SCN2A

gene
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Also known as Nav1.2HBSCIIHBSCI

Summary

SCN2A (sodium voltage-gated channel alpha subunit 2, HGNC:10588) is a protein-coding gene on chromosome 2q24.3, encoding Sodium channel protein type 2 subunit alpha (Q99250). Mediates the voltage-dependent sodium ion permeability of excitable membranes. It is haploinsufficient (ClinGen: sufficient evidence).

Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with four repeat domains, each of which is composed of six membrane-spanning segments, and one or more regulatory beta subunits. Voltage-gated sodium channels function in the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family. Allelic variants of this gene are associated with seizure disorders and autism spectrum disorder. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 6326 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): complex neurodevelopmental disorder (Definitive, ClinGen) — +10 more curated relationships
  • GWAS associations: 18
  • Clinical variants (ClinVar): 3,011 total — 353 pathogenic, 302 likely-pathogenic
  • Phenotypes (HPO): 208
  • Druggable target: yes — 99 molecules with ChEMBL bioactivity
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_001040142

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10588
Approved symbolSCN2A
Namesodium voltage-gated channel alpha subunit 2
Location2q24.3
Locus typegene with protein product
StatusApproved
AliasesNav1.2, HBSCII, HBSCI
Ensembl geneENSG00000136531
Ensembl biotypeprotein_coding
OMIM182390
Entrez6326

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 8 protein_coding, 8 nonsense_mediated_decay, 3 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000283256, ENST00000375437, ENST00000424833, ENST00000480032, ENST00000486878, ENST00000631182, ENST00000635945, ENST00000636071, ENST00000636135, ENST00000636384, ENST00000636662, ENST00000636769, ENST00000636985, ENST00000637266, ENST00000637367, ENST00000638151, ENST00000640791, ENST00000673831, ENST00000673883, ENST00000674133

RefSeq mRNA: 5 — MANE Select: NM_001040142 NM_001040142, NM_001040143, NM_001371246, NM_001371247, NM_021007

CCDS: CCDS33313, CCDS33314

Canonical transcript exons

ENST00000375437 — 27 exons

ExonStartEnd
ENSE00003469366165309352165309443
ENSE00003476134165312025165312088
ENSE00003480100165354192165354671
ENSE00003515214165367217165367371
ENSE00003520813165377597165377650
ENSE00003534381165326852165326984
ENSE00003577130165331330165331568
ENSE00003578392165344555165344911
ENSE00003583124165323156165323500
ENSE00003607689165295773165296090
ENSE00003618158165297017165297135
ENSE00003622830165313902165314108
ENSE00003624540165310323165310595
ENSE00003632501165342296165342469
ENSE00003637082165307848165307937
ENSE00003646557165308666165308794
ENSE00003650170165315471165315758
ENSE00003667200165313620165313761
ENSE00003673050165365143165365263
ENSE00003692338165374685165374966
ENSE00003768497165386746165387016
ENSE00003793096165380592165380729
ENSE00003797234165381093165381197
ENSE00003797951165370126165370299
ENSE00003798346165373225165373347
ENSE00003843655165239414165239640
ENSE00003848820165388629165392304

Expression profiles

Bgee: expression breadth ubiquitous, 187 present calls, max score 98.77.

FANTOM5 (CAGE): breadth broad, TPM avg 15.1310 / max 2181.7494, expressed in 368 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
234157.1018138
234165.8147137
234181.8434304
234170.291368
234190.033617
234260.028613
234140.01759

Top tissues by expression

289 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
middle temporal gyrusUBERON:000277198.77gold quality
Brodmann (1909) area 23UBERON:001355498.30gold quality
cerebellar vermisUBERON:000472096.78gold quality
entorhinal cortexUBERON:000272896.62gold quality
cerebellar cortexUBERON:000212996.33gold quality
parietal lobeUBERON:000187296.27gold quality
cerebellar hemisphereUBERON:000224596.27gold quality
postcentral gyrusUBERON:000258196.21gold quality
superior frontal gyrusUBERON:000266196.17gold quality
right hemisphere of cerebellumUBERON:001489095.95gold quality
cerebellumUBERON:000203795.77gold quality
endothelial cellCL:000011595.41gold quality
primary visual cortexUBERON:000243694.15gold quality
occipital lobeUBERON:000202194.10gold quality
ponsUBERON:000098893.83gold quality
prefrontal cortexUBERON:000045191.75gold quality
cortical plateUBERON:000534391.48gold quality
dorsolateral prefrontal cortexUBERON:000983490.96gold quality
Brodmann (1909) area 9UBERON:001354090.83gold quality
superior vestibular nucleusUBERON:000722790.66gold quality
frontal cortexUBERON:000187090.52gold quality
cerebral cortexUBERON:000095689.86gold quality
substantia nigra pars compactaUBERON:000196589.69gold quality
neocortexUBERON:000195089.43gold quality
lateral globus pallidusUBERON:000247688.85gold quality
telencephalonUBERON:000189388.02gold quality
temporal lobeUBERON:000187187.96gold quality
right frontal lobeUBERON:000281087.72gold quality
Brodmann (1909) area 46UBERON:000648387.46gold quality
Ammon’s hornUBERON:000195487.33gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

ExperimentMarker?Max mean expression
E-GEOD-75140yes480.60
E-GEOD-93593yes309.30
E-CURD-119yes45.64
E-ANND-3yes7.71
E-GEOD-84465yes6.46
E-GEOD-83139yes3.96

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): IL10, KDM5C, KLF4, RCOR1, REST, TNF

miRNA regulators (miRDB)

169 targeting SCN2A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-4533100.0069.482758
HSA-MIR-3924100.0072.092394
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-98-3P100.0074.083907
HSA-MIR-3163100.0077.238605
HSA-MIR-340-5P100.0072.504437
HSA-MIR-186-5P99.9970.833707
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-1213699.9872.815713
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-477599.9875.006394
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-480399.9871.993117
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-314899.9775.066478

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 40)

  • in autism families, the variant R1902C in SCN2A is located in the calmodulin binding site and was found to reduce binding affinity for calcium-bound calmodulin. (PMID:12610651)
  • We found a nonsense mutation of SCN2A in a patient with intractable epilepsy and severe mental decline. The phenotype is like severe myoclonic epilepsy in infancy but distinct because of partial epilepsy, delayed onset and no temperature sensitivity (PMID:15028761)
  • a role for the hemizygous deletion of not one but two sodium channel genes (SCN1A and SCN2A) in another complicated and more severe epileptic phenotype. (PMID:15249644)
  • Calmodulin mediates Ca2+ sensitivity of Nav1.2 and Nav1.5 sodium channels (PMID:15316014)
  • Although data suggest that SCN2A1 activity does not directly influence membrane potential, intracellular Ca(2+) release, or proliferation in normal human pulmonary artery smooth muscle cells, its physiological functions remain unresolved. (PMID:16052353)
  • Genetic interaction between the combined mild alleles of monogenic epilepsy genes KCNQ2 and SCN2A1 results in severe epilepsy in transgenic mice. (PMID:16464983)
  • Data show that the varied effects of beta1 and beta2 on Nav1.5 and Nav1.2 gating are apparently synergistic and highlight the complex manner, through subunit- and sugar-dependent mechanisms, by which Nav activity is modulated. (PMID:16847056)
  • The SCN2A gene was tested for a possible role in hippocampal abnormalities in familial mesial temporal lobe epilepsy. We conclusively ruled out the SCN2A gene as a candidate in FMTLE. (PMID:16914293)
  • two large families with benign familial neonatal-infantile seizure (BFNIS) and novel SCN2A mutations; the families had 12 & 9 affected individuals, respectively, with phenotypes consistent with BFNIS; two mutations were discovered in SCN2A (E430Q; I1596S) (PMID:17386050)
  • analysis of neonatal & adult splice forms of NaV1.2 with a benign familial neonatal-infantile seizures mutation; developmentally regulated NaV1.2 splicing may be one mechanism that counters the normally high excitability of neonatal neurons (PMID:17467289)
  • Characterization of 5’ untranslated regions SCN2A, and identification of cis-conserved noncoding sequences (PMID:17544618)
  • In south china, the R188W mutation of the SCN2A gene not releate to children with febrile seizures. (PMID:17641256)
  • Allele frequencies of both the D2S111 and the D2S124 polymorphisms of the SCN2A gene were not significantly different between cases with a specific idiopathic generalized epilepsy subtype (with generalized tonic-clonic seizures) and healthy controls. (PMID:17715289)
  • Nav1.2 immunostaining was not observed along demyelinated axons in chronic lesions but was expressed by scar and reactive astrocytes within the plaque. (PMID:17805013)
  • SCN2A gene mutations are associated with inherited benign neonatal-infantile epilepsy. (PMID:18479388)
  • The association of antiepileptic drugs responsiveness with genetic polymorphisms was investigated and any association with mRNA expression of the neuronal sodium channels was correlated. (PMID:18784617)
  • Clinically significant mutations identified in the C-terminal region of NaV1 sodium channels cluster in the helix I-IV interface and the helix II-III interhelical segment or in helices III and IV of the NaV1.2 (1777-1882) structure. (PMID:19129176)
  • Data demonstrate that the two N-terminal alternatively spliced FGF14 variants, FGF14-1a and FGF14-1b, differentially regulate currents produced by Nav1.2 and Nav1.6 channels. (PMID:19465131)
  • The direct effect of heat on Nav1.2 channels localized to the site of action potential initiation potentially causes a profound increase in neuronal excitability. This is likely to contribute to febrile seizure genesis. (PMID:19743470)
  • This finding suggests that both nonsense mutations and missense SCN2A mutations cause Dravet syndrome. (PMID:19783390)
  • de novo mutations SCN2A-E1211K, -I1473M, and -R102X indicate that SCN2A is an etiologic candidate underlying a variety of intractable childhood epilepsies (PMID:19786696)
  • Deletions in SCN2A gene is associated with autistic features and developmental delay. (PMID:20346423)
  • Transient expression of seizures occur due to a gain-of-function of mutant Na(V)1.2 channel. (PMID:20371507)
  • Genetic variants in the voltage-gated ion channel SCN2A dramatically influence the phenotype of mice carrying an SCN1A mutation as well as the seizures caused by the SCN1A mutation. (PMID:21156207)
  • We studied the developmental changes of Na(v)1.1 and Na(v)1.2 in the human hippocampus and temporal lobe (PMID:21377452)
  • Thermodynamic and structural studies of Calmodulin (CaM)-Na(v)1.2(IQp) interactions show that apo and (Ca(2+))(4)-CaM adopt distinct conformations that both permit tight association with Na(v)1.2(IQp) during gating. (PMID:21439835)
  • Environmental enrichment from birth reduces spontaneous seizures and neuronal damage in the Q54 model of temporal lobe epilepsy. (PMID:21762452)
  • Functional studies of SCN2A mutations show that they can cause divergent biophysical defects in Na(V)1.2 and impair cell surface expressions[review] (PMID:22029951)
  • association of the gene SCN2A, previously identified in epilepsy syndromes, with the risk of autism (PMID:22495306)
  • The results of this study shown that both A1685V (GEFS+) and A1685D (SMEI) mutant Nav1.1 channels are characterized by complete loss of function when they are expressed alone (PMID:22525008)
  • This finding suggests that SCN2A mutation is a predisposing factor for acute encephalopathy. (PMID:22591750)
  • This study demonistrated the detailed functional analysis of Na(v)1.2 mutant, R1312T, which was originally found in a child with Dravet syndrome. (PMID:22677033)
  • This study demonistrated that associated with a duplication of the SCN2A and SCN3A gene cluster on 2q24 in patient with early onset epilepsy. (PMID:23016767)
  • Identification of a novel SCN2A mutation in a family with infantile seizures with onset between 6 and 8 months provides further confirmation that this gene is involved in families with a delayed age of onset. (PMID:23360469)
  • study identified a de novo SCN2A mutation as the etiology for Ohtahara syndrome in monozygotic twins associated with a unique dentate-olivary dysplasia in the deceased twin (PMID:23550958)
  • Mutation of SCN2A induces neuronal hyperexcitability, resulting in infantile epilepsy with favorable outcome (PMID:23758435)
  • An SCN2A missense mutation is associated with infantile spasms and bitemporal hypometabolism. (PMID:23827426)
  • Our data from the Hong Kong and Malaysia cohorts showed no significant allele, genotype and haplotype association of polymorphisms in the SCN1A, SCN2A, and SCN3A genes with drug responsiveness in epilepsy. (PMID:23859570)
  • SCN2A mutations are an important genetic cause of Ohtahara syndrome. Given the wide clinical spectrum associated with SCN2A mutations, genetic testing for SCN2A should be considered for children with different epileptic conditions. (PMID:23935176)
  • Following SCN2A knockdown, the concentration of Cu-Zn SOD declined and the si-SCN2A vector group showed a repeated discharge. (PMID:24220630)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusScn2aENSMUSG00000075318
rattus_norvegicusScn2aENSRNOG00000005018

