SCN9A encodes the pore-forming alpha subunit of Nav1.7, a tetrodotoxin-sensitive voltage-gated sodium channel. It is a single large polypeptide (~1977 aa) with the canonical Nav architecture of four internal homologous repeats (domains I-IV), each containing six transmembrane segments (S1-S6); the S4 segments are the voltage sensors and the S5-S6 re-entrant loops form the Na+-selective pore. The channel is functional on its own as a multi-pass plasma membrane protein and is modulated by auxiliary beta subunits (SCN1B, SCN2B, SCN3B, SCN4B). On membrane depolarization the channel opens and selectively conducts Na+ down its electrochemical gradient, mediating the rising (depolarizing) phase of the action potential. Nav1.7 is strongly expressed in peripheral sensory neurons, most notably small-diameter nociceptive dorsal root ganglion neurons, and in sympathetic ganglion neurons; in nociceptors it localizes to the soma membrane, axons, axon/nerve terminals, and nodes of Ranvier, where it acts as a threshold/amplifier channel that boosts subthreshold depolarizations and sets the gain for action potential firing. Loss-of-function mutations cause complete congenital inability to perceive pain, while gain-of-function mutations cause inherited erythromelalgia and paroxysmal extreme pain disorder, establishing Nav1.7 as an essential, non-redundant determinant of human pain sensation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0001518
voltage-gated sodium channel complex
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Nav1.7 is the pore-forming alpha subunit of a voltage-gated sodium channel that assembles with auxiliary beta subunits (SCN1B-SCN4B) into the channel complex. Membership in the VGSC complex is directly demonstrated by cryo-EM (PMID:30765606) and is consistent across the phylogenetic family.
Reason: Well-supported by phylogenetic inference and corroborated by direct structural evidence; correct cellular component for the alpha subunit.
Supporting Evidence:
PMID:30765606
Here we report the cryo-electron microscopy structures of the human Nav1.7-Ξ²1-Ξ²2 complex
|
|
GO:0005248
voltage-gated sodium channel activity
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: Voltage-gated sodium channel activity is the defining molecular function of Nav1.7, demonstrated directly by functional expression (PMID:7720699, PMID:17145499) and broadly conserved across the Nav family.
Reason: Core molecular function, supported by both IBA and multiple experimental IDA annotations.
Supporting Evidence:
PMID:7720699
The channel exhibited rapid activation and inactivation kinetics, and was blocked by tetrodotoxin and cadmium with IC50 values of 24.5 nM and 1.1 mM, respectively.
|
|
GO:0035725
sodium ion transmembrane transport
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: As a Na+-selective channel, Nav1.7 mediates transmembrane movement of Na+ ions (Na(+)(in) = Na(+)(out)), the process directly underlying its channel activity.
Reason: Accurate and specific process term for a sodium channel; directly tied to the enabling molecular function and supported by the catalytic activity (Rhea:RHEA:34963).
Supporting Evidence:
PMID:7720699
A member of a new subclass of the voltage-activated sodium channel genes has been cloned from the human medullary thyroid carcinoma (hMTC) cell line.
|
|
GO:0086002
cardiac muscle cell action potential involved in contraction
|
IBA
GO_REF:0000033 |
MARK AS OVER ANNOTATED |
Summary: This cardiac process term is over-propagated from the Nav family tree. Nav1.7 is not a cardiac channel; the cardiac voltage-gated sodium channel is Nav1.5 (SCN5A). The original cloning study explicitly failed to detect SCN9A transcripts in heart.
Reason: Phylogenetic over-propagation. Nav1.7 is expressed in peripheral sensory and sympathetic neurons, not in cardiomyocytes, and has no established role in cardiac muscle contraction. The IBA WITH/FROM set (P35498 Nav1.1, Q14524 Nav1.5) reflects cardiac-channel paralogs, not SCN9A.
Supporting Evidence:
PMID:7720699
Transcripts were not identified in pituitary gland, brain, heart, liver or kidney, indicating that the hNE-Na is a sodium channel solely expressed in neuroendocrine cells.
|
|
GO:0001508
action potential
|
IEA
GO_REF:0000117 |
KEEP AS NON CORE |
Summary: Nav1.7 contributes to action potential generation, but this is a high-level parent of the more specific experimentally-supported terms neuronal action potential (GO:0019228) and membrane depolarization during action potential (GO:0086010) already annotated.
Reason: Correct but redundant general term; the specific neuronal terms capture the biology more informatively.
Supporting Evidence:
PMID:7720699
Action potentials were generated in cells expressing high levels of hNE-Na.
|
|
GO:0001518
voltage-gated sodium channel complex
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: InterPro-based electronic annotation of VGSC complex membership; redundant with the experimental IPI (PMID:30765606) and IBA annotations to the same term.
Reason: Correct component, consistent with the experimentally and phylogenetically supported annotations to the identical term.
|
|
GO:0005216
monoatomic ion channel activity
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: High-level parent of the specific, experimentally-supported voltage-gated sodium channel activity (GO:0005248).
Reason: Correct but uninformatively general; superseded by the specific MF term.
|
|
GO:0005248
voltage-gated sodium channel activity
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Electronic assertion of the core molecular function, redundant with the experimental IDA and IBA annotations to the same term.
Reason: Correct core molecular function; consistent with experimental evidence.
|
|
GO:0005261
monoatomic cation channel activity
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: High-level parent of voltage-gated sodium channel activity (GO:0005248).
Reason: Correct but uninformatively general; superseded by the specific Na+ channel MF term.
|
|
GO:0005886
plasma membrane
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: Nav1.7 is a multi-pass plasma membrane protein, directly demonstrated by multiple experimental studies.
Reason: Correct and core cellular location of the channel; supported by EXP/IMP annotations and UniProt subcellular location (Cell membrane).
Supporting Evidence:
PMID:30765606
Here we report the cryo-electron microscopy structures of the human Nav1.7-Ξ²1-Ξ²2 complex
|
|
GO:0006811
monoatomic ion transport
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: High-level parent of sodium ion transport / sodium ion transmembrane transport.
Reason: Correct but uninformatively general; superseded by the specific Na+ transport terms.
|
|
GO:0006814
sodium ion transport
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: Sodium ion transport is the process mediated by this Na+-selective channel, though the more specific GO:0035725 (sodium ion transmembrane transport, IBA) is preferable.
Reason: Correct but a less specific sibling/parent of the IBA-annotated sodium ion transmembrane transport term.
|
|
GO:0016020
membrane
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: High-level parent of plasma membrane (GO:0005886), the specific experimentally-supported location.
Reason: Correct but uninformatively general; superseded by plasma membrane.
|
|
GO:0030424
axon
|
IEA
GO_REF:0000044 |
KEEP AS NON CORE |
Summary: Nav1.7 localizes to axons of nociceptor neurons, directly demonstrated in human iPSC-derived nociceptors (PMID:30795902) and consistent with the UniProt subcellular location (Cell projection, axon).
Reason: Accurate location in sensory neurons; non-core relative to the channel's molecular function but a meaningful site of action. Redundant with the IDA-supported axon-related localizations.
Supporting Evidence:
PMID:30795902
localized at the soma membrane, axon, axon
|
|
GO:0043005
neuron projection
|
IEA
GO_REF:0000044 |
KEEP AS NON CORE |
Summary: Parent term encompassing axon/nerve terminals where Nav1.7 localizes; UniProt records Cell projection, neuron projection (PMID:30795902).
Reason: Correct but a general parent of the more specific axon, axon terminus, and node of Ranvier localizations.
Supporting Evidence:
PMID:30795902
localized at the soma membrane, axon, axon
|
|
GO:0055085
transmembrane transport
|
IEA
GO_REF:0000002 |
KEEP AS NON CORE |
Summary: High-level parent of sodium ion transmembrane transport (GO:0035725).
Reason: Correct but uninformatively general; superseded by the specific Na+ transmembrane transport term.
|
|
GO:0007623
circadian rhythm
|
IEA
GO_REF:0000107 |
REMOVE |
Summary: Electronic ortholog-transfer annotation from mouse Scn9a (Q62205) via Ensembl Compara. There is no established role for human Nav1.7 in circadian rhythm, and this is not part of the channel's well-characterized nociceptor biology.
Reason: Weakly supported ortholog-transfer (IEA) annotation with no experimental basis in human and no mechanistic link to the channel's core function. It does not appear in UniProt's curated function summary and risks implying an unsubstantiated role; better excluded than retained as non-core.
|
|
GO:0050965
detection of temperature stimulus involved in sensory perception of pain
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: Electronic ortholog-transfer from mouse Scn9a. Nav1.7 loss in humans produces thermal hypoesthesia and abolishes thermal/noxious pain, so a role in thermal pain signalling is biologically plausible, but Nav1.7 amplifies nociceptor excitability rather than directly transducing temperature.
Reason: Plausible peripheral role consistent with CIP thermal phenotypes, but IEA-only and not a core/direct molecular function; Nav1.7 is a downstream amplifier, not the thermal sensor. Keep as a non-core process annotation.
Supporting Evidence:
PMID:30795902
Cold and warm detection thresholds in both the hand and the foot were reduced when compared to the normative range
|
|
GO:0050974
detection of mechanical stimulus involved in sensory perception
|
IEA
GO_REF:0000107 |
KEEP AS NON CORE |
Summary: Electronic ortholog-transfer from mouse Scn9a. Nav1.7 contributes to mechanical pain sensitivity by amplifying nociceptor firing, but it is not the primary mechanotransducer; in CIP patients mechanical detection thresholds were normal while mechanical pain was abolished.
Reason: Nav1.7 supports mechanical nociception but does not detect mechanical stimuli directly; the term overstates a direct sensory-transduction role. Retain as non-core rather than core.
