SCN11A Gene

HGNC Family	Ion channels
Name	sodium channel, voltage gated, type XI alpha subunit
Description	Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family, and is highly expressed in nociceptive neurons of dorsal root ganglia and trigeminal ganglia. It mediates brain-derived neurotrophic factor-evoked membrane depolarization and is a major effector of peripheral inflammatory pain hypersensitivity. Mutations in this gene have been associated with hereditary sensory and autonomic neuropathy type VII and familial episodic pain syndrome-3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2017]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nSCN11A encodes the voltage‐gated sodium channel Nav1.9, which is predominantly expressed in nociceptive neurons and plays a pivotal role in controlling sensory excitability. A number of genetic studies have revealed that gain‐of‐function mutations in SCN11A lead to aberrant electrical activity by shifting channel gating properties and depolarizing the resting membrane potential. This can manifest clinically either as paradoxical insensitivity to pain—where excessive depolarization impairs action potential generation and leads to congenital inability to perceive pain with resultant self‐injury—or as painful conditions including familial episodic pain, small‐fiber neuropathy, and temperature‐dependent pain disorders. Indeed, human genetics in combination with knock‐in mouse models have illustrated that different mutations in SCN11A (e.g., p.Leu1302Phe, p.V1184A, p.Arg225Cys, and others) provoke hyperexcitability of dorsal root ganglion neurons and are strongly associated with diverse pain phenotypes, a finding further underscored by population screening of painful peripheral neuropathy patients."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "11"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nIn addition to its central role in pain transmission, Nav1.9 contributes to neurotrophin-mediated depolarization of neurons—a mechanism by which agents such as brain-derived neurotrophic factor trigger excitatory responses. Moreover, under inflammatory conditions Nav1.9 appears to be upregulated or redistributed (for example, along axons in the inflamed tissue) thereby exacerbating heat and mechanical pain hypersensitivity. Recent molecular studies have also identified a critical C-terminal motif that modulates the trafficking and membrane expression of Nav1.9, offering insights into how its functional density is regulated under normal and pathological conditions."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "12", "end_ref": "15"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nBeyond its established role in somatosensory pain processing, emerging evidence implicates Nav1.9 in additional sensory and neurophysiological functions. Altered channel function has been linked not only to changes in pain thresholds but also to abnormal itch sensations, essential tremor, gastrointestinal dysmotility, and even mood disturbances as observed in major depressive disorder. These observations suggest that SCN11A-mediated Nav1.9 activity exerts a broader influence on neuronal excitability across both peripheral and central circuits, thereby spotlighting the channel as a promising target for diagnostic and therapeutic strategies in a spectrum of disorders."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "16", "end_ref": "19"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Enrico Leipold, Lutz Liebmann, G Christoph Korenke, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A de novo gain-of-function mutation in SCN11A causes loss of pain perception."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Genet (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ng.2767"}], "href": "https://doi.org/10.1038/ng.2767"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24036948"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24036948"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Jianying Huang, Chongyang Han, Mark Estacion, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Gain-of-function mutations in sodium channel Na(v)1.9 in painful neuropathy."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Brain (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/brain/awu079"}], "href": "https://doi.org/10.1093/brain/awu079"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24776970"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24776970"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Xiang Yang Zhang, Jingmin Wen, Wei Yang, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Cold-aggravated pain in humans caused by a hyperactive NaV1.9 channel mutant."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nat Commun (2015)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/ncomms10049"}], "href": "https://doi.org/10.1038/ncomms10049"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "26645915"}], "href": "https://pubmed.ncbi.nlm.nih.gov/26645915"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Chongyang Han, Yang Yang, Bianca T A de Greef, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Sodium channel NaV1.9 mutations associated with insensitivity to pain dampen neuronal excitability."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Clin Invest (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1172/JCI92373"}], "href": "https://doi.org/10.1172/JCI92373"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28530638"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28530638"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Voraluck Phatarakijnirund, Steven Mumm, William H McAlister, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Yield of peripheral sodium channels gene screening in pure small fibre neuropathy."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Neurol Neurosurg Psychiatry (2019)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1136/jnnp-2018-319042"}], "href": "https://doi.org/10.1136/jnnp-2018-319042"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "30554136"}], "href": "https://pubmed.ncbi.nlm.nih.gov/30554136"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "Robert Blum, Karl W Kafitz, Arthur Konnerth "}, {"type": "b", "children": [{"type": "t", "text": "Neurotrophin-evoked depolarization requires the sodium channel Na(V)1.9."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nature (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/nature01085"}], "href": "https://doi.org/10.1038/nature01085"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12384689"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12384689"}]}, {"type": "r", "ref": 13, "children": [{"type": "t", "text": "Stéphane Lolignier, Muriel Amsalem, François Maingret, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Nav1.9 channel contributes to mechanical and heat pain hypersensitivity induced by subacute and chronic inflammation."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "PLoS One (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1371/journal.pone.0023083"}], "href": "https://doi.org/10.1371/journal.pone.0023083"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21857998"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21857998"}]}, {"type": "r", "ref": 14, "children": [{"type": "t", "text": "Mark D Baker, Mohammed A Nassar "}, {"type": "b", "children": [{"type": "t", "text": "Painful and painless mutations of SCN9A and SCN11A voltage-gated sodium channels."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Pflugers Arch (2020)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00424-020-02419-9"}], "href": "https://doi.org/10.1007/s00424-020-02419-9"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "32601768"}], "href": "https://pubmed.ncbi.nlm.nih.gov/32601768"}]}, {"type": "r", "ref": 15, "children": [{"type": "t", "text": "Luyao Yang, Lulu Li, Haiyan Tang, et al. 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"}, {"type": "b", "children": [{"type": "t", "text": "Elevated SCN11A concentrations associated with lower serum lipid levels in patients with major depressive disorder."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Transl Psychiatry (2024)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/s41398-024-02916-w"}], "href": "https://doi.org/10.1038/s41398-024-02916-w"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "38734669"}], "href": "https://pubmed.ncbi.nlm.nih.gov/38734669"}]}, {"type": "r", "ref": 19, "children": [{"type": "t", "text": "Chenyu Zhao, Xi Zhou, Xiaoliu Shi "}, {"type": "b", "children": [{"type": "t", "text": "The influence of Nav1.9 channels on intestinal hyperpathia and dysmotility."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Channels (Austin) (2023)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1080/19336950.2023.2212350"}], "href": "https://doi.org/10.1080/19336950.2023.2212350"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "37186898"}], "href": "https://pubmed.ncbi.nlm.nih.gov/37186898"}]}]}]}
Synonyms	NAV1.9, SCN12A, PN5, SNS-2, FEPS3, HSAN7, NAN
Proteins	SCNBA_HUMAN
NCBI Gene ID	11280
API
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Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