Paralogs (26): CACNA1G (ENSG00000006283), SCN4A (ENSG00000007314), CACNA1S (ENSG00000081248), CACNA1I (ENSG00000100346), CACNA1F (ENSG00000102001), NALCN (ENSG00000102452), SCN7A (ENSG00000136546), CACNA1A (ENSG00000141837), SCN1A (ENSG00000144285), CACNA1B (ENSG00000148408), CACNA1C (ENSG00000151067), CATSPER3 (ENSG00000152705), SCN3A (ENSG00000153253), CACNA1D (ENSG00000157388), TPCN2 (ENSG00000162341), CATSPER2 (ENSG00000166762), SCN11A (ENSG00000168356), SCN9A (ENSG00000169432), CATSPER1 (ENSG00000175294), SCN5A (ENSG00000183873), SCN10A (ENSG00000185313), TPCN1 (ENSG00000186815), CATSPER4 (ENSG00000188782), CACNA1H (ENSG00000196557), SCN8A (ENSG00000196876), CACNA1E (ENSG00000198216)

Protein

Protein identifiers

Sodium channel protein type 2 subunit alphaQ99250 (reviewed: Q99250)

Alternative names: HBSC II, Sodium channel protein brain II subunit alpha, Sodium channel protein type II subunit alpha, Voltage-gated sodium channel subunit alpha Nav1.2

All UniProt accessions (11): A0A0D9SGG2, A0A1B0GTS6, A0A1B0GTX0, A0A1B0GW40, A0A1B0GW67, A0A1B0GWA6, A0A669KAR0, A0A669KBL5, A0A669KBM3, Q99250, F6U291

UniProt curated annotations — full annotation on UniProt →

Function. Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient. Implicated in the regulation of hippocampal replay occurring within sharp wave ripples (SPW-R) important for memory.

Subunit / interactions. Heterooligomer of a large alpha subunit and a smaller beta subunit. Heterooligomer with SCN2B or SCN4B; disulfide-linked. Heterooligomer with SCN1B or SCN3B; non-covalently linked. Interacts with NEDD4L. Interacts with CALM. Interacts with TMEM233. Interacts with the conotoxin GVIIJ. Interacts with the spider beta/delta-theraphotoxin-Pre1a. Interacts with the conotoxin KIIIA. Interacts with the spider protoxin-II.

Subcellular location. Cell membrane.

Post-translational modifications. May be ubiquitinated by NEDD4L; which would promote its endocytosis. Phosphorylation at Ser-1506 by PKC in a highly conserved cytoplasmic loop slows inactivation of the sodium channel and reduces peak sodium currents. Sumoylated at Lys-38. Sumoylation is induced by hypoxia, increases voltage-gated sodium current and mediates the early response to acute hypoxia in neurons. Sumoylated SCN2A is located at the cell membrane.

Disease relevance. Seizures, benign familial infantile, 3 (BFIS3) [MIM:607745] A form of benign familial infantile epilepsy, a neurologic disorder characterized by afebrile seizures occurring in clusters during the first year of life, without neurologic sequelae. BFIS3 inheritance is autosomal dominant. The disease is caused by variants affecting the gene represented in this entry. Developmental and epileptic encephalopathy 11 (DEE11) [MIM:613721] An autosomal dominant seizure disorder characterized by neonatal or infantile onset of refractory seizures with resultant delayed neurologic development and persistent neurologic abnormalities. Patients may progress to West syndrome, which is characterized by tonic spasms with clustering, arrest of psychomotor development, and hypsarrhythmia on EEG. The disease is caused by variants affecting the gene represented in this entry. Defects in SCN2A are associated with genetic epilepsy with febrile seizures plus (GEFS+), a familial autosomal dominant epilepsy syndrome, a clinical subset of febrile seizures, characterized by frequent episodes after 6 years of age and various types of subsequent epilepsy. Defects in SCN2A are associated with autism spectrum disorders (ASD). It seems that mutations resulting in sodium channel gain of function and increased neuron excitability lead to infantile seizures, whereas variants resulting in sodium channel loss of function and decrease neuron excitability are associated with ASD. Episodic ataxia 9 (EA9) [MIM:618924] An autosomal dominant neurologic disorder characterized by episodic ataxia manifesting in the first years of life, early-onset seizures, difficulty walking, dizziness, slurred speech, headache, vomiting, and pain. The duration of ataxic episodes is heterogeneous. Most patients show episodes lasting minutes to maximum several hours, but periods lasting days up to weeks have been reported. Some patients have mildly delayed development with speech delay and/or autistic features or mildly impaired intellectual development. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1, S2, S3, S5, S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position.

Similarity. Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.2/SCN2A subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
Q99250-11, Adult, 6Ayes
Q99250-22, Neonatal, 6N

RefSeq proteins (5): NP_001035232, NP_001035233, NP_001358175, NP_001358176, NP_066287 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000048IQ_motif_EF-hand-BSBinding_site
IPR001696Na_channel_asuFamily
IPR005821Ion_trans_domDomain
IPR010526Na_trans_assoc_domDomain
IPR024583Na_trans_cytoplDomain
IPR027359Volt_channel_dom_sfHomologous_superfamily
IPR043203VGCC_Ca_NaFamily
IPR044564Na_chnl_inactivation_gateDomain
IPR058542IQ_SCN5A_CDomain

Pfam: PF00520, PF06512, PF11933, PF24609

Catalyzed reactions (Rhea), 1 shown:

  • Na(+)(in) = Na(+)(out) (RHEA:34963)

UniProt features (351 total): sequence variant 112, helix 67, topological domain 29, transmembrane region 24, modified residue 24, turn 21, strand 19, site 11, glycosylation site 10, disulfide bond 7, region of interest 6, compositionally biased region 5, intramembrane region 4, sequence conflict 4, repeat 4, chain 1, cross-link 1, splice variant 1, domain 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
4RLYX-RAY DIFFRACTION2.5
6J8EELECTRON MICROSCOPY3
4JPZX-RAY DIFFRACTION3.02
2KAVSOLUTION NMR
6BUTSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q99250-F169.280.17

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (11): 330 (binds mu-conotoxin kiiia); 362 (binds mu-conotoxin kiiia); 909 (binds scn2b; via carbonyl oxygen); 916 (binds mu-conotoxin kiiia; via amide nitrogen); 920 (binds mu-conotoxin kiiia; via carbonyl oxygen); 945 (binds mu-conotoxin kiiia); 949 (binds mu-conotoxin kiiia); 1374 (binds mu-conotoxin kiiia; via amide nitrogen); 1429 (binds mu-conotoxin kiiia); 1443 (binds mu-conotoxin kiiia); 1489 (important for channel closure)

Post-translational modifications (25): 686, 687, 721, 1506, 1930, 1943, 1963, 1966, 1971, 38, 4, 468, 471, 484, 526, 528, 531, 553, 554, 558 …

Disulfide bonds (7): 278–338, 910, 910, 912–918, 950–959, 1366–1386, 1731–1746

Glycosylation sites (10): 212, 285, 291, 297, 303, 308, 340, 1368, 1382, 1393

Function

Pathways and Gene Ontology

Reactome pathways

11 pathways

IDPathway
R-HSA-445095Interaction between L1 and Ankyrins
R-HSA-5576892Phase 0 - rapid depolarisation
R-HSA-9717207Sensory perception of sweet, bitter, and umami (glutamate) taste
R-HSA-1266738Developmental Biology
R-HSA-373760L1CAM interactions
R-HSA-397014Muscle contraction
R-HSA-422475Axon guidance
R-HSA-5576891Cardiac conduction
R-HSA-9675108Nervous system development
R-HSA-9709957Sensory Perception
R-HSA-9717189Sensory perception of taste

