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Aliases for SCN10A Gene

Aliases for SCN10A Gene

  • Sodium Voltage-Gated Channel Alpha Subunit 10 2 3 5
  • Sodium Channel, Voltage-Gated, Type X, Alpha Polypeptide 2 3
  • Sodium Channel, Voltage-Gated, Type X, Alpha Subunit 2 3
  • Voltage-Gated Sodium Channel Subunit Alpha Nav1.8 3 4
  • Sodium Channel Protein Type X Subunit Alpha 3 4
  • Peripheral Nerve Sodium Channel 3 3 4
  • HPN3 3 4
  • PN3 3 4
  • Sodium Channel, Voltage Gated, Type X Alpha Subunit 2
  • Sodium Channel Protein Type 10 Subunit Alpha 3
  • Nav1.8 3
  • FEPS2 3
  • SNS 3

External Ids for SCN10A Gene

Previous GeneCards Identifiers for SCN10A Gene

  • GC03U990071
  • GC03M038552
  • GC03M038699

Summaries for SCN10A Gene

Entrez Gene Summary for SCN10A Gene

  • The protein encoded by this gene is a tetrodotoxin-resistant voltage-gated sodium channel alpha subunit. The properties of the channel formed by the encoded transmembrane protein can be altered by interaction with different beta subunits. This protein may be involved in the onset of pain associated with peripheral neuropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

GeneCards Summary for SCN10A Gene

SCN10A (Sodium Voltage-Gated Channel Alpha Subunit 10) is a Protein Coding gene. Diseases associated with SCN10A include Episodic Pain Syndrome, Familial, 2 and Sodium Channelopathy-Related Small Fiber Neuropathy. Among its related pathways are Cardiac conduction and L1CAM interactions. Gene Ontology (GO) annotations related to this gene include ion channel activity and voltage-gated sodium channel activity. An important paralog of this gene is SCN5A.

UniProtKB/Swiss-Prot for SCN10A Gene

  • Tetrodotoxin-resistant channel that 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 sodium ions may pass in accordance with their electrochemical gradient. Plays a role in neuropathic pain mechanisms.

Tocris Summary for SCN10A 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 SCN10A Gene

Additional gene information for SCN10A Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCN10A Gene

Genomics for SCN10A Gene

GeneHancer (GH) Regulatory Elements for SCN10A Gene

Promoters and enhancers for SCN10A 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
GH03I038527 Enhancer 0.5 FANTOM5 dbSUPER 5 +266.6 266572 0.6 PIR31167 PIR44083 PIR53009 RPL18AP7 PIR61865 PIR49321 GC03P038527 EXOG SCN10A SLC22A14
GH03I039274 Enhancer 0.5 FANTOM5 dbSUPER 3.9 -480.6 -480640 0.3 NFIC XIRP1 TTC21A GORASP1 CCR8 HNRNPA1P21 RNU6-1227P MOBP SCN10A CX3CR1 LOC102724104
GH03I039271 Enhancer 1.1 FANTOM5 Ensembl ENCODE dbSUPER 1.5 -478.7 -478703 3.4 CTCF ZNF687 IKZF1 XIRP1 TTC21A GORASP1 CCR8 HNRNPA1P21 RNU6-1227P RPSA CSRNP1 SCN10A WDR48
GH03I038722 Enhancer 1.4 VISTA ENCODE 0.2 +69.5 69484 4.8 PKNOX1 SMAD1 ATF1 ARNT NCOA2 TCF12 ZNF766 GATA2 E2F8 FOS GORASP1 SNORA62 ENSG00000231243 RNU6-1227P OXSR1 SCN10A SCN5A
GH03I038649 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 0.1 +144.3 144309 0.6 HDAC1 HDGF ATF1 ZNF133 SIN3A ZNF335 GLIS2 ZNF213 EGR1 EGR2 SCN5A SCN10A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCN10A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCN10A gene promoter:

Genomic Locations for SCN10A Gene

Genomic Locations for SCN10A Gene
chr3:38,696,802-38,794,010
(GRCh38/hg38)
Size:
97,209 bases
Orientation:
Minus strand
chr3:38,738,293-38,835,501
(GRCh37/hg19)

Genomic View for SCN10A Gene

Genes around SCN10A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCN10A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCN10A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCN10A Gene

Proteins for SCN10A Gene

  • Protein details for SCN10A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5Y9-SCNAA_HUMAN
    Recommended name:
    Sodium channel protein type 10 subunit alpha
    Protein Accession:
    Q9Y5Y9
    Secondary Accessions:
    • A6NDQ1

    Protein attributes for SCN10A Gene

    Size:
    1956 amino acids
    Molecular mass:
    220626 Da
    Quaternary structure:
    • The channel consists of an ion conducting pore forming alpha-subunit regulated by one or more associated auxiliary subunits SCN1B, SCN2B and SCN3B; electrophysiological properties may vary depending on the type of the associated beta subunits. Found in a number of complexes with PRX, DYNLT1 and PDZD2. Interacts with proteins such as FSTL1, PRX, DYNLT1, PDZD2, S100A10 and many others (By similarity). Interacts with NEDD4 and NEDD4L.