Supporting Evidence:
PMID:30795902
Mechanical and vibration detection thresholds were normal
|
|
GO:0001518
voltage-gated sodium channel complex
|
IPI
PMID:30765606 Structures of human Na(v)1.7 channel in complex with auxilia... |
ACCEPT |
Summary: Cryo-EM structures of human Nav1.7 in complex with auxiliary subunits (SCN1B/SCN2B) directly establish that SCN9A is part of the voltage-gated sodium channel complex.
Reason: Directly experimentally demonstrated complex membership (ComplexPortal/structure-based); core cellular component.
Supporting Evidence:
PMID:30765606
Here we report the cryo-electron microscopy structures of the human Nav1.7-Ξ²1-Ξ²2 complex
|
|
GO:0086010
membrane depolarization during action potential
|
IDA
PMID:30765606 Structures of human Na(v)1.7 channel in complex with auxilia... |
ACCEPT |
Summary: Nav1.7 conducts the Na+ influx that produces membrane depolarization during the rising phase of the action potential, consistent with its established channel function.
Reason: Accurate and specific process directly mediated by the channel; well aligned with UniProt FUNCTION ("influx of Na(+) ions provokes membrane depolarization").
Supporting Evidence:
PMID:30765606
Voltage-gated sodium channel Nav1.7 represents a promising target for pain relief.
|
|
GO:0005886
plasma membrane
|
EXP
PMID:15385606 Electrophysiological properties of mutant Nav1.7 sodium chan... |
ACCEPT |
Summary: Experimental localization of Nav1.7 (including erythromelalgia mutants) to the cell membrane.
Reason: Correct, experimentally-supported core location of the channel.
Supporting Evidence:
PMID:15385606
Electrophysiological properties of mutant Nav1.7 sodium channels in a painful inherited neuropathy.
|
|
GO:0005886
plasma membrane
|
EXP
PMID:17167479 An SCN9A channelopathy causes congenital inability to experi... |
ACCEPT |
Summary: Functional expression of wild-type and mutant Nav1.7 in HEK293 cells demonstrating plasma-membrane Na+ currents (loss of function in CIP mutants).
Reason: Correct, experimentally-supported core location.
Supporting Evidence:
PMID:17167479
Whole-cell voltage clamp recordings from cells co-expressing wild-type Nav1.7 with the Ξ²1Ξ²2 subunits, revealed a voltage-gated Na+ current
|
|
GO:0005886
plasma membrane
|
EXP
PMID:19369487 Early- and late-onset inherited erythromelalgia: genotype-ph... |
ACCEPT |
Summary: Experimental characterization of inherited erythromelalgia mutants with cell-membrane localization/function.
Reason: Correct, experimentally-supported core location.
Supporting Evidence:
PMID:19369487
Early- and late-onset inherited erythromelalgia: genotype-phenotype correlation.
|
|
GO:0005886
plasma membrane
|
EXP
PMID:24311784 Inherited pain: sodium channel Nav1.7 A1632T mutation causes... |
ACCEPT |
Summary: Functional study of the A1632T erythromelalgia mutant with surface expression and altered fast inactivation.
Reason: Correct, experimentally-supported core location.
Supporting Evidence:
PMID:24311784
sodium channel Nav1.7 A1632T mutation causes erythromelalgia due to a shift of fast inactivation
|
|
GO:0005886
plasma membrane
|
EXP
PMID:25240195 Protein kinase C enhances human sodium channel hNav1.7 resur... |
ACCEPT |
Summary: Functional study showing PKC phosphorylation enhances Nav1.7 resurgent currents at the cell membrane.
Reason: Correct, experimentally-supported core location.
Supporting Evidence:
PMID:25240195
Protein kinase C enhances human sodium channel hNav1.7 resurgent currents via a serine residue in the domain III-IV linker.
|
|
GO:0005886
plasma membrane
|
EXP
PMID:26680203 Structural basis of Nav1.7 inhibition by an isoform-selectiv... |
ACCEPT |
Summary: Structural/functional study of Nav1.7 inhibition by a small-molecule antagonist, consistent with the channel residing in the cell membrane.
Reason: Correct, experimentally-supported core location.
Supporting Evidence:
PMID:26680203
Structural basis of Nav1.7 inhibition by an isoform-selective small-molecule antagonist.
|
|
GO:0005886
plasma membrane
|
EXP
PMID:7720699 Structure and functional expression of a new member of the t... |
ACCEPT |
Summary: Original functional expression of hNE-Na (Nav1.7) producing voltage-gated Na+ currents and action potentials at the cell surface.
Reason: Correct, experimentally-supported core location from the founding functional study.
Supporting Evidence:
PMID:7720699
The hNE-Na alpha subunit was transiently expressed in human embryonic kidney cells either alone or in combination with the human sodium channel beta 1 subunit.
|
|
GO:0005248
voltage-gated sodium channel activity
|
IDA
PMID:7720699 Structure and functional expression of a new member of the t... |
ACCEPT |
Summary: The founding study cloned hNE-Na (Nav1.7) and demonstrated voltage-gated, TTX-sensitive Na+ channel activity with rapid activation/inactivation kinetics upon heterologous expression.
Reason: Direct experimental demonstration of the core molecular function; primary evidence for GO:0005248.
Supporting Evidence:
PMID:7720699
The channel exhibited rapid activation and inactivation kinetics, and was blocked by tetrodotoxin and cadmium with IC50 values of 24.5 nM and 1.1 mM, respectively.
|
|
GO:0019228
neuronal action potential
|
IDA
PMID:30795902 Defining the Functional Role of Na(V)1.7 in Human Nociceptio... |
ACCEPT |
Summary: In human iPSC-derived nociceptors and CIP studies, Nav1.7 is required for normal nociceptor action potential firing, defining its role in the neuronal action potential.
Reason: Specific, experimentally-supported neuronal process directly reflecting Nav1.7's threshold/amplifier role in sensory neurons.
Supporting Evidence:
PMID:30795902
Defining the Functional Role of Na(V)1.7 in Human Nociception.
|
|
GO:0019233
sensory perception of pain
|
IMP
PMID:30795902 Defining the Functional Role of Na(V)1.7 in Human Nociceptio... |
ACCEPT |
Summary: Loss of functional Nav1.7 in CIP participants abolishes the perception of noxious thermal and mechanical stimuli as painful, demonstrating an essential role in pain sensation.
Reason: Decisive human-genetics evidence; core biological process of Nav1.7.
Supporting Evidence:
PMID:30795902
neither noxious temperature nor noxious mechanical stimuli were felt as painful
|
|
GO:0033268
node of Ranvier
|
IDA
PMID:30795902 Defining the Functional Role of Na(V)1.7 in Human Nociceptio... |
ACCEPT |
Summary: CRISPR-tagged endogenous Nav1.7 localized to the great majority of nodes of Ranvier in myelinated human iPSC-nociceptor co-cultures.
Reason: Directly demonstrated localization in human neurons; specific and informative cellular component.
Supporting Evidence:
PMID:30795902
NaV1.7 could be seen localized to >90% of nodes of Ranvier in myelinated axons
|
|
GO:0043679
axon terminus
|
IDA
PMID:30795902 Defining the Functional Role of Na(V)1.7 in Human Nociceptio... |
ACCEPT |
Summary: Endogenous tagged Nav1.7 was enriched in terminal structures of human iPSC nociceptors, consistent with prior reports of axon-terminal localization in rodent DRG neurons.
Reason: Directly demonstrated localization; specific and informative component relevant to action potential initiation/propagation at terminals.
Supporting Evidence:
PMID:30795902
staining revealed enrichment of NaV1.7 in terminal structures of our iPSC nociceptors
|
|
GO:0098870
action potential propagation
|
IDA
PMID:17145499 SCN9A mutations in paroxysmal extreme pain disorder: allelic... |
ACCEPT |
Summary: PEPD gain-of-function mutations impair Nav1.7 fast inactivation, producing persistent Na+ current and hyperexcitability that alters action potential firing/propagation in sensory neurons.
Reason: Consistent with Nav1.7's role in conducting/propagating depolarization; supported by an experimental electrophysiology study (full text read by curator).
Supporting Evidence:
PMID:17145499
Functional analysis in vitro of three of these mutant Na(v)1.7 channels revealed a reduction in fast inactivation, leading to persistent sodium current.
|
|
GO:0098870
action potential propagation
|
IDA
PMID:7720699 Structure and functional expression of a new member of the t... |
ACCEPT |
Summary: Cells expressing high levels of hNE-Na (Nav1.7) generated action potentials, consistent with the channel's role in initiating and propagating electrical signals.
Reason: Experimentally supported; the channel drives the depolarizing phase required for action potential propagation.
Supporting Evidence:
PMID:7720699
Action potentials were generated in cells expressing high levels of hNE-Na.
|
|
GO:0005515
protein binding
|
IPI
PMID:37117223 Pain-causing stinging nettle toxins target TMEM233 to modula... |
MARK AS OVER ANNOTATED |
Summary: This IPI annotation records the experimentally-demonstrated interaction between Nav1.7 and TMEM233 (B4DJY2), a transmembrane protein required for nettle-toxin modulation of Nav1.7 gating. The generic "protein binding" term is uninformative and does not capture the regulatory nature of this interaction.
Reason: Per curation guidelines, generic protein binding should be avoided in favour of an informative molecular function. The underlying biology is a channel-regulator/auxiliary-protein interaction (TMEM233 modulates Nav1.7 gating), but no sufficiently specific GO molecular-function term is clearly applicable; the specific interaction partner and regulatory role are better captured in notes/SUBUNIT than by this uninformative term.
Supporting Evidence:
PMID:37117223
Pain-causing stinging nettle toxins target TMEM233 to modulate Na(V)1.7 function.
file:human/SCN9A/SCN9A-deep-research-falcon.md
identified **TMEM233 (a dispanin-family protein)** as an essential **NaV1.7-interacting accessory protein** for the action of the plant-derived knottin toxin **Excelsatoxin A (ExTxA)**.
|
|
GO:0030424
axon
|
ISS
GO_REF:0000024 |
KEEP AS NON CORE |
Summary: Sequence-similarity transfer (from rat Pn1/O08562) of axonal localization; consistent with experimental human IDA data placing Nav1.7 in axons.