MSigDB gene sets: 599 (showing top): GOBP_MEMORY, GOBP_MEMBRANE_DEPOLARIZATION, GOBP_COGNITION, GOBP_BEHAVIOR, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOBP_SODIUM_ION_TRANSMEMBRANE_TRANSPORT, GOBP_MEMBRANE_DEPOLARIZATION_DURING_ACTION_POTENTIAL, GOBP_MONOATOMIC_CATION_TRANSPORT, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_LEVELS, GOBP_MUSCLE_CONTRACTION, GOBP_APOPTOTIC_SIGNALING_PATHWAY, GOBP_RESPONSE_TO_OXYGEN_LEVELS, GOBP_ENSHEATHMENT_OF_NEURONS, chr2q24, TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP

GO Biological Process (19): sodium ion transport (GO:0006814), nervous system development (GO:0007399), memory (GO:0007613), intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627), neuronal action potential (GO:0019228), sodium ion transmembrane transport (GO:0035725), myelination (GO:0042552), neuron apoptotic process (GO:0051402), cellular response to hypoxia (GO:0071456), cardiac muscle cell action potential involved in contraction (GO:0086002), action potential (GO:0001508), regulation of heart rate (GO:0002027), monoatomic ion transport (GO:0006811), monoatomic ion transmembrane transport (GO:0034220), regulation of membrane potential (GO:0042391), transmembrane transport (GO:0055085), cardiac muscle cell action potential (GO:0086001), regulation of muscle system process (GO:0090257), monoatomic cation transmembrane transport (GO:0098655)

GO Molecular Function (6): voltage-gated sodium channel activity (GO:0005248), calmodulin binding (GO:0005516), monoatomic ion channel activity (GO:0005216), monoatomic cation channel activity (GO:0005261), sodium channel activity (GO:0005272), protein binding (GO:0005515)

GO Cellular Component (6): voltage-gated sodium channel complex (GO:0001518), plasma membrane (GO:0005886), membrane (GO:0016020), axon (GO:0030424), node of Ranvier (GO:0033268), monoatomic ion channel complex (GO:0034702)

Reactome top-level categories

Rollup of top-8 pathways:

CategoryPathways
L1CAM interactions1
Cardiac conduction1
Sensory perception of taste1
Axon guidance1
Nervous system development1
Muscle contraction1
Developmental Biology1
Sensory Perception1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
action potential2
regulation of biological quality2
transport2
monoatomic ion transmembrane transport2
cellular anatomical structure2
metal ion transport1
system development1
learning or memory1
cellular response to osmotic stress1
intrinsic apoptotic signaling pathway1
transmission of nerve impulse1
sodium ion transport1
monoatomic cation transmembrane transport1
axon ensheathment1
apoptotic process1
response to hypoxia1
cellular response to stress1
cellular response to decreased oxygen levels1
cardiac muscle cell action potential1
cardiac muscle cell contraction1
regulation of membrane potential1
regulation of heart contraction1
monoatomic ion transport1
transmembrane transport1
cellular process1
muscle system process1
regulation of system process1
monoatomic cation transport1
sodium channel activity1
protein binding1
monoatomic ion transmembrane transporter activity1
channel activity1
monoatomic ion channel activity1
monoatomic cation transmembrane transporter activity1
monoatomic cation channel activity1
sodium ion transmembrane transporter activity1
binding1
sodium channel complex1
plasma membrane protein complex1
membrane1

Protein interactions and networks

STRING

2714 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SCN2AANK3Q12955937
SCN2ASCN1BQ07699930
SCN2APRRT2Q7Z6L0898
SCN2AKCNQ2O43526887
SCN2ASCN1AP35498875
SCN2ANAV1Q8NEY1871
SCN2ASCN4BQ8IWT1865
SCN2APCDH19Q8TAB3844
SCN2ASTXBP1P61764833
SCN2ACALM1P02593825
SCN2AHBBP02023820
SCN2ACDKL5O76039813
SCN2ASCN3BQ9NY72808
SCN2AKCNA1Q09470791
SCN2APCDH10Q9P2E7781

IntAct

17 interactions, top by confidence:

ABTypeScore
CALM1FGF13psi-mi:“MI:0915”(physical association)0.700
SCN2ACALM1psi-mi:“MI:0915”(physical association)0.690
SCN2AELAVL3psi-mi:“MI:0915”(physical association)0.500
Dlg4SCN2Apsi-mi:“MI:0407”(direct interaction)0.440
SCN2AATP5F1Apsi-mi:“MI:0915”(physical association)0.400
SCN2AATP5PDpsi-mi:“MI:0915”(physical association)0.400
CALM1psi-mi:“MI:0915”(physical association)0.400
SCN2AIGLL5psi-mi:“MI:0914”(association)0.350
CACNA1CDISP2psi-mi:“MI:0914”(association)0.350
HCN1POTEFpsi-mi:“MI:0914”(association)0.350
SCN2AIGF2BP3psi-mi:“MI:0914”(association)0.350
ATG16L1psi-mi:“MI:0914”(association)0.350
ARHGEF10LSCN2Apsi-mi:“MI:0915”(physical association)0.000
MPP3SCN2Apsi-mi:“MI:0915”(physical association)0.000
RNF130SCN2Apsi-mi:“MI:0915”(physical association)0.000

BioGRID (79): SCN2A (Proximity Label-MS), SCN2A (Proximity Label-MS), SCN2A (Affinity Capture-MS), SCN2A (Cross-Linking-MS (XL-MS)), TPT1 (Cross-Linking-MS (XL-MS)), SCN2A (Cross-Linking-MS (XL-MS)), SCN2A (Cross-Linking-MS (XL-MS)), CALM2 (Affinity Capture-MS), ELAVL2 (Affinity Capture-MS), IGF2BP2 (Affinity Capture-MS), RARG (Affinity Capture-MS), DNAJC16 (Affinity Capture-MS), ATP1A3 (Affinity Capture-MS), KARS (Affinity Capture-MS), GNAI1 (Affinity Capture-MS)

ESM2 similar proteins: A2APX8, A2ASI5, B1AWN6, C9D7C2, D0E0C2, O08562, O35505, O46669, O73700, O88420, O88457, P02719, P04774, P04775, P08104, P0DMA5, P15381, P15389, P15390, P22002, P27732, P35498, P35499, P35500, Q01815, Q07652, Q13936, Q14524, Q15858, Q20JQ7, Q28371, Q28644, Q2XVR3, Q2XVR4, Q2XVR5, Q2XVR6, Q2XVR7, Q62205, Q62968, Q6QIY3

Diamond homologs: A2APX8, A2ASI5, B1AWN6, B1AYL1, D0E0C2, F1LQQ7, O00555, O08562, O46669, O73705, O73706, O73707, O88420, O88457, P02719, P04774, P04775, P08104, P0DMA5, P15389, P15390, P27884, P35498, P35499, P35500, P54282, P56699, P97445, Q01118, Q02789, Q05973, Q14524, Q15858, Q15878, Q20JQ7, Q28371, Q28644, Q2XVR3, Q2XVR4, Q2XVR5

SIGNOR signaling

33 interactions.

AEffectBMechanism
RCOR1“down-regulates quantity by repression”SCN2A“transcriptional regulation”
REST“down-regulates quantity by repression”SCN2A“transcriptional regulation”
SCN2A“up-regulates quantity”sodium(1+)relocalization
FGF13“down-regulates activity”SCN2Abinding
FGF12“down-regulates activity”SCN2Abinding
FGF14“down-regulates activity”SCN2Abinding
FGF11“down-regulates activity”SCN2Abinding
SCN2Aup-regulatesAction_potential
“CoREST-HDAC complex”“down-regulates quantity by repression”SCN2A“transcriptional regulation”
GSK3B“down-regulates activity”SCN2Aphosphorylation
PKA“down-regulates activity”SCN2Aphosphorylation
PKC“down-regulates activity”SCN2Aphosphorylation
CSNK2A3“up-regulates activity”SCN2Aphosphorylation
CSNK2B“up-regulates activity”SCN2Aphosphorylation
CSNK2A1“up-regulates activity”SCN2Aphosphorylation
CSNK2A2“up-regulates activity”SCN2Aphosphorylation
NEDD4L“down-regulates quantity by destabilization”SCN2Aubiquitination
TNF“up-regulates quantity by expression”SCN2A“transcriptional regulation”
TNF“up-regulates activity”SCN2A
KDM5C“down-regulates quantity by repression”SCN2A“transcriptional regulation”
IL10“down-regulates quantity by repression”SCN2A“transcriptional regulation”
phenytoin“down-regulates activity”SCN2A“chemical inhibition”

Disease & clinical

Clinical variants and AI predictions

ClinVar

3011 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic353
Likely pathogenic302
Uncertain significance1250
Likely benign707
Benign131