neXtProt entry for SCN10A Gene

Post-translational modifications for SCN10A Gene

  • Lacks the cysteine which covalently binds the conotoxin GVIIJ. This cysteine (position 816) 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-1451 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents.
  • Ubiquitinated by NEDD4L; which promotes its endocytosis.
  • Glycosylation at isoforms=284, isoforms=288, isoforms=312, posLast=335335, posLast=819819, isoforms=1312, isoforms=1328, isoforms=1336, and isoforms=1686
  • Modification sites at PhosphoSitePlus

Other Protein References for SCN10A Gene

No data available for DME Specific Peptides for SCN10A Gene

Domains & Families for SCN10A Gene

Gene Families for SCN10A Gene

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

Suggested Antigen Peptide Sequences for SCN10A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y5Y9

UniProtKB/Swiss-Prot:

SCNAA_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. Nav1.8/SCN10A 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. Nav1.8/SCN10A subfamily.
genes like me logo Genes that share domains with SCN10A: view

Function for SCN10A Gene

Molecular function for SCN10A Gene

GENATLAS Biochemistry:
sodium channel voltage-gated,type X,alpha polypeptide,tetrodotoxin resistant,specific to sensory neurons,expressed in dorsal root ganglia
UniProtKB/Swiss-Prot Function:
Tetrodotoxin-resistant channel that 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 sodium ions may pass in accordance with their electrochemical gradient. Plays a role in neuropathic pain mechanisms.

Phenotypes From GWAS Catalog for SCN10A Gene

Gene Ontology (GO) - Molecular Function for SCN10A 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 IDA 9839820
GO:0005272 sodium channel activity IEA --
GO:0044325 ion channel binding IPI 24998131
genes like me logo Genes that share ontologies with SCN10A: view
genes like me logo Genes that share phenotypes with SCN10A: view

Human Phenotype Ontology for SCN10A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SCN10A Gene

MGI Knock Outs for SCN10A:

Animal Model Products

  • Taconic Biosciences Mouse Models for SCN10A

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for SCN10A Gene

Localization for SCN10A Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCN10A Gene

Cell membrane; Multi-pass membrane protein. Note=It can be translocated to the cell membrane through association with S100A10. {ECO:0000250}.

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 SCN10A gene
Compartment Confidence
plasma membrane 5
extracellular 5
nucleus 2
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for SCN10A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001518 voltage-gated sodium channel complex IDA 9839820
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome HDA,IDA 19056867
genes like me logo Genes that share ontologies with SCN10A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SCN10A Gene

Pathways & Interactions for SCN10A Gene

genes like me logo Genes that share pathways with SCN10A: view

Pathways by source for SCN10A Gene

Gene Ontology (GO) - Biological Process for SCN10A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002027 regulation of heart rate IMP 20062061
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006814 sodium ion transport IEA --
GO:0007600 sensory perception TAS 9839820
genes like me logo Genes that share ontologies with SCN10A: view

No data available for SIGNOR curated interactions for SCN10A Gene

Drugs & Compounds for SCN10A Gene

(33) Drugs for SCN10A Gene - From: DrugBank, PharmGKB, ClinicalTrials, ApexBio, DGIdb, IUPHAR, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Benzocaine Approved, Investigational Pharma Target, inhibitor, blocker 2232
Bupivacaine Approved, Investigational Pharma Pore Blocker, Target, inhibitor, blocker 1425
Chloroprocaine Approved Pharma Target, inhibitor, blocker 27
Cocaine Approved, Illicit Pharma Target, inhibitor 533
Dibucaine Approved, Vet_approved Pharma Target, inhibitor, blocker 0

(2) Additional Compounds for SCN10A 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 SCN10A 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

(3) ApexBio Compounds for SCN10A Gene

Compound Action Cas Number
A 887826 Voltage-dependent NaV1.8 channel blocker 1266212-81-0
A-803467 NaV1.8 channel blocker,potent and selective 944261-79-4
GS967 inhibitor of cardiac late sodium current 1262618-39-2
genes like me logo Genes that share compounds with SCN10A: view

Drug Products

Transcripts for SCN10A Gene

mRNA/cDNA for SCN10A Gene

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

Unigene Clusters for SCN10A Gene

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

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCN10A Gene

No ASD Table

Relevant External Links for SCN10A Gene

GeneLoc Exon Structure for
SCN10A
ECgene alternative splicing isoforms for
SCN10A

Expression for SCN10A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCN10A Gene

mRNA differential expression in normal tissues according to GTEx for SCN10A Gene

This gene is overexpressed in Heart - Left Ventricle (x17.9), Testis (x11.4), and Heart - Atrial Appendage (x7.8).