Reason: Accurate location supported by stronger human evidence; non-core relative to molecular function and redundant with the IEA axon annotation.
Supporting Evidence:
PMID:30795902
localized at the soma membrane, axon, axon
|
|
GO:0005248
voltage-gated sodium channel activity
|
IDA
PMID:17145499 SCN9A mutations in paroxysmal extreme pain disorder: allelic... |
ACCEPT |
Summary: Functional in vitro analysis of PEPD mutant Nav1.7 channels confirmed voltage-gated sodium channel activity (with altered fast inactivation in mutants).
Reason: Direct experimental evidence for the core molecular function.
Supporting Evidence:
PMID:17145499
Functional analysis in vitro of three of these mutant Na(v)1.7 channels revealed a reduction in fast inactivation, leading to persistent sodium current.
|
|
GO:0005886
plasma membrane
|
IMP
PMID:17145499 SCN9A mutations in paroxysmal extreme pain disorder: allelic... |
ACCEPT |
Summary: Functional expression of PEPD mutant channels demonstrates plasma-membrane Na+ currents, supporting cell-membrane localization.
Reason: Correct, experimentally-supported core location.
Supporting Evidence:
PMID:17145499
Functional analysis in vitro of three of these mutant Na(v)1.7 channels revealed a reduction in fast inactivation, leading to persistent sodium current.
|
|
GO:0019233
sensory perception of pain
|
IMP
PMID:17145499 SCN9A mutations in paroxysmal extreme pain disorder: allelic... |
ACCEPT |
Summary: Gain-of-function SCN9A mutations cause paroxysmal extreme pain disorder, directly linking Nav1.7 dysfunction to abnormal pain perception.
Reason: Human-genetics (mutant-phenotype) evidence for the core pain-perception role of Nav1.7.
Supporting Evidence:
PMID:17145499
an inherited condition characterized by paroxysms of rectal, ocular, or submandibular pain with flushing
|
This report is retrieval-only and is generated directly from Asta results.
search_papers_by_relevance with snippet_search.The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The target protein is the human voltageβgated sodium channel NaV1.7 Ξ±βsubunit, encoded by SCN9A, and is explicitly linked to UniProt accession Q15858 in a biochemical study analyzing the full-length channel (βfullβlength NaV1.7 (SCN9A, Uniprot Q15858)β). (wright2023thecterminalof pages 2-3)
NaV1.7 is a voltage-gated sodium (Na+) channel that supports membrane excitability by permitting selective Na+ flux during action potentials; in nociceptors it is strongly implicated in determining excitability near threshold and thereby controlling pain signaling. (toffano2020computationalpipelineto pages 1-2, meents2019theroleof pages 1-2)
Selectivity/substrate specificity: NaV1.7 is selective for Na+ and shares the canonical NaV architecture and DEKA selectivity filter (Asp-Glu-Lys-Ala across DIβDIV) described for eukaryotic NaV Ξ± subunits. (toffano2020computationalpipelineto pages 1-2)
The NaV Ξ±-subunit is a single ~2,000 aminoβacid polypeptide organized into four homologous domains (DIβDIV); each domain contains six transmembrane helices (S1βS6). S1βS4 form the voltage-sensing domain (VSD) and S5βS6 plus the extracellular P-loop form the pore domain and selectivity filter. (toffano2020computationalpipelineto pages 1-2, wood2025sensoryneuronsodium pages 1-2)
NaV1.7 is a plasma-membrane channel enriched in nociceptive neurons, with high expression reported in dorsal root ganglia (DRG), trigeminal ganglia, and sympathetic gangliaβan expression pattern central to its role in pain pathways. (dormer2023areviewof pages 8-9)
SCN9A is among the strongest βhuman-validatedβ targets in pain biology:
- Gain-of-function (GOF) variants cause painful channelopathies (e.g., inherited erythromelalgia, paroxysmal extreme pain disorder, and subsets of small fiber neuropathy). (baker2020painfulandpainless pages 1-2, meents2019theroleof pages 1-2)
- Loss-of-function (LOF) variants cause congenital insensitivity to pain. (baker2020painfulandpainless pages 1-2, meents2019theroleof pages 1-2)
These genotypeβphenotype links provide unusually direct causal evidence connecting a single ion channel to a clinically meaningful sensory modality. (baker2020painfulandpainless pages 1-2, meents2019theroleof pages 1-2)
A major 2023 advance was the publication of high-resolution cryoβEM structures of human NaV1.7 bound to multiple clinically used drugs and investigational compounds (2.6β3.2 Γ
). This work mapped multiple druggable binding sites including:
- a site beneath the intracellular gate (βsite BIGβ) accommodating carbamazepine, bupivacaine, and lacosamide,
- binding in pore fenestrations (e.g., vixotrigine in the IVβI fenestration; vinpocetine and hardwickiic acid at the IIIβIV fenestration),
- an unexpected second lacosamide molecule plugging into the selectivity filter from the central cavity. (wu2023structuralmappingof pages 1-2)
A figure from this study provides a consolidated schematic of the mapped druggable sites and is useful for functional annotation because it links channel anatomy directly to chemical mechanisms of inhibition/modulation. (wu2023structuralmappingof media a264241d)
A 2023 Nature Communications study demonstrated that voltage-gated sodium channels can behave as multiprotein signaling complexes, and identified TMEM233 (a dispanin-family protein) as an essential NaV1.7-interacting accessory protein for the action of the plant-derived knottin toxin Excelsatoxin A (ExTxA). ExTxA inhibits fast inactivation and induces persistent currents in sensory neurons; in human iPSC-derived sensory neurons this persistent current was largely blocked by a selective NaV1.7 blocker (Pn3a 100 nM), implicating NaV1.7 as a major mediator. (jami2023paincausingstingingnettle pages 1-2)
This establishes a contemporary concept: native accessory proteins can be required to reproduce pharmacology observed in sensory neurons, which may help explain discrepancies between heterologous assays and clinical outcomes. (jami2023paincausingstingingnettle pages 1-2)
A 2023 ACS Bio & Med Chem Au study provided direct biochemical evidence that the E3 ligase NEDD4L ubiquitinates the cytoplasmic Cβterminus of NaV1.7. The work also documents motifs in the Cβterminus relevant to regulation (including an IQ motif and a NEDD4L-recognized PY motif) and identifies ubiquitinated lysines by mass spectrometry. (wright2023thecterminalof pages 1-2, wright2023thecterminalof pages 2-3)
This supports a functional annotation element often missing from older descriptions: post-translational modification and trafficking/turnover regulation are likely important determinants of NaV1.7 surface density and nociceptor excitability. (wright2023thecterminalof pages 1-2, wright2023thecterminalof pages 2-3)
A 2023 Journal of General Physiology study used a tractable bacterial NaV homolog (NaVAb) carrying human-analogous inherited erythromelalgia mutations to provide structural explanations for negative shifts in activation (gain-of-function): widening of the gating-charge translocation pathway or altered hydrophobic/phospholipid interactions favoring outward S4 movement. (wisedchaisri2023structuralbasisfor pages 1-2)
A 2024 PNAS study solved cryoβEM structures (2.9β3.4 Γ ) of engineered human NaV1.7 mutants and linked pore-domain contraction to right-shifted activation/static inactivation, refining how structural states map onto electrophysiological behavior. (li2024dissectionofthe pages 1-2)
Two notable 2024 directions go beyond classic small-molecule pore blockers:
- Single-domain antibody (VHH) against human NaV1.7: an Aug 2024 study reported a VHH that binds NaV1.7, slows deactivation, reduces nociceptor action potential firing, and reverses hyperalgesia in rodent models. (martina2024anovelantigen pages 1-2)
- AAV-delivered engineered transcriptional repressors: a Sep 2024 preprint reported zinc-finger repressors achieving ~90% SCN9A repression in human iPSC-derived neurons, up to 70% repression in mouse DRG, and up to 60% repression in nonhuman primate DRG after intrathecal delivery, with short-term tolerability in NHP. (samie2024potentandselective pages 1-3)
Together these illustrate a shift from βblock the poreβ to modulate gating with biologics or reduce SCN9A expression as potentially more durable analgesic strategies. (martina2024anovelantigen pages 1-2, samie2024potentandselective pages 1-3)
Real-world implementation is best captured by registered clinical trial protocols:
PFβ05089771 (Pfizer) in painful diabetic peripheral neuropathy (DPN):
- NCT02215252 (Phase 2; randomized, double-blind, parallel; COMPLETED) tested PFβ05089771 150 mg BID as monotherapy and as add-on to pregabalin 150 mg BID (300 mg/day).
- Enrollment: 141 participants.
- Primary endpoint: daily pain numeric rating scale (mean of last 7 days).
- Key secondary endpoints: responder rates (30%/50%), Neuropathic Pain Symptom Inventory, PGIC, sleep interference, rescue medication use. (NCT02215252 chunk 1, NCT02215252 chunk 2)
Genotype-guided NaV1.7 strategy in small fiber neuropathy (SFN):
- NCT01911975 (Phase 3; randomized; quadruple-masked; crossover; COMPLETED) evaluated lacosamide 200 mg BID vs placebo in patients with gain-of-function SCN9A mutations and SFN.
- Enrollment: 25.