SCN11A has 4,794 functional associations with biological entities spanning 9 categories (molecular profile, organism, chemical, disease, phenotype or trait, functional term, phrase or reference, structural feature, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 120 datasets.

Click the + buttons to view associations for SCN11A from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

SCN11A Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by SCN11A gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SCN11A gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of SCN11A gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of SCN11A gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of SCN11A gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of SCN11A gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of SCN11A gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of SCN11A gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of SCN11A gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of SCN11A gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of SCN11A gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of SCN11A gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of SCN11A gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with SCN11A protein from the CCLE Cell Line Proteomics dataset.
	CellMarker Gene-Cell Type Associations	cell types associated with SCN11A gene from the CellMarker Gene-Cell Type Associations dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of SCN11A gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of SCN11A gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of SCN11A gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations	phenotypes associated with SCN11A gene from the curated ClinVar Gene-Phenotype Associations dataset.
	ClinVar Gene-Phenotype Associations 2025	phenotypes associated with SCN11A gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CM4AI KOLF21J CRISPRi Gene Perturbation Atlas	gene perturbations changing expression of SCN11A gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of SCN11A gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing SCN11A protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing SCN11A protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with SCN11A protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with SCN11A protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of SCN11A gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with SCN11A gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with SCN11A gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with SCN11A gene/protein from the curated CTD Gene-Disease Associations dataset.
	dbGAP Gene-Trait Associations	traits associated with SCN11A gene in GWAS and other genetic association datasets from the dbGAP Gene-Trait Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of SCN11A protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DepMap CRISPR Gene Dependency	cell lines with fitness changed by SCN11A gene knockdown relative to other cell lines from the DepMap CRISPR Gene Dependency dataset.
	DGIdb Drug Targets 2026	interacting drugs for SCN11A protein from the DGIdb Drug Targets 2026 dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores	diseases involving SCN11A gene from the DISEASES Curated Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving SCN11A gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with SCN11A gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with SCN11A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with SCN11A gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with SCN11A gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.