Protein differential expression in normal tissues from HIPED for SCN10A Gene

This gene is overexpressed in Monocytes (22.5), Tlymphocyte (18.7), Blymphocyte (17.3), and Neutrophil (9.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SCN10A Gene



Protein tissue co-expression partners for SCN10A Gene

NURSA nuclear receptor signaling pathways regulating expression of SCN10A Gene:

SCN10A

SOURCE GeneReport for Unigene cluster for SCN10A Gene:

Hs.250443

mRNA Expression by UniProt/SwissProt for SCN10A Gene:

Q9Y5Y9-SCNAA_HUMAN
Tissue specificity: Expressed in the dorsal root ganglia and sciatic nerve.

Evidence on tissue expression from TISSUES for SCN10A Gene

  • Nervous system(4.6)
  • Lymph node(3.1)
  • Skin(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SCN10A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
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
  • heart
  • heart valve
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • intestine
  • large intestine
  • small intestine
Pelvis:
  • pelvis
  • rectum
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • spinal column
  • spinal cord
  • sweat gland
  • vertebrae
genes like me logo Genes that share expression patterns with SCN10A: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for SCN10A Gene

Orthologs for SCN10A Gene

This gene was present in the common ancestor of animals.

Orthologs for SCN10A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCN10A 33 34
  • 99.25 (n)
dog
(Canis familiaris)
Mammalia SCN10A 33 34
  • 88.82 (n)
cow
(Bos Taurus)
Mammalia SCN10A 33 34
  • 86.75 (n)
mouse
(Mus musculus)
Mammalia Scn10a 34 16 33
  • 82.37 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Scn10a 33
  • 82.13 (n)
oppossum
(Monodelphis domestica)
Mammalia SCN10A 34
  • 65 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SCN10A 34
  • 61 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCN10A 34
  • 59 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SCN10A 34
  • 58 (a)
OneToOne
zebrafish
(Danio rerio)
Actinopterygii scn1a 34
  • 55 (a)
ManyToMany
CABZ01063402.1 34
  • 53 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta NaCP60E 35
  • 62 (a)
Species where no ortholog for SCN10A 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCN10A Gene

ENSEMBL:
Gene Tree for SCN10A (if available)
TreeFam:
Gene Tree for SCN10A (if available)

Paralogs for SCN10A Gene

(11) SIMAP similar genes for SCN10A Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SCN10A: view

Variants for SCN10A Gene

Sequence variations from dbSNP and Humsavar for SCN10A Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1060501715 uncertain-significance, Brugada syndrome 38,709,538(-) G/T coding_sequence_variant, missense_variant
rs1060501716 uncertain-significance, Brugada syndrome 38,752,244(-) A/T coding_sequence_variant, intron_variant, missense_variant
rs1060501717 uncertain-significance, Brugada syndrome 38,793,768(-) A/T coding_sequence_variant, missense_variant
rs1060504317 likely-benign, Brugada syndrome 38,710,859(-) A/G coding_sequence_variant, synonymous_variant
rs112374164 benign, Brugada syndrome 38,697,724(-) A/G coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for SCN10A Gene

Variant ID Type Subtype PubMed ID
esv3358507 CNV insertion 20981092
esv3595914 CNV loss 21293372
nsv1160931 CNV deletion 26073780
nsv527515 CNV loss 19592680

Variation tolerance for SCN10A Gene

Residual Variation Intolerance Score: 91.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.59; 82.59% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCN10A Gene

Human Gene Mutation Database (HGMD)
SCN10A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCN10A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCN10A Gene

Disorders for SCN10A Gene

MalaCards: The human disease database

(16) MalaCards diseases for SCN10A Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SCNAA_HUMAN
  • Episodic pain syndrome, familial, 2 (FEPS2) [MIM:615551]: An autosomal dominant neurologic disorder characterized by adult-onset of paroxysmal pain mainly affecting the distal lower extremities. {ECO:0000269 PubMed:23115331}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SCN10A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SCN10A: view

No data available for Genatlas for SCN10A Gene

Publications for SCN10A Gene

  1. A tetrodotoxin-resistant voltage-gated sodium channel from human dorsal root ganglia, hPN3/SCN10A. (PMID: 9839820) Rabert DK … Sangameswaran L (Pain 1998) 2 3 4 22 58
  2. Gain-of-function Nav1.8 mutations in painful neuropathy. (PMID: 23115331) Faber CG … Waxman SG (Proceedings of the National Academy of Sciences of the United States of America 2012) 3 4 58
  3. Genome-wide association study of PR interval. (PMID: 20062060) Pfeufer A … Heckbert SR (Nature genetics 2010) 3 44 58
  4. Genetic variation in SCN10A influences cardiac conduction. (PMID: 20062061) Chambers JC … Kooner JS (Nature genetics 2010) 3 44 58
  5. Several common variants modulate heart rate, PR interval and QRS duration. (PMID: 20062063) Holm H … Stefansson K (Nature genetics 2010) 3 44 58

Products for SCN10A Gene

Sources for SCN10A Gene

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