- Primary endpoint: mean daily pain intensity recorded twice daily over 33 weeks. (NCT01911975 chunk 1)
Inherited erythromelalgia (IEM) precision trial:
- NCT07262268 (Phase 1b; randomized crossover; quadruple-masked; start 2026) enrolls IEM participants with characterized NaV1.7 gain-of-function SCN9A mutations; enrollment 5; primary outcome uses frequent pain scoring. (NCT07262268 chunk 1)
These protocols show how SCN9A biology is operationalized clinically: either by targeting NaV1.7 pharmacologically (often with mixed efficacy historically) or by selecting subjects with SCN9A GOF variants to increase mechanistic alignment and effect size potential. (dormer2023areviewof pages 4-5, NCT02215252 chunk 1)
SCN9A variation is also implemented in prospective genotypeβphenotype studies:
- NCT02496455: postoperative pain after cesarean section (n=200) with SCN9A SNP genotyping and outcomes including 24-hour VAS pain and tramadol consumption. (NCT02496455 chunk 1)
A 2024 Pain review analyzing the mismatch between preclinical and clinical testing concludes that despite strong genetic support for NaV1.7, NaV1.7-selective inhibitors have not yet proven effective in clinical trials, and highlights key design mismatches: species/population differences, inflammatory pain models vs neuropathic pain trials, evoked pain endpoints vs average pain intensity, and single-dose preclinical studies vs repeat dosing clinically. ()
A 2023 review focusing on SCN9A/Nav1.7 clinical trials similarly concludes that small-molecule programs have often been inconclusive, motivating exploration of alternative approaches (including gene therapy-like strategies). (dormer2023areviewof pages 8-9, dormer2023areviewof pages 4-5)
The following figure (cropped from the primary 2023 cryoβEM study) summarizes multiple druggable binding sites mapped onto NaV1.7 and supports the structural pharmacology narrative in Sections 2.1 and 5. (wu2023structuralmappingof media a264241d)
The table below consolidates key functional annotation points, evidence types, and translational status with DOIs/URLs.
| Category | Key points | Representative recent sources (DOI/URL) | Evidence type |
|---|---|---|---|
| Identity | Human SCN9A encodes NaV1.7; explicit match to UniProt Q15858 in biochemical study of the full-length channel. C-terminal region includes IQ motif and PY (PPSY) motif relevant to regulation. (wright2023thecterminalof pages 2-3, wright2023thecterminalof pages 1-2) | Wright et al., 2023. DOI: 10.1021/acsbiomedchemau.3c00031; https://doi.org/10.1021/acsbiomedchemau.3c00031 | Biochemistry |
| Structure | Canonical voltage-gated sodium channel Ξ±-subunit architecture: ~2,000 aa, 4 homologous domains (DIβDIV), each with 6 TM helices (S1βS6); S1βS4 form VSDs, S5βS6 + P-loop form pore/selectivity filter; DEKA selectivity filter. (toffano2020computationalpipelineto pages 1-2, wood2025sensoryneuronsodium pages 1-2) | Toffano et al., 2020. DOI: 10.1038/s41598-020-74591-y; https://doi.org/10.1038/s41598-020-74591-y. Wood et al., 2025. DOI: 10.1085/jgp.202513778; https://doi.org/10.1085/jgp.202513778 | Structural/functional review, computational synthesis |
| Localization | NaV1.7 is highly expressed in nociceptive neurons of dorsal root ganglia (DRG), trigeminal ganglia, and sympathetic ganglia; positioned at the plasma membrane to regulate excitability. (dormer2023areviewof pages 8-9) | Dormer et al., 2023. DOI: 10.2147/JPR.S388896; https://doi.org/10.2147/JPR.S388896 | Review |
| Physiology | In human iPSC-derived nociceptors from inherited erythromelalgia, SCN9A/NaV1.7 gain-of-function shifts activation to more negative voltages, lowers firing threshold, and enhances AP upstroke; supports NaV1.7 as a threshold channel for action-potential initiation in pain pathways. (meents2019theroleof pages 1-2, meents2019theroleof pages 10-12) | Meents et al., 2019. DOI: 10.1097/j.pain.0000000000001511; https://doi.org/10.1097/j.pain.0000000000001511 | Human electrophysiology, iPSC nociceptors |
| Regulation | NaV1.7 C-terminus is ubiquitinated by NEDD4L; study identified ubiquitinated lysines and defined a CT region containing an EF-hand-like bundle, IQ motif, and PY motif that can regulate channel trafficking/turnover. (wright2023thecterminalof pages 1-2, wright2023thecterminalof pages 2-3) | Wright et al., 2023. DOI: 10.1021/acsbiomedchemau.3c00031; https://doi.org/10.1021/acsbiomedchemau.3c00031 | Biochemistry, mass spectrometry |
| Regulation / accessory proteins | Plant toxin ExTxA requires TMEM233 (a sensory-neuron dispanin) for pharmacological activity at NaV1.7; toxin-induced persistent current in human sensory neurons was largely blocked by Pn3a 100 nM, showing accessory-protein dependence of Nav1.7 modulation. (jami2023paincausingstingingnettle pages 1-2) | Jami et al., 2023. DOI: 10.1038/s41467-023-37963-2; https://doi.org/10.1038/s41467-023-37963-2 | Electrophysiology, molecular pharmacology |
| Structural pharmacology | Cryo-EM structures of human NaV1.7 bound to drugs/lead compounds at 2.6β3.2 Γ mapped multiple binding sites, including site BIG beneath the intracellular gate; vixotrigine occupies a fenestration site; lacosamide also showed unexpected occupancy near the selectivity filter. Figure-level structural atlas of druggable sites was retrieved. (wu2023structuralmappingof pages 1-2, wu2023structuralmappingof media a264241d) | Wu et al., 2023. DOI: 10.1038/s41467-023-38942-3; https://doi.org/10.1038/s41467-023-38942-3 | Cryo-EM structural pharmacology |
| Structural mechanism | Engineered Nav1.7 mutants solved at 2.9β3.4 Γ showed correlation between pore-domain contraction and right-shifted activation/static inactivation, refining structureβfunction understanding of gating states relevant to drug design. (li2024dissectionofthe pages 1-2) | Li et al., 2024. DOI: 10.1073/pnas.2322899121; https://doi.org/10.1073/pnas.2322899121 | Cryo-EM, electrophysiology |
| Genetics | Human genetics strongly validate SCN9A: gain-of-function variants cause painful syndromes including inherited erythromelalgia (IEM), paroxysmal extreme pain disorder (PEPD), and some small-fiber neuropathy (SFN); loss-of-function variants cause congenital insensitivity to pain (CIP). (baker2020painfulandpainless pages 1-2, meents2019theroleof pages 1-2, yogi2025preclinicalanimalmodels pages 1-3) | Baker & Nassar, 2020. DOI: 10.1007/s00424-020-02419-9; https://doi.org/10.1007/s00424-020-02419-9. Meents et al., 2019. DOI above | Review, human genetics, electrophysiology |
| Clinical translation | Small-molecule clinical development has been active but disappointing overall; review notes ~30% of idiopathic SFN linked to SCN9A and summarizes funapide/TV-45070, PF-05089771, vixotrigine, and lacosamide programs; expression in DRG/TG/sympathetic neurons supports target rationale but efficacy has often been modest. (dormer2023areviewof pages 4-5) | Dormer et al., 2023. DOI: 10.2147/JPR.S388896; https://doi.org/10.2147/JPR.S388896 | Review, clinical landscape |
| Clinical translation / registry | PF-05089771 Phase 2 painful diabetic peripheral neuropathy study NCT02215252: completed; n=141; monotherapy 150 mg BID and add-on pregabalin 150 mg BID arms; endpoints included daily pain NRS, responder rates, NPSI, PGIC, sleep interference, rescue medication. (NCT02215252 chunk 1, NCT02215252 chunk 2) | ClinicalTrials.gov NCT02215252; https://clinicaltrials.gov/study/NCT02215252 | Clinical trial registry |
| Clinical translation / precision medicine | Lacosamide genotype-guided SCN9A gain-of-function SFN study NCT01911975: randomized quadruple-masked crossover; n=25; 200 mg BID vs placebo; pain assessed over 33 weeks. (NCT01911975 chunk 1) | ClinicalTrials.gov NCT01911975; https://clinicaltrials.gov/study/NCT01911975 | Clinical trial registry |
| Clinical translation / observational genomics | SCN9A polymorphism study NCT02496455: prospective postoperative-pain cohort after cesarean section; n=200; genotyped rs6746030, rs7604448, rs10930214, rs7595255; outcomes were VAS pain and 24 h tramadol consumption. (NCT02496455 chunk 1) | ClinicalTrials.gov NCT02496455; https://clinicaltrials.gov/study/NCT02496455 | Clinical trial registry, observational genetics |
| Emerging therapeutics | Single-domain antibody (VHH) against human NaV1.7 slowed deactivation, reduced nociceptor firing, and reversed hyperalgesia in rodent models, demonstrating feasibility of a biologic modality. (martina2024anovelantigen pages 1-2) | Martina et al., 2024. DOI: 10.1002/advs.202405432; https://doi.org/10.1002/advs.202405432 | Biologic engineering, electrophysiology, animal models |
| Emerging therapeutics | Engineered zinc-finger repressors (ZFRs) targeting SCN9A achieved 90% repression in human iPSC-derived neurons, up to 70% repression in mouse DRG, and up to 60% repression in nonhuman-primate DRG after AAV delivery, supporting gene-regulatory analgesic strategies. (samie2024potentandselective pages 1-3) | Samie et al., 2024. DOI: 10.1101/2024.09.06.609976; https://doi.org/10.1101/2024.09.06.609976 | Preclinical gene regulation, AAV, transcript repression |
| Emerging clinical precision medicine | BHV-7000/opakalim inherited erythromelalgia study NCT07262268: Phase 1b, double-blind crossover, n=5, enrolling participants with characterized NaV1.7 gain-of-function SCN9A mutations; endpoints include maximum pain intensity and attack metrics. (NCT07262268 chunk 1) | ClinicalTrials.gov NCT07262268; https://clinicaltrials.gov/study/NCT07262268 | Clinical trial registry |
Table: This table summarizes functional annotation, mechanism, genetics, and clinical translation for human SCN9A/Nav1.7 using the most relevant gathered evidence, prioritizing 2023β2024 sources where possible. It is useful as a compact reference linking molecular function to experimental support and translational status.