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1000049NM_001040142.2(SCN2A):c.4901G>T (p.Gly1634Val)Pathogenic
1013421NM_001040142.2(SCN2A):c.4948C>T (p.Leu1650Phe)Pathogenic
1066198NM_001040142.2(SCN2A):c.4551+1G>APathogenic
1068258NM_001040142.2(SCN2A):c.4501A>G (p.Met1501Val)Pathogenic
1070304NM_001040142.2(SCN2A):c.787G>A (p.Ala263Thr)Pathogenic
1071664NM_001040142.2(SCN2A):c.718del (p.Ala240fs)Pathogenic
1071677NM_001040142.2(SCN2A):c.1497del (p.Glu500fs)Pathogenic
1072191NM_001040142.2(SCN2A):c.1267G>T (p.Val423Leu)Pathogenic
1073234NM_001040142.2(SCN2A):c.4533dup (p.Pro1512fs)Pathogenic
1074161NM_001040142.2(SCN2A):c.3782G>A (p.Trp1261Ter)Pathogenic
1074300NM_001040142.2(SCN2A):c.4543C>T (p.Arg1515Ter)Pathogenic
1074301NM_001040142.2(SCN2A):c.4787T>G (p.Ile1596Ser)Pathogenic
1098322NM_001040142.2(SCN2A):c.1940del (p.Ala647fs)Pathogenic
1173107NM_001040142.2(SCN2A):c.330C>A (p.Tyr110Ter)Pathogenic
1180439NM_001040142.2(SCN2A):c.986dup (p.Leu329fs)Pathogenic
1196824NM_001040142.2(SCN2A):c.5405G>A (p.Trp1802Ter)Pathogenic
1198013NM_001040142.2(SCN2A):c.721del (p.Ala240_Leu241insTer)Pathogenic
1206719NM_001040142.2(SCN2A):c.476+1G>APathogenic
1219256NM_001040142.2(SCN2A):c.1729del (p.Leu577fs)Pathogenic
1256055NM_001040142.2(SCN2A):c.2588C>A (p.Ser863Tyr)Pathogenic
12876NM_001040142.2(SCN2A):c.3988C>T (p.Leu1330Phe)Pathogenic
12877NM_001040142.2(SCN2A):c.4687C>G (p.Leu1563Val)Pathogenic
12880NM_001040142.2(SCN2A):c.3956G>A (p.Arg1319Gln)Pathogenic
1298832NM_001040142.2(SCN2A):c.2017-2A>GPathogenic
1300201NM_001040142.2(SCN2A):c.4018G>A (p.Val1340Ile)Pathogenic
130220NM_001040142.2(SCN2A):c.3374del (p.Glu1125fs)Pathogenic
1318908NM_001040142.2(SCN2A):c.718G>T (p.Ala240Ser)Pathogenic
1323562NM_001040142.2(SCN2A):c.4446+1A>GPathogenic
1342670NM_001040142.2(SCN2A):c.1261T>G (p.Leu421Val)Pathogenic
1342671NM_001040142.2(SCN2A):c.4364T>A (p.Ile1455Asn)Pathogenic

SpliceAI

4238 predictions. Top by Δscore:

VariantEffectΔscore
2:165296087:GAAA:Gdonor_gain1.0000
2:165296088:A:Tdonor_gain1.0000
2:165296091:G:GGdonor_gain1.0000
2:165307837:C:CAacceptor_gain1.0000
2:165307859:T:Gacceptor_gain1.0000
2:165307868:T:Gacceptor_gain1.0000
2:165312087:GG:Gdonor_gain1.0000
2:165312088:GG:Gdonor_gain1.0000
2:165313619:GCCA:Gacceptor_gain1.0000
2:165313896:TTGCA:Tacceptor_loss1.0000
2:165313897:TGCA:Tacceptor_loss1.0000
2:165313898:GCAGA:Gacceptor_loss1.0000
2:165313899:CA:Cacceptor_loss1.0000
2:165313900:A:ACacceptor_loss1.0000
2:165313900:A:AGacceptor_gain1.0000
2:165313901:G:GCacceptor_gain1.0000
2:165313901:GA:Gacceptor_gain1.0000
2:165313901:GAC:Gacceptor_gain1.0000
2:165313901:GACA:Gacceptor_gain1.0000
2:165313901:GACAC:Gacceptor_gain1.0000
2:165313993:T:TAacceptor_gain1.0000
2:165314105:TCAG:Tdonor_loss1.0000
2:165314106:CAG:Cdonor_loss1.0000
2:165314107:AG:Adonor_loss1.0000
2:165314108:GG:Gdonor_loss1.0000
2:165314109:GT:Gdonor_loss1.0000
2:165314110:T:Gdonor_loss1.0000
2:165323153:T:Gacceptor_gain1.0000
2:165323154:A:AGacceptor_gain1.0000
2:165323155:G:GGacceptor_gain1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000005741 (2:165377563 G>A), RS1000026430 (2:165268028 A>G), RS1000076153 (2:165325519 G>A), RS1000084150 (2:165313222 C>T), RS1000098009 (2:165345784 C>T), RS1000139270 (2:165377562 T>G), RS1000142152 (2:165357422 C>A), RS1000161115 (2:165305047 A>G), RS1000177567 (2:165241179 T>C), RS1000189145 (2:165291418 C>T), RS1000191130 (2:165266791 G>T), RS1000192036 (2:165357469 A>G), RS1000205736 (2:165254545 G>A), RS1000225061 (2:165266488 T>G), RS1000232833 (2:165248134 A>C)

Disease associations

OMIM: gene MIM:182390 | disease phenotypes: MIM:607745, MIM:613721, MIM:618924, MIM:108600, MIM:601764, MIM:604233, MIM:606369, MIM:160120, MIM:616341, MIM:117100, MIM:308350, MIM:209850, MIM:613863, MIM:201300, MIM:616421, MIM:613722, MIM:128235, MIM:156200, MIM:617080, MIM:618468, MIM:616373

GenCC curated gene-disease

DiseaseClassificationInheritance
developmental and epileptic encephalopathy, 11DefinitiveAutosomal dominant
complex neurodevelopmental disorderDefinitiveAutosomal dominant
intellectual disabilityDefinitiveAutosomal dominant
seizures, benign familial infantile, 3StrongAutosomal dominant
episodic ataxia, type 9StrongAutosomal dominant
benign familial neonatal-infantile seizuresSupportiveAutosomal dominant
genetic developmental and epileptic encephalopathySupportiveAutosomal dominant
malignant migrating partial seizures of infancySupportiveAutosomal dominant
benign familial infantile epilepsySupportiveAutosomal dominant
Dravet syndromeSupportiveAutosomal dominant
infantile spasmsSupportiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
complex neurodevelopmental disorderDefinitiveAD

Mondo (40): seizures, benign familial infantile, 3 (MONDO:0011904), developmental and epileptic encephalopathy, 11 (MONDO:0013388), (MONDO:0100025), episodic ataxia, type 9 (MONDO:0030064), complex neurodevelopmental disorder (MONDO:0100038), spastic ataxia (MONDO:0017845), neurodevelopmental disorder (MONDO:0700092), benign familial infantile epilepsy (MONDO:0017615), developmental and epileptic encephalopathy (MONDO:0100620), pyridoxine-dependent epilepsy (MONDO:0009945), Dravet syndrome (MONDO:0100135), infantile spasms (MONDO:0018097), generalized epilepsy with febrile seizures plus (MONDO:0018214), Lennox-Gastaut syndrome (MONDO:0016532), autism spectrum disorder (MONDO:0005258)

Orphanet (21): Self-limited neonatal-infantile epilepsy (Orphanet:140927), Early infantile developmental and epileptic encephalopathy (Orphanet:1934), Self-limited infantile epilepsy (Orphanet:306), Non-specific syndromic intellectual disability (Orphanet:528084), Spastic ataxia (Orphanet:316226), Pyridoxine-dependent-developmental and epileptic encephalopathy (Orphanet:3006), Dravet syndrome (Orphanet:33069), West syndrome (Orphanet:3451), Infantile epileptic spasms syndrome (Orphanet:697160), Genetic epilepsy with febrile seizure plus (Orphanet:36387), Lennox-Gastaut syndrome (Orphanet:2382), Hereditary episodic ataxia (Orphanet:211062), Self-limited epilepsy with centrotemporal spikes (Orphanet:1945), Hereditary sensory and autonomic neuropathy type 2 (Orphanet:970), Epilepsy with myoclonic-atonic seizures (Orphanet:1942)

HPO phenotypes

208 total (30 of 208 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000054Micropenis
HP:0000070Ureterocele
HP:0000110Renal dysplasia
HP:0000175Cleft palate
HP:0000252Microcephaly
HP:0000297Facial hypotonia
HP:0000340Sloping forehead
HP:0000348High forehead
HP:0000463Anteverted nares
HP:0000466Limited neck range of motion
HP:0000486Strabismus
HP:0000505Visual impairment
HP:0000565Esotropia
HP:0000577Exotropia
HP:0000639Nystagmus
HP:0000657Oculomotor apraxia
HP:0000707Abnormality of the nervous system
HP:0000708Atypical behavior
HP:0000712Emotional lability
HP:0000717Autism
HP:0000718Aggressive behavior
HP:0000729Autistic behavior
HP:0000736Short attention span
HP:0000739Anxiety
HP:0000750Delayed speech and language development
HP:0000752Hyperactivity
HP:0000826Precocious puberty
HP:0000961Cyanosis
HP:0000975Hyperhidrosis

GWAS associations

18 associations (top):

StudyTraitp-value
GCST002129_12Periodontitis (DPAL)5.000000e-06
GCST002672_4Febrile seizures3.000000e-10
GCST002673_3Febrile seizures (MMR vaccine-unrelated)2.000000e-07
GCST002674_5Febrile seizures (MMR vaccine-related)4.000000e-06
GCST006630_51Diastolic blood pressure3.000000e-10
GCST007343_2Epilepsy2.000000e-13
GCST007352_1Focal epilepsy7.000000e-09
GCST007353_3Generalized epilepsy5.000000e-08
GCST007401_10Factor VII activity8.000000e-07
GCST008103_11Bipolar disorder2.000000e-09
GCST008154_50Trunk fat mass3.000000e-06
GCST008647_39Urinary sodium excretion1.000000e-10
GCST010002_403Refractive error1.000000e-11
GCST010988_192Adult body size2.000000e-08
GCST011102_2Bipolar disorder2.000000e-09
GCST012465_47Bipolar disorder3.000000e-08
GCST90000047_75Age at first sexual intercourse1.000000e-08
GCST90000050_17Age at first birth2.000000e-08

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0006519MMR-related febrile seizures
EFO:0006336diastolic blood pressure
EFO:0004619factor VII measurement
EFO:0009282sodium measurement
EFO:0009749age at first sexual intercourse measurement
EFO:0009101age at first birth measurement

MeSH disease descriptors (12)

DescriptorNameTree numbers
D001321Autistic DisorderF03.625.164.113.500
D004828Epilepsies, PartialC10.228.140.490.360
D004827EpilepsyC10.228.140.490
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D065768Lennox Gastaut SyndromeC10.228.140.490.493.750; C16.320.495
D009069Movement DisordersC10.228.662
D065886Neurodevelopmental DisordersF03.625
C538001Dystonia 12 (supp.)
C567827Generalized Epilepsy With Febrile Seizures Plus, 7 (supp.)
C565808Generalized Epilepsy with Febrile Seizures Plus (supp.)
C536254Pyridoxine-dependent epilepsy (supp.)
C564815Spastic Ataxia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (4): CHEMBL2096682 (PROTEIN FAMILY), CHEMBL2331043 (PROTEIN FAMILY), CHEMBL4187 (SINGLE PROTEIN), CHEMBL4523672 (PROTEIN COMPLEX)

