for SCN9A Gene

Aliases for SCN9A Gene

  • Sodium Voltage-Gated Channel Alpha Subunit 9 2 3 5
  • 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
  • Sodium Channel, Voltage Gated, Type IX Alpha Subunit 2
  • Voltage-Gated Sodium Channel Alpha Subunit Nav1.7 3
  • Sodium Channel Protein Type 9 Subunit Alpha 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 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 L1CAM interactions. 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 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 , fRNAdb sequence ontologies and piRNA Summary for SCN9A Gene

Genomics for SCN9A Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for SCN9A Gene

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
GH02I166375 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 562.9 -0.1 -110 2.2 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 SCN9A GC02M166405 GC02M166406
GH02I166373 Enhancer 0.8 Ensembl 573 +1.8 1799 0.4 ATF1 SMAD1 NFIB ZNF529 ZNF366 SCRT2 ZEB2 TSHZ1 ZNF843 SP1 SCN9A GC02M166198
GH02I166371 Enhancer 1.1 Ensembl ENCODE 12.7 +3.7 3668 2.2 FOXA2 ARID4B DMAP1 ETS1 YY1 ZNF213 ATF7 RXRA SP5 MIER2 SCN9A GC02M166198
GH02I166493 Promoter/Enhancer 1.2 Ensembl ENCODE 6.2 -118.3 -118331 1.3 MCM2 ZFHX2 CTBP1 ZBTB48 EGR1 ZNF547 SCRT2 VEZF1 CBFA2T2 EGR2 SCN7A SCN9A PIR55994
GH02I166344 Enhancer 0.7 ENCODE 10.5 +31.1 31061 0.8 ELF3 SOX13 ATF1 FOXA2 SAP130 CTBP1 EGR1 RCOR1 ATF7 SMARCE1 SCN9A GC02M166198
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCN9A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCN9A gene promoter:

Genomic Locations for SCN9A Gene

Genomic Locations for SCN9A Gene
chr2:166,195,185-166,375,993
(GRCh38/hg38)
Size:
180,809 bases
Orientation:
Minus strand
chr2:167,051,695-167,232,503
(GRCh37/hg19)

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

Products:

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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 and 2-3 smaller, ancillary beta subunits (PubMed:7720699, PubMed:17167479, PubMed:25240195). 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 toxins huwentoxin-IV and ProTx-II (PubMed:20855463, PubMed:21659528). 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 posLast=209209, posLast=283283, posLast=13521352, isoforms=2, 31366, and isoforms=2, 31375

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:
ProtoNet:

Suggested Antigen Peptide Sequences for SCN9A Gene

GenScript: Design optimal peptide antigens:

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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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 (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).

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 TAS,IDA 17145499
GO:0005272 sodium channel activity IEA --
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

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 Model Products

Clone 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

Cell membrane; Multi-pass membrane protein. Cell 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
endoplasmic reticulum 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 --
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

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

Pathways by source for SCN9A Gene

1 Cell Signaling Technology pathway for SCN9A Gene
1 KEGG pathway for SCN9A Gene

Gene Ontology (GO) - Biological Process for SCN9A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006814 sodium ion transport TAS 7720699
GO:0006954 inflammatory response IEA --
GO:0009636 response to toxic substance 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

Products:

  1. Drug

(47) Drugs for SCN9A Gene - From: DrugBank, ClinicalTrials, ApexBio, DGIdb, IUPHAR, HMDB, 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 82
Lidocaine Approved, Vet_approved Pharma Antagonist, Pore Blocker, Target, inhibitor, blocker Anasthetic and class Ib antiarrhythmic agent 1477
Ranolazine Approved, Investigational Pharma Target, inhibitor, blocker 82
Zonisamide Approved, Investigational Pharma Target, inhibitor, blocker Antiepileptic with anticonvulsant and mechanistic effect 69
Brivaracetam Approved, Investigational Pharma Target, inhibitor ligand for SV2A, selective and high-affinity 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Sodium
  • Sodium ion
 7440-23-5

(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

Transcripts for SCN9A Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for SCN9A Gene

(8) REFSEQ mRNAs :
(12) Additional mRNA sequences :
(26) Selected AceView cDNA sequences:
(6) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SCN9A Gene

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

Clone 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

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCN9A Gene

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



Protein tissue co-expression partners for SCN9A Gene

NURSA nuclear receptor signaling pathways regulating expression of SCN9A Gene:

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. 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(4.1)

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

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 33 34
  • 99.43 (n)
cow
(Bos Taurus)
 Mammalia SCN9A 33 34
  • 91.27 (n)
dog
(Canis familiaris)
 Mammalia SCN9A 33 34
  • 91.09 (n)
rat
(Rattus norvegicus)
 Mammalia Scn9a 33
  • 86.72 (n)
mouse
(Mus musculus)
 Mammalia Scn9a 33 16 34
  • 86.37 (n)
oppossum
(Monodelphis domestica)
 Mammalia SCN9A 34
  • 84 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia SCN9A 34
  • 83 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves SCN9A 33 34
  • 75.3 (n)
lizard
(Anolis carolinensis)
 Reptilia SCN9A 34
  • 73 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia scn2a 33
  • 71.83 (n)
zebrafish
(Danio rerio)
 Actinopterygii scn1lab 34
  • 73 (a)
 OneToMany
fruit fly
(Drosophila melanogaster)
 Insecta NaCP60E 35
  • 64 (a)
NaCP37B 35
  • 57 (a)
para 35
  • 49 (a)
Species where no ortholog for SCN9A 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 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

Paralogs for SCN9A Gene

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

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 Variation AA Info Type
rs1024152367 to pain, congenital, autosomal recessive (CIP) [MIM:243000] 166,277,137(-) C/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1034452097 uncertain-significance, Generalized epilepsy with febrile seizures plus, type 7, Hereditary sensory and autonomic neuropathy type IIA 166,198,713(-) T/C coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs1055160615 likely-benign, Generalized epilepsy with febrile seizures plus, type 7, Hereditary sensory and autonomic neuropathy type IIA 166,303,241(-) G/A/T coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs1057518900 pathogenic, Pain insensitivity 166,284,785(-) G/A coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs1060502047 likely-pathogenic, Generalized epilepsy with febrile seizures plus, type 7, Hereditary sensory and autonomic neuropathy type IIA 166,198,763(-) T/G coding_sequence_variant, genic_downstream_transcript_variant, missense_variant

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

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

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

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

Disorders for SCN9A Gene

MalaCards: The human disease database

(23) MalaCards diseases for SCN9A Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- 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
  • 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: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 mutations affecting the gene represented in this entry.

Additional Disease Information for SCN9A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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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 44 58
  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 (The EMBO journal 1995) 2 3 4 22 58
  3. Pain perception is altered by a nucleotide polymorphism in SCN9A. (PMID: 20212137) Reimann F … Woods CG (Proceedings of the National Academy of Sciences of the United States of America 2010) 3 22 44 58
  4. Association analysis of SCN9A gene variants with borderline personality disorder. (PMID: 18439623) Tadić A … Dahmen N (Journal of psychiatric research 2008) 3 22 44 58
  5. An SCN9A channelopathy causes congenital inability to experience pain. (PMID: 17167479) Cox JJ … Woods CG (Nature 2006) 3 4 22 58

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