UniProt lists historical names such as βneuroendocrine sodium channel,β βPN1,β and βhNEβNa.β These aliases were not directly encountered in the retrieved primary texts; this report therefore treats them as database-derived synonyms and relies on primary literature for functional claims. The SCN9A β NaV1.7 β UniProt Q15858 mapping is explicitly supported in Wright et al. 2023. (wright2023thecterminalof pages 2-3)
References
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UniProt: Q15858 | HGNC: SCN9A | Taxon: NCBITaxon:9606 (human)
PANTHER family: PTHR10037 (VOLTAGE-GATED CATION CHANNEL CALCIUM AND SODIUM)
SCN9A encodes the pore-forming alpha subunit of Nav1.7, a tetrodotoxin-sensitive
voltage-gated sodium channel. It is a single-polypeptide channel of ~1977 aa with the
canonical Nav architecture: 4 internal homologous repeats (domains IβIV), each with 6
transmembrane segments (S1βS6); S4 segments are the voltage sensors and the S5βS6
re-entrant loops form the Na+-selective pore. The channel is functional on its own but
is modulated by beta subunits (SCN1B/SCN2B/SCN3B/SCN4B).
Strongly expressed in dorsal root ganglion (nociceptors), sympathetic neurons, with
minor levels elsewhere (smooth muscle, MTC cell line, C-cell carcinoma, vagus nerve).
Original cloning paper explicitly: "Transcripts were not identified in pituitary gland,
brain, heart, liver or kidney" β i.e. NOT a cardiac channel (cardiac Nav is
Nav1.5/SCN5A). PMID:7720699
Nav1.7 function is exceptionally well validated by human Mendelian genetics:
- Congenital insensitivity to pain (CIP) β autosomal recessive, biallelic nonsense/LOF
mutations (S459X, I767X, W897X); complete loss of function abolishes pain. "SCN9A is an
essential and non-redundant requirement for nociception in humans." PMID:17167479
- Inherited/primary erythromelalgia (PERYTHM) β gain-of-function (hyperpolarizing shift
of activation) β burning extremity pain. [PMID:15385606, PMID:19369487, PMID:24311784]
- Paroxysmal extreme pain disorder (PEPD) β gain-of-function (impaired fast
inactivation β persistent current). PMID:17145499
These establish GO:0019233 sensory perception of pain (IMP) on the firmest possible footing.
id: Q15858
gene_symbol: SCN9A
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:9606
label: Homo sapiens
description: SCN9A encodes the pore-forming alpha subunit of Nav1.7, a tetrodotoxin-sensitive
voltage-gated sodium channel. It is a single large polypeptide (~1977 aa) with the
canonical Nav architecture of four internal homologous repeats (domains I-IV), each
containing six transmembrane segments (S1-S6); the S4 segments are the voltage sensors
and the S5-S6 re-entrant loops form the Na+-selective pore. The channel is functional
on its own as a multi-pass plasma membrane protein and is modulated by auxiliary
beta subunits (SCN1B, SCN2B, SCN3B, SCN4B). On membrane depolarization the channel
opens and selectively conducts Na+ down its electrochemical gradient, mediating the
rising (depolarizing) phase of the action potential. Nav1.7 is strongly expressed
in peripheral sensory neurons, most notably small-diameter nociceptive dorsal root
ganglion neurons, and in sympathetic ganglion neurons; in nociceptors it localizes
to the soma membrane, axons, axon/nerve terminals, and nodes of Ranvier, where it
acts as a threshold/amplifier channel that boosts subthreshold depolarizations and
sets the gain for action potential firing. Loss-of-function mutations cause complete
congenital inability to perceive pain, while gain-of-function mutations cause inherited
erythromelalgia and paroxysmal extreme pain disorder, establishing Nav1.7 as an essential,
non-redundant determinant of human pain sensation.
alternative_products:
- name: '1'
id: Q15858-1
- name: '2'
id: Q15858-2
sequence_note: VSP_012028
- name: '3'
id: Q15858-3
sequence_note: VSP_012029
- name: '4'
id: Q15858-4
sequence_note: VSP_012028, VSP_012029
existing_annotations:
- term:
id: GO:0001518
label: voltage-gated sodium channel complex
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: part_of
review:
summary: Nav1.7 is the pore-forming alpha subunit of a voltage-gated sodium channel
that assembles with auxiliary beta subunits (SCN1B-SCN4B) into the channel complex.
Membership in the VGSC complex is directly demonstrated by cryo-EM (PMID:30765606)
and is consistent across the phylogenetic family.
action: ACCEPT
reason: Well-supported by phylogenetic inference and corroborated by direct structural
evidence; correct cellular component for the alpha subunit.
supported_by:
- reference_id: PMID:30765606
supporting_text: Here we report the cryo-electron microscopy structures of the
human Nav1.7-Ξ²1-Ξ²2 complex
- term:
id: GO:0005248
label: voltage-gated sodium channel activity
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: enables
review:
summary: Voltage-gated sodium channel activity is the defining molecular function
of Nav1.7, demonstrated directly by functional expression (PMID:7720699, PMID:17145499)
and broadly conserved across the Nav family.
action: ACCEPT
reason: Core molecular function, supported by both IBA and multiple experimental
IDA annotations.
supported_by:
- reference_id: PMID:7720699
supporting_text: The channel exhibited rapid activation and inactivation kinetics,
and was blocked by tetrodotoxin and cadmium with IC50 values of 24.5 nM and
1.1 mM, respectively.
- term:
id: GO:0035725
label: sodium ion transmembrane transport
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: As a Na+-selective channel, Nav1.7 mediates transmembrane movement of
Na+ ions (Na(+)(in) = Na(+)(out)), the process directly underlying its channel
activity.
action: ACCEPT
reason: Accurate and specific process term for a sodium channel; directly tied
to the enabling molecular function and supported by the catalytic activity (Rhea:RHEA:34963).
supported_by:
- reference_id: PMID:7720699
supporting_text: A member of a new subclass of the voltage-activated sodium
channel genes has been cloned from the human medullary thyroid carcinoma (hMTC)
cell line.
- term:
id: GO:0086002
label: cardiac muscle cell action potential involved in contraction
evidence_type: IBA
original_reference_id: GO_REF:0000033
qualifier: involved_in
review:
summary: This cardiac process term is over-propagated from the Nav family tree.
Nav1.7 is not a cardiac channel; the cardiac voltage-gated sodium channel is
Nav1.5 (SCN5A). The original cloning study explicitly failed to detect SCN9A
transcripts in heart.
action: MARK_AS_OVER_ANNOTATED
reason: Phylogenetic over-propagation. Nav1.7 is expressed in peripheral sensory
and sympathetic neurons, not in cardiomyocytes, and has no established role in
cardiac muscle contraction. The IBA WITH/FROM set (P35498 Nav1.1, Q14524 Nav1.5)
reflects cardiac-channel paralogs, not SCN9A.
supported_by:
- reference_id: PMID:7720699
supporting_text: Transcripts were not identified in pituitary gland, brain,
heart, liver or kidney, indicating that the hNE-Na is a sodium channel solely
expressed in neuroendocrine cells.
- term:
id: GO:0001508
label: action potential
evidence_type: IEA
original_reference_id: GO_REF:0000117
qualifier: involved_in
review:
summary: Nav1.7 contributes to action potential generation, but this is a high-level
parent of the more specific experimentally-supported terms neuronal action potential
(GO:0019228) and membrane depolarization during action potential (GO:0086010)
already annotated.
action: KEEP_AS_NON_CORE
reason: Correct but redundant general term; the specific neuronal terms capture
the biology more informatively.
supported_by:
- reference_id: PMID:7720699
supporting_text: Action potentials were generated in cells expressing high levels
of hNE-Na.
- term:
id: GO:0001518
label: voltage-gated sodium channel complex
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: part_of
review:
summary: InterPro-based electronic annotation of VGSC complex membership; redundant
with the experimental IPI (PMID:30765606) and IBA annotations to the same term.
action: ACCEPT
reason: Correct component, consistent with the experimentally and phylogenetically
supported annotations to the identical term.
- term:
id: GO:0005216
label: monoatomic ion channel activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: High-level parent of the specific, experimentally-supported voltage-gated
sodium channel activity (GO:0005248).
action: KEEP_AS_NON_CORE
reason: Correct but uninformatively general; superseded by the specific MF term.
- term:
id: GO:0005248
label: voltage-gated sodium channel activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: enables
review:
summary: Electronic assertion of the core molecular function, redundant with the
experimental IDA and IBA annotations to the same term.
action: ACCEPT
reason: Correct core molecular function; consistent with experimental evidence.
- term:
id: GO:0005261
label: monoatomic cation channel activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: enables
review:
summary: High-level parent of voltage-gated sodium channel activity (GO:0005248).
action: KEEP_AS_NON_CORE
reason: Correct but uninformatively general; superseded by the specific Na+ channel
MF term.
- term:
id: GO:0005886
label: plasma membrane
evidence_type: IEA
original_reference_id: GO_REF:0000120
qualifier: located_in
review:
summary: Nav1.7 is a multi-pass plasma membrane protein, directly demonstrated
by multiple experimental studies.
action: ACCEPT
reason: Correct and core cellular location of the channel; supported by EXP/IMP
annotations and UniProt subcellular location (Cell membrane).
supported_by:
- reference_id: PMID:30765606
supporting_text: Here we report the cryo-electron microscopy structures of the
human Nav1.7-Ξ²1-Ξ²2 complex
- term:
id: GO:0006811
label: monoatomic ion transport
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: High-level parent of sodium ion transport / sodium ion transmembrane
transport.
action: KEEP_AS_NON_CORE
reason: Correct but uninformatively general; superseded by the specific Na+ transport
terms.