Molecules with ChEMBL bioactivity

99 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 507,182 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1008BEPRIDIL411,776
CHEMBL1086DIBUCAINE417,231
CHEMBL1093ARTICAINE46,583
CHEMBL1098BUPIVACAINE437,899
CHEMBL11IMIPRAMINE448,893
CHEMBL1108DROPERIDOL416,888
CHEMBL1123DICYCLOMINE48,691
CHEMBL117785TETRABENAZINE49,645
CHEMBL1193PHENIRAMINE411,218
CHEMBL1194PRILOCAINE415,137
CHEMBL1195PROPOXYCAINE45,653
CHEMBL1196PROPARACAINE412,973
CHEMBL1197HEXYLCAINE44,372
CHEMBL1198PRAMOXINE410,295
CHEMBL1200BENOXINATE46,712
CHEMBL1294QUINIDINE471,943
CHEMBL1480FELODIPINE430,761
CHEMBL16PHENYTOIN453,375
CHEMBL170QUININE4108,216
CHEMBL1726NISOLDIPINE418,921
CHEMBL193NIFEDIPINE4
CHEMBL2PRAZOSIN4
CHEMBL23DILTIAZEM4
CHEMBL24072PRENYLAMINE4
CHEMBL370805COCAINE4
CHEMBL422TRIFLUOPERAZINE4
CHEMBL43064CINNARIZINE4
CHEMBL479THIORIDAZINE4
CHEMBL492ETIDOCAINE4
CHEMBL505CHLORPHENIRAMINE4

PharmGKB: 1 entry (VIP=true, CPIC=false)

PharmGKB clinical annotations

7 annotations.

VariantTypeLevelDrugsPhenotypes
rs17183814Efficacy4antiepileptics;carbamazepine;phenobarbital;phenytoin;valproic acidEpilepsy
rs2304016Efficacy3antiepilepticsEpilepsy
rs2304016Efficacy3carbamazepineEpilepsy
rs2304016Efficacy3lamotrigineEpilepsy
rs2304016Efficacy3oxcarbazepineEpilepsy
rs2304016Efficacy3phenytoinEpilepsy
rs2304016Efficacy3topiramateEpilepsy

PharmGKB variants

2 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs2304016SCN2A33.256oxcarbazepine;antiepileptics;carbamazepine;lamotrigine;phenytoin;topiramate
rs17183814SCN2A4-2.501antiepileptics;carbamazepine;phenobarbital;phenytoin;valproic acid

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: vgic — Voltage-gated sodium channels (NaV)

Most potent curated ligand interactions (25 total), top 25:

LigandActionAffinityParameter
β-scorpion toxin Css IVPartial agonist9.7pKd
batrachotoxinAgonist9.1pKd
μ-conotoxin SmIIIAPore blocker8.9pKd
saxitoxinPore blocker8.8pIC50
α-scorpion toxin 2Slows inactivation8.7pKd
GNE-131Inhibition8.15pIC50
ATX-IISlows inactivation8.1pEC50
tetrodotoxinPore blocker8.0pIC50
XPC-5462Channel blocker7.96pIC50
GNE-616Inhibition7.92pKd
huwentoxin IVVoltage-dependent inhibition7.8pKd
protoxin IIVoltage-dependent inhibition7.4pKi
relutrigineInhibition6.76pIC50
funapideInhibition6.22pIC50
etidocainePore blocker6.0pIC50
aconitinePartial agonist5.9pKd
Bc-IIISlows inactivation5.8pEC50
AFT-IISlows inactivation5.7pEC50
cannabidiolChannel blocker5.54pIC50
veratridinePartial agonist5.2pKd
lidocainePore blocker5.0pIC50
phenytoinPore blocker4.9pIC50
lacosamideAntagonist4.52pIC50
lamotriginePore blocker4.5pIC50
δ-hexatoxin-Mg1aSlows inactivation4.5pEC50

Binding affinities (BindingDB)

577 measured of 587 human assays (587 total across all organisms); most potent 50 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValuePatent
5-cyclopropyl-4-[(3R)-1-[(3,5-dichlorophenyl)methyl]piperidin-3-yl]oxy-2-fluoro-N-methylsulfonylbenzamideIC500.3 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-N-cyclopropylsulfonyl-4-[[1-[(3,5-dichlorophenyl)-phenylmethyl]piperidin-4-yl]methoxy]-2-fluorobenzamideIC500.8 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[(3R)-1-[[3-chloro-5-(trifluoromethoxy)phenyl]methyl]piperidin-3-yl]oxy-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC501.3 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(3,5-dichlorophenyl)-phenylmethyl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC501.5 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(2S)-2-(3,5-dichlorophenyl)-1-methoxypropan-2-yl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC501.6 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(1S)-1-(3,5-dichlorophenyl)-2-methoxy-2-methylpropyl]piperidin-4-yl]methoxy]-N-ethylsulfonyl-2-fluorobenzamideIC501.6 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(1S)-1-(3,5-dichloro-2-fluorophenyl)ethyl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC501.6 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[[1-[1-(2-chloro-4-fluorophenyl)-2,2,2-trifluoroethyl]piperidin-4-yl]methoxy]-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC501.6 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[(3R)-1-[(2-chlorophenyl)methyl]piperidin-3-yl]oxy-5-cyclopropyl-N-cyclopropylsulfonyl-2-fluorobenzamideIC501.7 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[(3R)-1-[(2,4-dichlorophenyl)methyl]piperidin-3-yl]oxy-2-fluoro-N-methylsulfonylbenzamideIC501.7 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(1R)-1-(3,5-dichlorophenyl)-2-methoxy-2-methylpropyl]piperidin-4-yl]methoxy]-N-ethylsulfonyl-2-fluorobenzamideIC501.7 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[2-(3,5-dichlorophenyl)propan-2-yl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC501.7 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(1S)-1-(3,5-dichlorophenyl)ethyl]-4-methylpiperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC501.7 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(1S)-1-(3,5-dichlorophenyl)-2-methoxy-2-methylpropyl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC501.8 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-2-fluoro-4-[(3R)-1-[[4-fluoro-2-(trifluoromethyl)phenyl]methyl]piperidin-3-yl]oxy-N-methylsulfonylbenzamideIC501.9 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[(3R)-1-[(1S)-1-(3,5-dichlorophenyl)ethyl]piperidin-3-yl]oxy-2-fluoro-N-methylsulfonylbenzamideIC501.9 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[[1-[[3-chloro-5-(trifluoromethoxy)phenyl]methyl]piperidin-4-yl]methoxy]-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC501.9 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[2-(3,5-dichlorophenyl)propan-2-yl]piperidin-4-yl]methoxy]-N-ethylsulfonyl-2-fluorobenzamideIC501.9 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[1-(3,5-dichlorophenyl)-2,2,2-trifluoroethyl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC501.9 nMUS-9694002: Substituted benzamides and methods of use thereof
N-(azetidin-1-ylsulfonyl)-4-[(3R,6R)-1-[(2-chloro-4-fluorophenyl)methyl]-6-methylpiperidin-3-yl]oxy-5-cyclopropyl-2-fluorobenzamideIC501.9 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[(3R,6R)-1-[(2-chloro-4-fluorophenyl)methyl]-6-methylpiperidin-3-yl]oxy-5-cyclopropyl-N-cyclopropylsulfonyl-2-fluorobenzamideIC501.9 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[1-(3,5-dichlorophenyl)propyl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC502 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[[1-[bis(3-chlorophenyl)methyl]piperidin-4-yl]methoxy]-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC502 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[[1-[bis(2-chlorophenyl)methyl]piperidin-4-yl]methoxy]-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC502 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-N-cyclopropylsulfonyl-4-[(3R)-1-(3,5-dichlorophenyl)piperidin-3-yl]oxy-2-fluorobenzamideIC502.1 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[[1-[[2,5-bis(trifluoromethyl)phenyl]methyl]-4-methylpiperidin-4-yl]methoxy]-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC502.1 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[[1-[[3-chloro-5-(trifluoromethyl)phenyl]methyl]piperidin-4-yl]methoxy]-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC502.1 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[[1-[bis(4-chlorophenyl)methyl]piperidin-4-yl]methoxy]-5-cyclopropyl-N-cyclopropylsulfonyl-2-fluorobenzamideIC502.1 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[(3R)-1-[(2,4-dimethylphenyl)methyl]piperidin-3-yl]oxy-2-fluoro-N-methylsulfonylbenzamideIC502.1 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[[1-[5-chloro-4-(trifluoromethyl)-2-pyridinyl]-4-methylpiperidin-4-yl]methoxy]-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC502.1 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(1S)-1-(2,4-dichlorophenyl)ethyl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC502.2 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-N-cyclopropylsulfonyl-4-[[1-[(3,5-dichlorophenyl)methyl]piperidin-4-yl]methoxy]-2-fluorobenzamideIC502.2 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[(3R)-1-[(2-chloro-4-fluorophenyl)methyl]piperidin-3-yl]oxy-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC502.2 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[[(1R,5S)-3-[3-chloro-5-(trifluoromethoxy)phenoxy]-8-azabicyclo[3.2.1]octan-8-yl]methyl]-5-cyclopropyl-N-cyclopropylsulfonyl-2-fluorobenzamideIC502.2 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[4-(3,5-dichlorophenyl)sulfanylpiperidin-1-yl]methyl]-2-fluorobenzamideIC502.2 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-N-cyclopropylsulfonyl-4-[[1-[(1S)-1-(3,5-dichlorophenyl)-2-methoxyethyl]piperidin-4-yl]methoxy]-2-fluorobenzamideIC502.3 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[(3R)-1-[(1S)-1-(2-chloro-4-fluorophenyl)ethyl]piperidin-3-yl]oxy-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC502.3 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[(3R)-1-[(1S)-1-(5-chloro-6-cyclopropyl-2-pyridinyl)ethyl]piperidin-3-yl]oxy-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC502.3 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[(3R)-1-[2-(3-chlorophenyl)propan-2-yl]piperidin-3-yl]oxy-5-cyclopropyl-2-fluorobenzamideIC502.3 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-N-cyclopropylsulfonyl-2-fluoro-4-[(3R)-1-[[4-fluoro-2-(trifluoromethyl)phenyl]methyl]piperidin-3-yl]oxybenzamideIC502.4 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[[1-[[5-chloro-2-(trifluoromethyl)phenyl]methyl]-4-methylpiperidin-4-yl]methoxy]-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC502.4 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(1R)-1-(3,5-dichlorophenyl)propyl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC502.4 nMUS-9694002: Substituted benzamides and methods of use thereof
N-(azetidin-1-ylsulfonyl)-4-[(3R,6S)-1-[(2-chloro-4-fluorophenyl)methyl]-6-methylpiperidin-3-yl]oxy-5-cyclopropyl-2-fluorobenzamideIC502.4 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(3,5-dichlorophenyl)-phenylmethyl]-3-methylazetidin-3-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC502.4 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-N-cyclopropylsulfonyl-4-[[1-[1-(3,5-dichlorophenyl)ethyl]piperidin-4-yl]methoxy]-2-fluorobenzamideIC502.5 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(1R)-1-(3,5-dichlorophenyl)-2-methoxy-2-methylpropyl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamideIC502.5 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-4-[[1-[(2,4-dichlorophenyl)methyl]piperidin-4-yl]methoxy]-N-ethylsulfonyl-2-fluorobenzamideIC502.5 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-N-cyclopropylsulfonyl-4-[[1-[(3,5-dichlorophenyl)-phenylmethyl]-3-methylazetidin-3-yl]methoxy]-2-fluorobenzamideIC502.5 nMUS-9694002: Substituted benzamides and methods of use thereof
4-[(3R)-1-[(2-chloro-4-methylphenyl)methyl]piperidin-3-yl]oxy-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamideIC502.5 nMUS-9694002: Substituted benzamides and methods of use thereof
5-cyclopropyl-N-cyclopropylsulfonyl-4-[(3R)-1-[(3,5-dichlorophenyl)methyl]piperidin-3-yl]oxy-2-fluorobenzamideIC502.6 nMUS-9694002: Substituted benzamides and methods of use thereof