- term:
id: GO:0006814
label: sodium ion transport
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: Sodium ion transport is the process mediated by this Na+-selective channel,
though the more specific GO:0035725 (sodium ion transmembrane transport, IBA)
is preferable.
action: KEEP_AS_NON_CORE
reason: Correct but a less specific sibling/parent of the IBA-annotated sodium
ion transmembrane transport term.
- term:
id: GO:0016020
label: membrane
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: located_in
review:
summary: High-level parent of plasma membrane (GO:0005886), the specific experimentally-supported
location.
action: KEEP_AS_NON_CORE
reason: Correct but uninformatively general; superseded by plasma membrane.
- term:
id: GO:0030424
label: axon
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: Nav1.7 localizes to axons of nociceptor neurons, directly demonstrated
in human iPSC-derived nociceptors (PMID:30795902) and consistent with the UniProt
subcellular location (Cell projection, axon).
action: KEEP_AS_NON_CORE
reason: Accurate location in sensory neurons; non-core relative to the channel's
molecular function but a meaningful site of action. Redundant with the IDA-supported
axon-related localizations.
supported_by:
- reference_id: PMID:30795902
supporting_text: localized at the soma membrane, axon, axon
- term:
id: GO:0043005
label: neuron projection
evidence_type: IEA
original_reference_id: GO_REF:0000044
qualifier: located_in
review:
summary: Parent term encompassing axon/nerve terminals where Nav1.7 localizes;
UniProt records Cell projection, neuron projection (PMID:30795902).
action: KEEP_AS_NON_CORE
reason: Correct but a general parent of the more specific axon, axon terminus,
and node of Ranvier localizations.
supported_by:
- reference_id: PMID:30795902
supporting_text: localized at the soma membrane, axon, axon
- term:
id: GO:0055085
label: transmembrane transport
evidence_type: IEA
original_reference_id: GO_REF:0000002
qualifier: involved_in
review:
summary: High-level parent of sodium ion transmembrane transport (GO:0035725).
action: KEEP_AS_NON_CORE
reason: Correct but uninformatively general; superseded by the specific Na+ transmembrane
transport term.
- term:
id: GO:0007623
label: circadian rhythm
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: involved_in
review:
summary: Electronic ortholog-transfer annotation from mouse Scn9a (Q62205) via
Ensembl Compara. There is no established role for human Nav1.7 in circadian
rhythm, and this is not part of the channel's well-characterized nociceptor
biology.
action: REMOVE
reason: Weakly supported ortholog-transfer (IEA) annotation with no experimental
basis in human and no mechanistic link to the channel's core function. It does
not appear in UniProt's curated function summary and risks implying an unsubstantiated
role; better excluded than retained as non-core.
- term:
id: GO:0050965
label: detection of temperature stimulus involved in sensory perception of pain
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: involved_in
review:
summary: Electronic ortholog-transfer from mouse Scn9a. Nav1.7 loss in humans
produces thermal hypoesthesia and abolishes thermal/noxious pain, so a role
in thermal pain signalling is biologically plausible, but Nav1.7 amplifies nociceptor
excitability rather than directly transducing temperature.
action: KEEP_AS_NON_CORE
reason: Plausible peripheral role consistent with CIP thermal phenotypes, but
IEA-only and not a core/direct molecular function; Nav1.7 is a downstream amplifier,
not the thermal sensor. Keep as a non-core process annotation.
supported_by:
- reference_id: PMID:30795902
supporting_text: Cold and warm detection thresholds in both the hand and the
foot were reduced when compared to the normative range
- term:
id: GO:0050974
label: detection of mechanical stimulus involved in sensory perception
evidence_type: IEA
original_reference_id: GO_REF:0000107
qualifier: involved_in
review:
summary: Electronic ortholog-transfer from mouse Scn9a. Nav1.7 contributes to
mechanical pain sensitivity by amplifying nociceptor firing, but it is not the
primary mechanotransducer; in CIP patients mechanical detection thresholds were
normal while mechanical pain was abolished.
action: KEEP_AS_NON_CORE
reason: Nav1.7 supports mechanical nociception but does not detect mechanical
stimuli directly; the term overstates a direct sensory-transduction role. Retain
as non-core rather than core.
supported_by:
- reference_id: PMID:30795902
supporting_text: Mechanical and vibration detection thresholds were normal
- term:
id: GO:0001518
label: voltage-gated sodium channel complex
evidence_type: IPI
original_reference_id: PMID:30765606
qualifier: part_of
review:
summary: Cryo-EM structures of human Nav1.7 in complex with auxiliary subunits
(SCN1B/SCN2B) directly establish that SCN9A is part of the voltage-gated sodium
channel complex.
action: ACCEPT
reason: Directly experimentally demonstrated complex membership (ComplexPortal/structure-based);
core cellular component.
supported_by:
- reference_id: PMID:30765606
supporting_text: Here we report the cryo-electron microscopy structures of the
human Nav1.7-Ξ²1-Ξ²2 complex
- term:
id: GO:0086010
label: membrane depolarization during action potential
evidence_type: IDA
original_reference_id: PMID:30765606
qualifier: involved_in
review:
summary: Nav1.7 conducts the Na+ influx that produces membrane depolarization
during the rising phase of the action potential, consistent with its established
channel function.
action: ACCEPT
reason: Accurate and specific process directly mediated by the channel; well aligned
with UniProt FUNCTION ("influx of Na(+) ions provokes membrane depolarization").
supported_by:
- reference_id: PMID:30765606
supporting_text: Voltage-gated sodium channel Nav1.7 represents a promising
target for pain relief.
- term:
id: GO:0005886
label: plasma membrane
evidence_type: EXP
original_reference_id: PMID:15385606
qualifier: located_in
review:
summary: Experimental localization of Nav1.7 (including erythromelalgia mutants)
to the cell membrane.
action: ACCEPT
reason: Correct, experimentally-supported core location of the channel.
supported_by:
- reference_id: PMID:15385606
supporting_text: Electrophysiological properties of mutant Nav1.7 sodium channels
in a painful inherited neuropathy.
- term:
id: GO:0005886
label: plasma membrane
evidence_type: EXP
original_reference_id: PMID:17167479
qualifier: located_in
review:
summary: Functional expression of wild-type and mutant Nav1.7 in HEK293 cells
demonstrating plasma-membrane Na+ currents (loss of function in CIP mutants).
action: ACCEPT
reason: Correct, experimentally-supported core location.
supported_by:
- reference_id: PMID:17167479
supporting_text: Whole-cell voltage clamp recordings from cells co-expressing
wild-type Nav1.7 with the Ξ²1Ξ²2 subunits, revealed a voltage-gated Na+ current
- term:
id: GO:0005886
label: plasma membrane
evidence_type: EXP
original_reference_id: PMID:19369487
qualifier: located_in
review:
summary: Experimental characterization of inherited erythromelalgia mutants with
cell-membrane localization/function.
action: ACCEPT
reason: Correct, experimentally-supported core location.
supported_by:
- reference_id: PMID:19369487
supporting_text: 'Early- and late-onset inherited erythromelalgia: genotype-phenotype
correlation.'
- term:
id: GO:0005886
label: plasma membrane
evidence_type: EXP
original_reference_id: PMID:24311784
qualifier: located_in
review:
summary: Functional study of the A1632T erythromelalgia mutant with surface expression
and altered fast inactivation.
action: ACCEPT
reason: Correct, experimentally-supported core location.
supported_by:
- reference_id: PMID:24311784
supporting_text: 'sodium channel Nav1.7 A1632T mutation causes erythromelalgia
due to a shift of fast inactivation'
- term:
id: GO:0005886
label: plasma membrane
evidence_type: EXP
original_reference_id: PMID:25240195
qualifier: located_in
review:
summary: Functional study showing PKC phosphorylation enhances Nav1.7 resurgent
currents at the cell membrane.
action: ACCEPT
reason: Correct, experimentally-supported core location.
supported_by:
- reference_id: PMID:25240195
supporting_text: Protein kinase C enhances human sodium channel hNav1.7 resurgent
currents via a serine residue in the domain III-IV linker.
- term:
id: GO:0005886
label: plasma membrane
evidence_type: EXP
original_reference_id: PMID:26680203
qualifier: located_in
review:
summary: Structural/functional study of Nav1.7 inhibition by a small-molecule
antagonist, consistent with the channel residing in the cell membrane.
action: ACCEPT
reason: Correct, experimentally-supported core location.
supported_by:
- reference_id: PMID:26680203
supporting_text: Structural basis of Nav1.7 inhibition by an isoform-selective
small-molecule antagonist.
- term:
id: GO:0005886
label: plasma membrane
evidence_type: EXP
original_reference_id: PMID:7720699
qualifier: located_in
review:
summary: Original functional expression of hNE-Na (Nav1.7) producing voltage-gated
Na+ currents and action potentials at the cell surface.
action: ACCEPT
reason: Correct, experimentally-supported core location from the founding functional
study.
supported_by:
- reference_id: PMID:7720699
supporting_text: The hNE-Na alpha subunit was transiently expressed in human
embryonic kidney cells either alone or in combination with the human sodium
channel beta 1 subunit.
- term:
id: GO:0005248
label: voltage-gated sodium channel activity
evidence_type: IDA
original_reference_id: PMID:7720699
qualifier: enables
review:
summary: The founding study cloned hNE-Na (Nav1.7) and demonstrated voltage-gated,
TTX-sensitive Na+ channel activity with rapid activation/inactivation kinetics
upon heterologous expression.
action: ACCEPT
reason: Direct experimental demonstration of the core molecular function; primary
evidence for GO:0005248.
supported_by:
- reference_id: PMID:7720699
supporting_text: The channel exhibited rapid activation and inactivation kinetics,
and was blocked by tetrodotoxin and cadmium with IC50 values of 24.5 nM and
1.1 mM, respectively.