ChEMBL bioactivities

261 potent at pChembl≥5 of 343 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
9.70IC500.2nMCHEMBL3617063
9.55IC500.28nMCHEMBL4060338
9.35IC500.45nMCHEMBL4060338
9.00IC501nMSAXITOXIN
8.70IC502nMCHEMBL4070670
8.70IC502nMCHEMBL3662190
8.68IC502.1nMCHEMBL4070670
8.60IC502.519nMCHEMBL4217988
8.52IC503nMCHEMBL4217988
8.38IC504.2nMCHEMBL3341983
8.28EC505.3nMCHEMBL4064160
8.22IC506nMCHEMBL3662077
8.15IC507nMCHEMBL4290579
8.12IC507.5nMCHEMBL4082248
8.00IC5010nMCHEMBL4285790
7.92EC5012nMCHEMBL4060338
7.92Kd12nMCHEMBL4464990
7.92IC5012nMCHEMBL4854735
7.89IC5013nMCHEMBL4580996
7.85IC5014nMCHEMBL4279238
7.85IC5014nMTETRODOTOXIN
7.82IC5015.02nMBREVETOXIN B
7.82IC5015nMCHEMBL6143914
7.72IC5018.9nMCHEMBL3657855
7.70IC5020nMCHEMBL3657855
7.58IC5026nMCHEMBL4064160
7.54IC5029nMCHEMBL4068937
7.51IC5031nMCHEMBL4460028
7.46IC5035nMCHEMBL4082248
7.42IC5038nMCHEMBL5094715
7.39IC5041nMCHEMBL4224739
7.33IC5047nMCHEMBL4466858
7.30IC5050nMCHEMBL1269990
7.27IC5054nMPIMOZIDE
7.19Kd64nMCHEMBL4444707
7.19IC5065nMCHEMBL5598329
7.18IC5066nMCHEMBL4435054
7.16IC5070nMCHEMBL1270301
7.10EC5079nMCHEMBL4082248
7.10IC5079nMCHEMBL3318132
7.00IC50100nMCHEMBL486495
6.96IC50110nMPF-05089771
6.96IC50110nMCHEMBL1269882
6.92EC50120nMCHEMBL4070670
6.92IC50119nMPF-05089771
6.92IC50120nMCHEMBL4588728
6.92IC50120nMCHEMBL5598304
6.92IC50120nMCHEMBL1269991
6.90IC50125nMCHEMBL4471825
6.85Kd140nMCHEMBL4471012