- term:
id: GO:0019228
label: neuronal action potential
evidence_type: IDA
original_reference_id: PMID:30795902
qualifier: involved_in
review:
summary: In human iPSC-derived nociceptors and CIP studies, Nav1.7 is required
for normal nociceptor action potential firing, defining its role in the neuronal
action potential.
action: ACCEPT
reason: Specific, experimentally-supported neuronal process directly reflecting
Nav1.7's threshold/amplifier role in sensory neurons.
supported_by:
- reference_id: PMID:30795902
supporting_text: Defining the Functional Role of Na(V)1.7 in Human Nociception.
- term:
id: GO:0019233
label: sensory perception of pain
evidence_type: IMP
original_reference_id: PMID:30795902
qualifier: involved_in
review:
summary: Loss of functional Nav1.7 in CIP participants abolishes the perception
of noxious thermal and mechanical stimuli as painful, demonstrating an essential
role in pain sensation.
action: ACCEPT
reason: Decisive human-genetics evidence; core biological process of Nav1.7.
supported_by:
- reference_id: PMID:30795902
supporting_text: neither noxious temperature nor noxious mechanical stimuli
were felt as painful
- term:
id: GO:0033268
label: node of Ranvier
evidence_type: IDA
original_reference_id: PMID:30795902
qualifier: located_in
review:
summary: CRISPR-tagged endogenous Nav1.7 localized to the great majority of nodes
of Ranvier in myelinated human iPSC-nociceptor co-cultures.
action: ACCEPT
reason: Directly demonstrated localization in human neurons; specific and informative
cellular component.
supported_by:
- reference_id: PMID:30795902
supporting_text: NaV1.7 could be seen localized to >90% of nodes of Ranvier
in myelinated axons
- term:
id: GO:0043679
label: axon terminus
evidence_type: IDA
original_reference_id: PMID:30795902
qualifier: located_in
review:
summary: Endogenous tagged Nav1.7 was enriched in terminal structures of human
iPSC nociceptors, consistent with prior reports of axon-terminal localization
in rodent DRG neurons.
action: ACCEPT
reason: Directly demonstrated localization; specific and informative component
relevant to action potential initiation/propagation at terminals.
supported_by:
- reference_id: PMID:30795902
supporting_text: staining revealed enrichment of NaV1.7 in terminal structures
of our iPSC nociceptors
- term:
id: GO:0098870
label: action potential propagation
evidence_type: IDA
original_reference_id: PMID:17145499
qualifier: involved_in
review:
summary: PEPD gain-of-function mutations impair Nav1.7 fast inactivation, producing
persistent Na+ current and hyperexcitability that alters action potential firing/propagation
in sensory neurons.
action: ACCEPT
reason: Consistent with Nav1.7's role in conducting/propagating depolarization;
supported by an experimental electrophysiology study (full text read by curator).
supported_by:
- reference_id: PMID:17145499
supporting_text: Functional analysis in vitro of three of these mutant Na(v)1.7
channels revealed a reduction in fast inactivation, leading to persistent
sodium current.
- term:
id: GO:0098870
label: action potential propagation
evidence_type: IDA
original_reference_id: PMID:7720699
qualifier: involved_in
review:
summary: Cells expressing high levels of hNE-Na (Nav1.7) generated action potentials,
consistent with the channel's role in initiating and propagating electrical
signals.
action: ACCEPT
reason: Experimentally supported; the channel drives the depolarizing phase required
for action potential propagation.
supported_by:
- reference_id: PMID:7720699
supporting_text: Action potentials were generated in cells expressing high levels
of hNE-Na.
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:37117223
qualifier: enables
review:
summary: This IPI annotation records the experimentally-demonstrated interaction
between Nav1.7 and TMEM233 (B4DJY2), a transmembrane protein required for nettle-toxin
modulation of Nav1.7 gating. The generic "protein binding" term is uninformative
and does not capture the regulatory nature of this interaction.
action: MARK_AS_OVER_ANNOTATED
reason: Per curation guidelines, generic protein binding should be avoided in
favour of an informative molecular function. The underlying biology is a channel-regulator/auxiliary-protein
interaction (TMEM233 modulates Nav1.7 gating), but no sufficiently specific
GO molecular-function term is clearly applicable; the specific interaction partner
and regulatory role are better captured in notes/SUBUNIT than by this uninformative
term.
supported_by:
- reference_id: PMID:37117223
supporting_text: Pain-causing stinging nettle toxins target TMEM233 to modulate
Na(V)1.7 function.
- reference_id: file:human/SCN9A/SCN9A-deep-research-falcon.md
supporting_text: identified **TMEM233 (a dispanin-family protein)** as an essential
**NaV1.7-interacting accessory protein** for the action of the plant-derived
knottin toxin **Excelsatoxin A (ExTxA)**.
- term:
id: GO:0030424
label: axon
evidence_type: ISS
original_reference_id: GO_REF:0000024
qualifier: located_in
review:
summary: Sequence-similarity transfer (from rat Pn1/O08562) of axonal localization;
consistent with experimental human IDA data placing Nav1.7 in axons.
action: KEEP_AS_NON_CORE
reason: Accurate location supported by stronger human evidence; non-core relative
to molecular function and redundant with the IEA axon annotation.
supported_by:
- reference_id: PMID:30795902
supporting_text: localized at the soma membrane, axon, axon
- term:
id: GO:0005248
label: voltage-gated sodium channel activity
evidence_type: IDA
original_reference_id: PMID:17145499
qualifier: enables
review:
summary: Functional in vitro analysis of PEPD mutant Nav1.7 channels confirmed
voltage-gated sodium channel activity (with altered fast inactivation in mutants).
action: ACCEPT
reason: Direct experimental evidence for the core molecular function.
supported_by:
- reference_id: PMID:17145499
supporting_text: Functional analysis in vitro of three of these mutant Na(v)1.7
channels revealed a reduction in fast inactivation, leading to persistent
sodium current.
- term:
id: GO:0005886
label: plasma membrane
evidence_type: IMP
original_reference_id: PMID:17145499
qualifier: located_in
review:
summary: Functional expression of PEPD mutant channels demonstrates plasma-membrane
Na+ currents, supporting cell-membrane localization.
action: ACCEPT
reason: Correct, experimentally-supported core location.
supported_by:
- reference_id: PMID:17145499
supporting_text: Functional analysis in vitro of three of these mutant Na(v)1.7
channels revealed a reduction in fast inactivation, leading to persistent
sodium current.
- term:
id: GO:0019233
label: sensory perception of pain
evidence_type: IMP
original_reference_id: PMID:17145499
qualifier: involved_in
review:
summary: Gain-of-function SCN9A mutations cause paroxysmal extreme pain disorder,
directly linking Nav1.7 dysfunction to abnormal pain perception.
action: ACCEPT
reason: Human-genetics (mutant-phenotype) evidence for the core pain-perception
role of Nav1.7.
supported_by:
- reference_id: PMID:17145499
supporting_text: an inherited condition characterized by paroxysms of rectal,
ocular, or submandibular pain with flushing
core_functions:
- description: Nav1.7 is the pore-forming alpha subunit of a tetrodotoxin-sensitive
voltage-gated sodium channel that opens on membrane depolarization and selectively
conducts Na+ down its electrochemical gradient across the plasma membrane, mediating
the rising/depolarizing phase of the action potential.
molecular_function:
id: GO:0005248
label: voltage-gated sodium channel activity
directly_involved_in:
- id: GO:0035725
label: sodium ion transmembrane transport
- id: GO:0086010
label: membrane depolarization during action potential
locations:
- id: GO:0005886
label: plasma membrane
in_complex:
id: GO:0001518
label: voltage-gated sodium channel complex
substrates:
- id: CHEBI:29101
label: sodium(1+)
supported_by:
- reference_id: PMID:7720699
supporting_text: The channel exhibited rapid activation and inactivation kinetics,
and was blocked by tetrodotoxin and cadmium with IC50 values of 24.5 nM and
1.1 mM, respectively.
reference_section_type: ABSTRACT
- reference_id: PMID:30765606
supporting_text: Here we report the cryo-electron microscopy structures of the
human Nav1.7-Ξ²1-Ξ²2 complex
reference_section_type: ABSTRACT
- reference_id: file:human/SCN9A/SCN9A-deep-research-falcon.md
supporting_text: NaV1.7 is selective for Na+ and shares the canonical NaV architecture
and **DEKA selectivity filter** (Asp-Glu-Lys-Ala across DI-DIV) described for
eukaryotic NaV alpha subunits.
- description: In peripheral nociceptor (and sympathetic) neurons, Nav1.7 acts as a
threshold/amplifier channel that boosts subthreshold depolarizations and sets the
gain for neuronal action potential firing, making it an essential, non-redundant
determinant of pain sensation. It localizes to the soma membrane, axons, axon/nerve
terminals, and nodes of Ranvier.
molecular_function:
id: GO:0005248
label: voltage-gated sodium channel activity
directly_involved_in:
- id: GO:0019228
label: neuronal action potential
- id: GO:0019233
label: sensory perception of pain
locations:
- id: GO:0030424
label: axon
- id: GO:0043679
label: axon terminus
- id: GO:0033268
label: node of Ranvier
supported_by:
- reference_id: PMID:17167479
supporting_text: Our data suggest that SCN9A is an essential and non-redundant
requirement for nociception in humans.
full_text_unavailable: false
reference_section_type: ABSTRACT
- reference_id: PMID:30795902
supporting_text: neither noxious temperature nor noxious mechanical stimuli were
felt as painful
full_text_unavailable: false
reference_section_type: RESULTS
- reference_id: PMID:30795902
supporting_text: NaV1.7 could be seen localized to >90% of nodes of Ranvier in
myelinated axons
full_text_unavailable: false
reference_section_type: RESULTS
- reference_id: file:human/SCN9A/SCN9A-deep-research-falcon.md
supporting_text: in nociceptors it is strongly implicated in determining excitability
near threshold and thereby controlling pain signaling.
proposed_new_terms: []
suggested_questions: []
suggested_experiments: []
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings: []
- id: GO_REF:0000024
title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
by curator judgment of sequence similarity
findings: []
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
vocabulary mapping, accompanied by conservative changes to GO terms applied by
UniProt
findings: []
- id: GO_REF:0000107
title: Automatic transfer of experimentally verified manual GO annotation data to
orthologs using Ensembl Compara
findings: []
- id: GO_REF:0000117
title: Electronic Gene Ontology annotations created by ARBA machine learning models
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:15385606
title: Electrophysiological properties of mutant Nav1.7 sodium channels in a painful
inherited neuropathy.
findings:
- statement: Erythromelalgia (PERYTHM) gain-of-function mutations shift Nav1.7 activation
to more hyperpolarized potentials, supporting cell-membrane localization and
a role in nociceptor hyperexcitability.
supporting_text: Electrophysiological properties of mutant Nav1.7 sodium channels
in a painful inherited neuropathy.
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: PubMed-verified; supports plasma-membrane localization and gain-of-function
mechanism in inherited erythromelalgia.
- id: PMID:17145499
title: 'SCN9A mutations in paroxysmal extreme pain disorder: allelic variants underlie
distinct channel defects and phenotypes.'
findings:
- statement: PEPD is caused by SCN9A gain-of-function missense mutations that reduce
Nav1.7 fast inactivation, producing persistent sodium current and linking the
channel to a heritable pain disorder.
supporting_text: Functional analysis in vitro of three of these mutant Na(v)1.7
channels revealed a reduction in fast inactivation, leading to persistent sodium
current.
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified abstract; establishes Nav1.7 channel activity and
pain-perception role via PEPD gain-of-function mutations.
- id: PMID:17167479
title: An SCN9A channelopathy causes congenital inability to experience pain.
findings:
- statement: Biallelic SCN9A nonsense mutations (S459X, I767X, W897X) cause complete
loss of Nav1.7 function and congenital inability to perceive pain, with all
other sensory modalities preserved.
supporting_text: Our data suggest that SCN9A is an essential and non-redundant
requirement for nociception in humans.
- statement: Nav1.7 is the alpha-subunit of a TTX-sensitive voltage-gated sodium
channel strongly expressed in nociceptive DRG neurons.
supporting_text: encoding the alpha-subunit of the voltage-gated sodium channel,
Na(v)1.7, which is strongly expressed in nociceptive neurons
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified, full text available; decisive loss-of-function
human genetics for the core pain-perception role.
- id: PMID:19369487
title: 'Early- and late-onset inherited erythromelalgia: genotype-phenotype correlation.'
findings:
- statement: Inherited erythromelalgia gain-of-function Nav1.7 mutations correlate
with age of onset, supporting cell-membrane localization and the channel's role
in pain.
supporting_text: 'Early- and late-onset inherited erythromelalgia: genotype-phenotype
correlation.'
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: PubMed-verified abstract-only; supports plasma-membrane localization
via EXP annotation.
- id: PMID:24311784
title: 'Inherited pain: sodium channel Nav1.7 A1632T mutation causes erythromelalgia
due to a shift of fast inactivation.'
findings:
- statement: The A1632T erythromelalgia mutation alters Nav1.7 fast inactivation,
a gain-of-function mechanism, with the channel expressed at the cell membrane.
supporting_text: 'sodium channel Nav1.7 A1632T mutation causes erythromelalgia
due to a shift of fast inactivation'
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: PubMed-verified; supports plasma-membrane localization and gain-of-function
mechanism.
- id: PMID:25240195
title: Protein kinase C enhances human sodium channel hNav1.7 resurgent currents
via a serine residue in the domain III-IV linker.
findings:
- statement: PKC phosphorylation at Ser-1490 in the domain III-IV linker enhances
Nav1.7 resurgent sodium currents, modulating the membrane-resident channel.
supporting_text: Protein kinase C enhances human sodium channel hNav1.7 resurgent
currents via a serine residue in the domain III-IV linker.
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: PubMed-verified; supports plasma-membrane localization and post-translational
regulation of channel activity.
- id: PMID:26680203
title: Structural basis of Nav1.7 inhibition by an isoform-selective small-molecule
antagonist.
findings:
- statement: Crystallographic study of a Nav1.7 voltage-sensor domain bound by an
isoform-selective antagonist, consistent with the channel as a membrane-embedded
drug target.
supporting_text: Structural basis of Nav1.7 inhibition by an isoform-selective
small-molecule antagonist.
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: PubMed-verified abstract-only; supports plasma-membrane localization
and channel pharmacology.
- id: PMID:30765606
title: Structures of human Na(v)1.7 channel in complex with auxiliary subunits and
animal toxins.
findings:
- statement: Cryo-EM structures show human Nav1.7 alpha subunit assembled with auxiliary
beta subunits (SCN1B/SCN2B) into the voltage-gated sodium channel complex, a
multi-pass membrane protein.
supporting_text: Here we report the cryo-electron microscopy structures of the
human Nav1.7-Ξ²1-Ξ²2 complex
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified; structural basis for VGSC complex membership and
membrane-depolarization function.
- id: PMID:30795902
title: Defining the Functional Role of Na(V)1.7 in Human Nociception.
findings:
- statement: In CIP participants with biallelic loss-of-function SCN9A mutations,
noxious thermal and mechanical stimuli are not perceived as painful, while mechanical/vibration
detection thresholds remain normal.
supporting_text: neither noxious temperature nor noxious mechanical stimuli were
felt as painful
- statement: CRISPR-tagged endogenous Nav1.7 localizes to the soma membrane, axons,
axon terminals, and >90% of nodes of Ranvier in human iPSC-derived nociceptors.
supporting_text: NaV1.7 could be seen localized to >90% of nodes of Ranvier in
myelinated axons
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified, full text available; primary human evidence for
neuronal action potential, pain perception, and subcellular localization (node
of Ranvier, axon terminus).
- id: PMID:37117223
title: Pain-causing stinging nettle toxins target TMEM233 to modulate Na(V)1.7 function.
findings:
- statement: Nav1.7 interacts with the transmembrane protein TMEM233 (B4DJY2), which
modulates channel gating; this is the basis of the GO:0005515 protein binding
annotation.
supporting_text: Pain-causing stinging nettle toxins target TMEM233 to modulate
Na(V)1.7 function.
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: PubMed-verified, full text available; underlying interaction (TMEM233)
is real but the generic protein binding term is uninformative.
- id: PMID:7720699
title: Structure and functional expression of a new member of the tetrodotoxin-sensitive
voltage-activated sodium channel family from human neuroendocrine cells.
findings:
- statement: hNE-Na (Nav1.7) is a 1977-aa TTX-sensitive voltage-activated sodium
channel; heterologous expression yields rapidly activating/inactivating Na+
currents and generates action potentials.
supporting_text: The channel exhibited rapid activation and inactivation kinetics,
and was blocked by tetrodotoxin and cadmium with IC50 values of 24.5 nM and
1.1 mM, respectively.
- statement: SCN9A transcripts are not detectable in heart, indicating Nav1.7 is
not a cardiac sodium channel.
supporting_text: Transcripts were not identified in pituitary gland, brain, heart,
liver or kidney
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: PubMed-verified abstract-only; founding functional study establishing
channel activity, plasma-membrane localization, and absence from heart.
- id: file:human/SCN9A/SCN9A-deep-research-falcon.md
title: Falcon deep research report for human SCN9A
findings:
- statement: Falcon deep research affirms the core molecular function as a voltage-gated
Na+ channel selective for Na+ via the canonical DEKA selectivity filter (Asp-Glu-Lys-Ala
across DI-DIV), supporting the GO:0005248 / GO:0005261 annotations.
supporting_text: NaV1.7 is selective for Na+ and shares the canonical NaV architecture
and **DEKA selectivity filter** (Asp-Glu-Lys-Ala across DI-DIV) described for
eukaryotic NaV alpha subunits.
- statement: Falcon deep research frames Nav1.7 as a nociceptor "threshold channel"
enriched at the plasma membrane of DRG, trigeminal and sympathetic ganglion
neurons, consistent with the sensory-perception-of-pain and plasma-membrane annotations.
supporting_text: NaV1.7 is a **plasma-membrane** channel enriched in **nociceptive
neurons**, with high expression reported in **dorsal root ganglia (DRG)**, **trigeminal
ganglia**, and **sympathetic ganglia**.
- statement: Falcon deep research corroborates that TMEM233 (a dispanin-family protein)
is an essential Nav1.7-interacting accessory protein, supporting the regulatory
interpretation of the GO:0005515 (TMEM233) annotation rather than generic protein binding.
supporting_text: identified **TMEM233 (a dispanin-family protein)** as an essential
**NaV1.7-interacting accessory protein** for the action of the plant-derived
knottin toxin **Excelsatoxin A (ExTxA)**.
- statement: Falcon deep research highlights regulation of Nav1.7 surface density
by NEDD4L-mediated ubiquitination of a C-terminal PY motif - a trafficking/turnover
regulatory axis (consistent with the UniProt NEDD4/NEDD4L SUBUNIT note) that is
not captured by any current GOA annotation.
supporting_text: the E3 ligase **NEDD4L ubiquitinates the cytoplasmic C-terminus
of NaV1.7** ... **post-translational modification and trafficking/turnover regulation**
are likely important determinants of NaV1.7 surface density and nociceptor excitability.
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: LLM-generated literature synthesis (Edison/falcon); used only as
corroborating context. Its core-function, localization, and TMEM233-accessory
claims are consistent with the primary literature and UniProt cited elsewhere
in this review; the NEDD4L/trafficking point is supported by UniProt's curated
SUBUNIT annotation (interaction with NEDD4/NEDD4L).