PubChem BioAssay actives

259 with measured affinity, of 897 total; 50 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
[(3R,5S,6S,11R,12S,16S)-14,17-diamino-19,19-dihydroxy-6-(hydroxymethyl)-10-oxo-3-sulfooxy-8-oxa-1,9,13,15,18-pentazapentacyclo[9.5.2.13,16.05,9.012,16]nonadeca-14,17-dien-13-yl]methyl N-hydroxycarbamate1246042: Inhibition of NaV1.2 channel (unknown origin) expressed in Xenopus laevis oocytes by two-electrode oocyte voltage-clamp methodic50<0.0001uM
4-[2-(2-amino-3H-benzimidazol-5-yl)-4-chlorophenoxy]-2,5-difluoro-N-(1,2,4-thiadiazol-5-yl)benzenesulfonamide1300004: Inhibition of full length human Nav1.2 channel expressed in HEK cells co-expressing human sodium channel subunit beta1 at holding potential -35 mV by automated voltage clamp analysisic500.0002uM
(5R,7R)-7-decyl-1-oxa-8,10-diazaspiro[4.5]dec-8-en-9-amine1432176: Antagonist activity at human Nav1.2 expressed in HEK293T cells assessed as inhibition of VTD-induced tail current by whole cell patch clamp method relative to controlic500.0003uM
[(3aS,4R,10aS)-2,6-diamino-10,10-dihydroxy-3a,4,8,9-tetrahydro-1H-pyrrolo[1,2-c]purin-4-yl]methyl carbamate1525389: Inhibition of human Nav1.2 expressed in HEK293 cells by electrophysiology assayic500.0010uM
(5S,7S)-7-decyl-1-oxa-8,10-diazaspiro[4.5]dec-8-en-9-amine1432176: Antagonist activity at human Nav1.2 expressed in HEK293T cells assessed as inhibition of VTD-induced tail current by whole cell patch clamp method relative to controlic500.0020uM
5-cyclopropyl-N-cyclopropylsulfonyl-2-fluoro-4-[(6-methylspiro[2.5]octan-6-yl)methoxy]benzamide1525389: Inhibition of human Nav1.2 expressed in HEK293 cells by electrophysiology assayic500.0020uM
3-cyano-4-[2-[2-[(2-piperidin-4-ylethylamino)methyl]-4-pyridinyl]-4-[3-(trifluoromethyl)phenyl]phenoxy]-N-(1,2,4-thiadiazol-5-yl)benzenesulfonamide1365875: Inhibition of human Nav1.2 expressed in HEK cells by patch clamp electrophysiology methodic500.0025uM
4-[2-(3-amino-1,2-benzoxazol-5-yl)-4-chlorophenoxy]-2,5-difluoro-N-(1,2,4-thiadiazol-5-yl)benzenesulfonamide1300004: Inhibition of full length human Nav1.2 channel expressed in HEK cells co-expressing human sodium channel subunit beta1 at holding potential -35 mV by automated voltage clamp analysisic500.0042uM
(5R,6S,7R)-9-amino-7-decyl-1-oxa-8,10-diazaspiro[4.5]dec-8-ene-6-carboxylic acid1432177: Inhibition of Nav1.2 (unknown origin) by cell based assayec500.0053uM
5-cyclopropyl-N-cyclopropylsulfonyl-4-[(4,4-difluoro-1-methylcyclohexyl)methoxy]-2-fluorobenzamide1960144: Inhibition of human Nav1.2 alpha subunit expressed in HEK293 cells co-expressing beta1 subunit at -35 mV holding potential by PatchXpress automated voltage clamp electrophysiology techniqueic500.0060uM
N-[7-(1-adamantylmethoxy)-6-cyclopropyl-[1,2,4]triazolo[4,3-a]pyridin-3-yl]cyclopropanesulfonamide1410604: Inhibition of inactivated state of recombinant human NaV1.2 expressed in HEK293 cell membranes coexpressing Nav beta1 subunit assessed as decrease in sodium current amplitude at -35 mV holding potential by PX automated voltage clamp methodic500.0070uM
(5S,6R,7S)-9-amino-7-decyl-1-oxa-8,10-diazaspiro[4.5]dec-8-ene-6-carboxylic acid1432157: Antagonist activity at human Nav1.2 expressed in HEK293T cells assessed as inhibition of VTD-induced sustained current by whole cell patch clamp method relative to controlic500.0075uM
N-[6-cyclopropyl-7-[(3,5-dichlorophenoxy)methyl]-[1,2,4]triazolo[4,3-a]pyridin-3-yl]methanesulfonamide1410604: Inhibition of inactivated state of recombinant human NaV1.2 expressed in HEK293 cell membranes coexpressing Nav beta1 subunit assessed as decrease in sodium current amplitude at -35 mV holding potential by PX automated voltage clamp methodic500.0100uM
(4S)-6-fluoro-4-[(2R,4S)-2-pyridin-2-yl-4-(trifluoromethyl)piperidin-1-yl]-N-pyrimidin-4-yl-3,4-dihydro-2H-chromene-7-sulfonamide1587753: Inhibition of full length human Nav1.2 expressed in HEK293 cells at -60 mV holding potential by manual patch clamp electrophysiology methodkd0.0120uM
4-[(3S,4S)-3-(3,4-difluorophenyl)-1-(2,2,2-trifluoroethyl)piperidin-4-yl]oxy-3,5-difluoro-N-(6-fluoro-2-pyridinyl)benzenesulfonamide1754511: Inhibition of human Nav1.2 by V1/2 protocol based analysisic500.0120uM
5-chloro-4-[[(1S)-1-(2,5-difluorophenyl)ethyl]amino]-2-fluoro-N-(1,3-thiazol-4-yl)benzenesulfonamide1616312: Inhibition of recombinant human full length Nav1.2 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0130uM
(1R,5R,6R,7R,9S,11S,12S,13S,14S)-3-amino-14-(hydroxymethyl)-8,10-dioxa-2,4-diazatetracyclo[7.3.1.17,11.01,6]tetradec-3-ene-5,9,12,13,14-pentol1525389: Inhibition of human Nav1.2 expressed in HEK293 cells by electrophysiology assayic500.0140uM
N-[7-(1-adamantylmethoxy)-6-cyclopropyl-[1,2,4]triazolo[4,3-a]pyridin-3-yl]methanesulfonamide1410604: Inhibition of inactivated state of recombinant human NaV1.2 expressed in HEK293 cell membranes coexpressing Nav beta1 subunit assessed as decrease in sodium current amplitude at -35 mV holding potential by PX automated voltage clamp methodic500.0140uM
2-[[(1R,3S,5R,7S,9R,11S,12S,14R,16R,18S,20R,21Z,24S,26R,28S,30R,31R,33S,35R,37S,42R,44S,46R,48S)-12-hydroxy-1,3,11,24,31,41,44-heptamethyl-39-oxo-2,6,10,15,19,25,29,34,38,43,47-undecaoxaundecacyclo[26.22.0.03,26.05,24.07,20.09,18.011,16.030,48.033,46.035,44.037,42]pentaconta-21,40-dien-14-yl]methyl]prop-2-enal254847: Inhibitory concentration against synaptosome using [3H]PbTx-3ic500.0150uM
4-(1-adamantylmethoxy)-N-(azetidin-1-ylsulfonyl)-5-cyclopropyl-2-fluorobenzamide1831648: Inhibition of full length human Nav1.2 expressed in HEK cells by whole cell voltage clamp analysisic500.0189uM
2-oxo-3-[(1R)-1-(1,2,3,4-tetrahydroisoquinolin-8-yl)ethyl]-N-(1,2,4-thiadiazol-5-yl)-1,3-benzoxazole-6-sulfonamide1466785: Inhibition of Nav1.2 (unknown origin)ic500.0290uM
4-[[2-[(2,2-dimethylazetidin-1-yl)methyl]-6-fluorophenyl]methylamino]-2,6-difluoro-N-(1,3-thiazol-4-yl)benzenesulfonamide1616312: Inhibition of recombinant human full length Nav1.2 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0310uM
5-cyclopropyl-4-[[1-[(1S)-1-(3,5-dichlorophenyl)ethyl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamide1831648: Inhibition of full length human Nav1.2 expressed in HEK cells by whole cell voltage clamp analysisic500.0380uM
(2S)-2-[[(2S)-2-[[(2S)-6-amino-2-[[(2S)-6-amino-2-[[(2S)-6-amino-2-[[(1R,4S,7S,13S,16R,21R,24S,27S,30S,33S,36S,39S,42R,45S,48S,51S,54S,57S,60R,65R,68S,71S,74S)-27,57-bis(4-aminobutyl)-21-[[(2S)-2-amino-3-(4-hydroxyphenyl)propanoyl]amino]-24-(3-amino-3-oxopropyl)-54,74-bis(3-carbamimidamidopropyl)-13,51-bis(2-carboxyethyl)-45-(carboxymethyl)-39-[(1R)-1-hydroxyethyl]-48-(hydroxymethyl)-30,36,68-tris(1H-indol-3-ylmethyl)-71-(2-methylpropyl)-7,33-bis(2-methylsulfanylethyl)-3,6,9,12,15,22,25,28,31,34,37,40,43,46,49,52,55,58,67,70,73,76,81-tricosaoxo-4-propan-2-yl-18,19,62,63,78,79-hexathia-2,5,8,11,14,23,26,29,32,35,38,41,44,47,50,53,56,59,66,69,72,75,82-tricosazatricyclo[40.34.4.216,60]dooctacontane-65-carbonyl]amino]hexanoyl]amino]hexanoyl]amino]hexanoyl]amino]-4-methylpentanoyl]amino]-3-(1H-indol-3-yl)propanoic acid1388447: Inhibition of Nav1.2 (unknown origin) expressed in xenopus oocytes at -80 mV holding potential by two-electrode voltage-clamp methodic500.0410uM
2,6-difluoro-4-[[(1S)-1-(2-fluorophenyl)ethyl]amino]-N-(1,3-thiazol-4-yl)benzenesulfonamide1616312: Inhibition of recombinant human full length Nav1.2 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0470uM
5-(4-chlorophenyl)-N-[(2-piperidin-1-ylphenyl)methyl]pyridine-3-carboxamide527217: Inhibition of human NaV1.2 by electrophysiologyic500.0500uM
Pimozide1207165: Inhibition of Na channel (species unknown)ic500.0540uM
4-[[1-[[2-chloro-5-(trifluoromethyl)phenyl]methyl]piperidin-4-yl]methoxy]-5-cyclopropyl-2-fluoro-N-methylsulfonylbenzamide1525419: Binding affinity to human recombinant Nav1.2 by radioligand binding assaykd0.0640uM
4-(3-methoxyphenyl)-6-(8-methyl-1,3,4,5-tetrahydro-2-benzazepin-2-yl)pyrimidin-2-amine2120760: Inhibition of human Nav1.2 expressed in HEK293 cells at -40 mv holding potential measured after 5 mins by whole cell voltage clamp electrophysiological analysisic500.0650uM
2,6-difluoro-4-[[2-fluoro-6-[[methyl(propan-2-yl)amino]methyl]phenyl]methylamino]-N-(1,3-thiazol-4-yl)benzenesulfonamide1616312: Inhibition of recombinant human full length Nav1.2 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0660uM
5-(4-chlorophenyl)-N-[(2-piperidin-1-yl-3-pyridinyl)methyl]pyridine-3-carboxamide527217: Inhibition of human NaV1.2 by electrophysiologyic500.0700uM
[5-(4-tert-butylphenyl)furan-2-yl]-(4-cyclohexylpiperazin-1-yl)methanone404535: Inhibition of human recombinant Nav1.2 channel expressed in HEK293 cells by whole cell voltage clamp techniqueic500.1000uM
4-[2-(5-amino-1H-pyrazol-4-yl)-4-chlorophenoxy]-5-chloro-2-fluoro-N-(1,3-thiazol-4-yl)benzenesulfonamide1525389: Inhibition of human Nav1.2 expressed in HEK293 cells by electrophysiology assayic500.1100uM
5-(4-chlorophenyl)-N-[(2-methylphenyl)methyl]pyridine-3-carboxamide527217: Inhibition of human NaV1.2 by electrophysiologyic500.1100uM
(3S)-3-amino-4-oxo-4-[[(1R,4S,7S,10S,13S,16S,19R,24R,27S,30S,33S,36S,39S,42S,45R,51S,54S,57S,60R,65R,68S,71S,74S,77S,83S)-7,30,36,42,57-pentakis(4-aminobutyl)-77-benzyl-39,68-bis(3-carbamimidamidopropyl)-24-[[(2S)-1-[[(2S)-1-[[(2S)-3-carboxy-1-[[(2S)-1-[[(2S,3R)-1-[[(2S)-1-[[(1S,2R)-1-carboxy-2-hydroxypropyl]amino]-1-oxo-3-phenylpropan-2-yl]amino]-3-hydroxy-1-oxobutan-2-yl]amino]-1-oxo-3-phenylpropan-2-yl]amino]-1-oxopropan-2-yl]amino]-3-(1H-indol-3-yl)-1-oxopropan-2-yl]amino]-1-oxopropan-2-yl]carbamoyl]-4,13-bis(2-carboxyethyl)-10,16,83-tris(carboxymethyl)-27,71-bis[(4-hydroxyphenyl)methyl]-54-(1H-imidazol-5-ylmethyl)-51-(2-methylpropyl)-33,74-bis(2-methylsulfanylethyl)-2,5,8,11,14,17,26,29,32,35,38,41,44,47,50,53,56,59,66,69,72,75,78,81,84,91-hexacosaoxo-21,22,62,63,87,88-hexathia-3,6,9,12,15,18,25,28,31,34,37,40,43,46,49,52,55,58,67,70,73,76,79,82,85,90-hexacosazatricyclo[43.40.4.219,60]hennonacontan-65-yl]amino]butanoic acid1525389: Inhibition of human Nav1.2 expressed in HEK293 cells by electrophysiology assayic500.1200uM
4-(3-methoxyphenyl)-6-(1,3,4,5-tetrahydro-2-benzazepin-2-yl)pyrimidin-2-amine2120760: Inhibition of human Nav1.2 expressed in HEK293 cells at -40 mv holding potential measured after 5 mins by whole cell voltage clamp electrophysiological analysisic500.1200uM
5-(4-chlorophenyl)-N-[(2-morpholin-4-ylphenyl)methyl]pyridine-3-carboxamide527217: Inhibition of human NaV1.2 by electrophysiologyic500.1200uM
4-[[2-[[tert-butyl(methyl)amino]methyl]-6-fluorophenyl]methylamino]-2,6-difluoro-N-(1,3-thiazol-4-yl)benzenesulfonamide1616312: Inhibition of recombinant human full length Nav1.2 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.1250uM
N-cyclopropylsulfonyl-1-[(3R)-1-[(1R)-1-(3,5-dichlorophenyl)ethyl]pyrrolidin-3-yl]-6-fluoro-3-methylindazole-5-carboxamide1525419: Binding affinity to human recombinant Nav1.2 by radioligand binding assaykd0.1400uM
4-[4-chloro-2-(2-methylpyrazol-3-yl)phenoxy]-3-fluoro-N-(1,2,4-thiadiazol-5-yl)benzenesulfonamide1457691: Inhibition of human NaV1.2 expressed in HEK cells assessed as half inactivation potential at -120 mV holding potential by automated patch clamp methodic500.1490uM
2,6-ditert-butyl-4-[[3-(2,6-dimethylphenoxy)propylamino]methyl]phenol2120835: Inhibition of Nav1.2 (unknown origin)ic500.1800uM
2,5-bis[3-(trifluoromethyl)phenyl]-1H-imidazole351546: Inhibition of human Nav1.2 channel expressed in HEK cells by patch-clamp electrophysiology methodic500.2000uM
2,2-diphenyl-N-[4-(1,3-thiazol-2-ylsulfamoyl)phenyl]acetamide1246060: Inhibition of human NaV1.2 channel by patch clamp electrophysiology assayic500.2400uM
Loperamide205267: Inhibition of binding of Batrachotoxinin [3H]BTX-B to high affinity sites on voltage dependent sodium channels in a vesicular preparation from guinea pig cerebral cortexic500.2700uM
4-[4-chloro-2-(2-methylpyrazol-3-yl)phenoxy]-3-cyano-N-(1,2,4-thiadiazol-5-yl)benzenesulfonamide1457691: Inhibition of human NaV1.2 expressed in HEK cells assessed as half inactivation potential at -120 mV holding potential by automated patch clamp methodic500.2760uM
4-[4-[4-chloro-3-(trifluoromethyl)phenyl]-4-hydroxypiperidin-1-yl]-N,N-dimethyl-2,2-diphenylbutanamide205267: Inhibition of binding of Batrachotoxinin [3H]BTX-B to high affinity sites on voltage dependent sodium channels in a vesicular preparation from guinea pig cerebral cortexic500.2800uM
3,3-diphenyl-N-(1-phenylpropan-2-yl)propan-1-amine205267: Inhibition of binding of Batrachotoxinin [3H]BTX-B to high affinity sites on voltage dependent sodium channels in a vesicular preparation from guinea pig cerebral cortexic500.3000uM
[5-(4-chlorophenyl)furan-2-yl]-(4-cyclohexylpiperazin-1-yl)methanone404535: Inhibition of human recombinant Nav1.2 channel expressed in HEK293 cells by whole cell voltage clamp techniqueic500.3500uM
N-(3,5-dimethylphenyl)-6-(4-ethoxyphenyl)pyrazine-2-carboxamide536195: Inhibition of human recombinant NaV1.2 by electrophysiologyic500.3600uM
5-chloro-2-fluoro-4-[2-pyridazin-4-yl-4-(trifluoromethyl)phenoxy]-N-(1,3,4-thiadiazol-2-yl)benzenesulfonamide1457691: Inhibition of human NaV1.2 expressed in HEK cells assessed as half inactivation potential at -120 mV holding potential by automated patch clamp methodic500.3980uM

CTD chemical–gene interactions

45 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
mercuric bromideincreases expression, affects cotreatment2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideincreases expression, affects cotreatment2
Ascorbic Acidaffects cotreatment, increases expression, affects binding2
Benzo(a)pyreneincreases expression, increases methylation2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Tretinoinaffects binding, increases reaction, affects reaction, affects cotreatment, increases expression2
Valproic Acidincreases expression2
ascorbate-2-phosphateaffects binding, affects cotreatment, increases expression1
tris(2-butoxyethyl) phosphateaffects expression1
decamethrindecreases expression, decreases reaction1
sodium arseniteaffects methylation1
beta-methylcholineaffects expression1
1,2-bis(2-aminophenoxy)ethane N,N,N’,N’-tetraacetic acid acetoxymethyl esterdecreases expression, decreases reaction1
4-methoxycinnamate methyl esterincreases expression, increases reaction1
CGP 52608affects binding, increases reaction1
PD 150606decreases expression, decreases reaction1
1-hydroxy-2-oxo-3,3-bis(2-aminoethyl)-1-triazeneincreases expression, affects cotreatment1
pinostrobinincreases phosphorylation1
Chir 99021affects binding, affects cotreatment, increases expression1
Grape Seed Proanthocyanidinsaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangaffects cotreatment, increases expression1
XAV939increases expression, affects binding, affects cotreatment1
LDN 193189affects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
Temozolomidedecreases expression1
Lamotriginedecreases activity1
Arsenic Trioxideincreases expression1
Cyclic AMPincreases expression, affects cotreatment1
Atrazinedecreases expression1

ChEMBL screening assays

203 unique, capped per target: 172 binding, 20 functional, 10 admet, 1 toxicity

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL679768BindingInhibition of [3H]BTX binding to guinea pig voltage-dependent sodium channelAnticonvulsant activity of piperidinol and (dialkylamino)alkanol esters. — J Med Chem
CHEMBL749469FunctionalAntagonism of batrachotoxin-mediated sodium ion uptake into cultured neuroblastoma cellsBatrachotoxin binding site antagonists — Bioorg Med Chem Lett
CHEMBL3883160ADMETInhibition of human Nav1.2 expressed in CHO cells assessed as reduction in peak frequency currents by whole-cell voltage-clamp methodFused heterocyclic compounds as ion channel modulators

Cellosaurus cell lines

7 cell lines: 5 induced pluripotent stem cell, 2 spontaneously immortalized cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_C0Y9B’SYS CHO Nav1.2Spontaneously immortalized cell lineFemale
CVCL_C8H7FINi001-AInduced pluripotent stem cellFemale
CVCL_C8SPFINi003-AInduced pluripotent stem cellMale
CVCL_E4Q2KOLF2.1J SCN2A 94.3kbdel DEL/DELInduced pluripotent stem cellMale
CVCL_LC66PrecisION hNav1.2-CHOSpontaneously immortalized cell lineFemale
CVCL_VE79PFIZi031-AInduced pluripotent stem cellMale
CVCL_WN05CBTCi008-AInduced pluripotent stem cellFemale

Clinical trials (associated diseases)

511 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT01413711PHASE4WITHDRAWNAn Open-Label, Single and Multiple Oral Dose Pharmacokinetic Study of Vigabatrin in Infants With Infantile Spasms
NCT02092883PHASE4COMPLETEDEvaluation of Neuroinflammation in Children With Infantile Spasms
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT05044819PHASE4ACTIVE_NOT_RECRUITINGAssessment of Potential for Chronic Liver Injury in Participants Treated With Epidiolex (Cannabidiol) Oral Solution
NCT06598449PHASE4RECRUITINGAssessment of Safety of the Use of Fenfluramine in Children With Dravet Syndrome Under 24 Months of Age
NCT06924827PHASE4NOT_YET_RECRUITINGA Study to Investigate the Transition of Children From ‘Artisanal Cannabidiol (CBD) to Epidiolex
NCT07112365PHASE4NOT_YET_RECRUITINGThe FINTEPLA as an Anti-SUDEP Therapy in Dravet Syndrome Project
NCT06719141PHASE3RECRUITINGA Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathies (DEE)
NCT06908226PHASE3ENROLLING_BY_INVITATIONA Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathy (DEE)
NCT01575639PHASE3COMPLETEDPrednisolone in Infantile Spasms- High Dose Versus Usual Dose
NCT01828437PHASE3COMPLETEDAddition of Pyridoxine to Prednisolone in Infantile Spasms
NCT02299115PHASE3WITHDRAWNPrednisolone Versus Vigabatrin in the First-line Treatment of Infantile Spasms
NCT02953548PHASE3COMPLETEDTrial of Cannabidiol (CBD; GWP42003-P) for Infantile Spasms (GWPCARE7)
NCT02954887PHASE3COMPLETEDPhase 3 Trial of Cannabidiol (CBD; GWP42003-P) for Infantile Spasms: Open-label Extension Phase (GWPCARE7)
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT03347526PHASE3SUSPENDEDA Novel Approach to Infantile Spasms
NCT03421496PHASE3TERMINATEDA Study to Assess Cannabidiol Oral Solution With Vigabatrin as Initial Therapy in Participants With Infantile Spasms
NCT00098475PHASE3ACTIVE_NOT_RECRUITINGLenalidomide and Dexamethasone With or Without Thalidomide in Treating Patients With Multiple Myeloma
NCT00114101PHASE3ACTIVE_NOT_RECRUITINGLenalidomide in Treating Patients With Multiple Myeloma Undergoing Autologous Stem Cell Transplant
NCT00644228PHASE3ACTIVE_NOT_RECRUITINGLenalidomide and Dexamethasone With or Without Bortezomib in Treating Patients With Previously Untreated Multiple Myeloma
NCT00869206PHASE3COMPLETEDZoledronic Acid in Treating Patients With Metastatic Breast Cancer, Metastatic Prostate Cancer, or Multiple Myeloma With Bone Involvement
NCT02091375PHASE3COMPLETEDAntiepileptic Efficacy Study of GWP42003-P in Children and Young Adults With Dravet Syndrome (GWPCARE1)
NCT02174094PHASE3WITHDRAWNClobazam as Adjunctive Therapy in Paediatric Patients Aged ≥1 to ≤16 Years With Dravet Syndrome
NCT02187809PHASE3TERMINATEDSafety and Tolerability of Clobazam as Adjunctive Therapy in Paediatric Patients Aged ≥1 to ≤16 Years With Dravet Syndrome
NCT02224573PHASE3COMPLETEDAn Open Label Extension Study of Cannabidiol (GWP42003-P) in Children and Adults With Dravet or Lennox-Gastaut Syndromes
NCT02224703PHASE3COMPLETEDGWPCARE2 A Study to Investigate the Efficacy and Safety of Cannabidiol (GWP42003-P) in Children and Young Adults With Dravet Syndrome
NCT02318563PHASE3WITHDRAWNCannabidiol Oral Solution as an Adjunctive Therapy for Treatment of Participants With Inadequately Controlled Dravet Syndrome
NCT02682927PHASE3COMPLETEDA Trial of Two Fixed Doses of ZX008 (Fenfluramine HCl) in Children and Young Adults With Dravet Syndrome
NCT02823145PHASE3COMPLETEDAn Open-Label Extension Trial to Assess the Long-Term Safety of ZX008 (Fenfluramine Hydrochloride HCl) Oral Solution in Children and Young Adults With Dravet Syndrome
NCT02926898PHASE3COMPLETEDA 2-Part Study to Investigate the Dose-Ranging Safety and Pharmacokinetics, Followed by the Efficacy and Safety of ZX008 (Fenfluramine Hydrochloride) Oral Solution as an Adjunctive Therapy in Children ≥ 2 Years Old and Young Adults With Dravet Syndrome
NCT03299842PHASE3TERMINATEDA Study to Assess the Usability of the Embrace Seizure Detection Watch in Children and Young Adults With Dravet Syndrome