SCN1B

gene
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Summary

SCN1B (sodium voltage-gated channel beta subunit 1, HGNC:10586) is a protein-coding gene on chromosome 19q13.11, encoding Sodium channel regulatory subunit beta-1 (Q07699). Regulatory subunit of multiple voltage-gated sodium (Nav) channels directly mediating the depolarization of excitable membranes.

Voltage-gated sodium channels are heteromeric proteins that function in the generation and propagation of action potentials in muscle and neuronal cells. They are composed of one alpha and two beta subunits, where the alpha subunit provides channel activity and the beta-1 subunit modulates the kinetics of channel inactivation. This gene encodes a sodium channel beta-1 subunit. Mutations in this gene result in generalized epilepsy with febrile seizures plus, Brugada syndrome 5, and defects in cardiac conduction. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 6324 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): generalized epilepsy with febrile seizures plus (Definitive, ClinGen) — +8 more curated relationships
  • GWAS associations: 4
  • Clinical variants (ClinVar): 702 total — 27 pathogenic, 5 likely-pathogenic
  • Phenotypes (HPO): 148
  • Druggable target: yes — 2 molecules with ChEMBL bioactivity
  • Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_001037

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:10586
Approved symbolSCN1B
Namesodium voltage-gated channel beta subunit 1
Location19q13.11
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000105711
Ensembl biotypeprotein_coding
OMIM600235
Entrez6324

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000262631, ENST00000415950, ENST00000595652, ENST00000596348, ENST00000602150, ENST00000638536, ENST00000639260, ENST00000640135, ENST00000675741, ENST00000676410, ENST00000955983

RefSeq mRNA: 3 — MANE Select: NM_001037 NM_001037, NM_001321605, NM_199037

CCDS: CCDS12441, CCDS46047, CCDS86744

Canonical transcript exons

ENST00000262631 — 6 exons

ExonStartEnd
ENSE000008627353503963535039706
ENSE000008627363503979735040449
ENSE000012543043503911735039258
ENSE000035013723503349935033739
ENSE000035573973503252835032694
ENSE000038069383503047035030860

Expression profiles

Bgee: expression breadth ubiquitous, 133 present calls, max score 99.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.9798 / max 458.3845, expressed in 1337 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
1751845.34671073
1751861.6628595
1751891.5350436
1751910.9853217
1751880.3910163
1751850.3474139
1751830.3367177
1751900.155753
1751870.141068
1751920.078332

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primary visual cortexUBERON:000243699.43gold quality
right hemisphere of cerebellumUBERON:001489099.29gold quality
cerebellumUBERON:000203799.21gold quality
cerebellar cortexUBERON:000212999.21gold quality
cerebellar hemisphereUBERON:000224599.21gold quality
gastrocnemiusUBERON:000138899.13gold quality
right frontal lobeUBERON:000281098.50gold quality
hindlimb stylopod muscleUBERON:000425298.46gold quality
skeletal muscle tissueUBERON:000113498.20gold quality
muscle of legUBERON:000138398.16gold quality
dorsolateral prefrontal cortexUBERON:000983498.15gold quality
Brodmann (1909) area 9UBERON:001354097.92gold quality
frontal cortexUBERON:000187097.72gold quality
superior frontal gyrusUBERON:000266197.56gold quality
prefrontal cortexUBERON:000045197.17gold quality
cerebral cortexUBERON:000095696.59gold quality
putamenUBERON:000187496.43gold quality
right atrium auricular regionUBERON:000663196.29gold quality
anterior cingulate cortexUBERON:000983596.14gold quality
caudate nucleusUBERON:000187395.26gold quality
Ammon’s hornUBERON:000195494.85gold quality
substantia nigraUBERON:000203894.70gold quality
brainUBERON:000095594.69gold quality
apex of heartUBERON:000209894.16gold quality
nucleus accumbensUBERON:000188293.14gold quality
temporal lobeUBERON:000187193.10gold quality
amygdalaUBERON:000187693.06gold quality
muscle tissueUBERON:000238592.84gold quality
heart left ventricleUBERON:000208492.61gold quality
C1 segment of cervical spinal cordUBERON:000646992.56gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.33
E-CURD-112no3.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

25 targeting SCN1B, 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-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-368699.9070.532432
HSA-MIR-444799.8567.812900
HSA-MIR-76599.8468.242442
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-7154-5P99.6970.521900
HSA-MIR-486-3P99.5166.821901
HSA-MIR-318299.4068.152454
HSA-MIR-431199.3170.473041
HSA-MIR-504-3P99.3067.181745
HSA-MIR-60698.7267.34960
HSA-MIR-1227-5P98.6565.321549
HSA-MIR-92497.7866.21681
HSA-MIR-296-5P97.6164.02851
HSA-MIR-6787-5P97.5463.85457
HSA-MIR-431397.1863.15420
HSA-MIR-191397.0766.201417
HSA-MIR-6773-5P97.0464.30595
HSA-MIR-5591-3P96.2367.03489
HSA-MIR-6815-5P96.0565.55662
HSA-MIR-6865-5P96.0565.58675
HSA-MIR-10396B-5P94.9963.57358
HSA-MIR-744-5P93.7865.29230

Functional genomics

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

Literature-anchored findings (GeneRIF, showing 40)

  • Mutation of the sodium channel subunit SCN1B linked again to generalized epilepsy with febrile seizures (PMID:12011299)
  • Functional and biochemical analysis of a sodium channel beta1 subunit mutation responsible for generalized epilepsy with febrile seizures plus type 1. (PMID:12486163)
  • the expression of NaCh beta1 subunit protein in astrocytes is plastic, and indicate a novel mechanism for modulation of glial function in gliosis-associated pathologies. (PMID:12677453)
  • The IVS2-2A>C transition deletes AA 70-74 in the central hydrophobic core of the extracellular Ig domain, disrupting the hydrophobic interaction in the Ig-like fold & proper [beta]1 folding & causing a persistent inward Na+ current & hyperexcitability. (PMID:14504340)
  • identification and characterization of a novel splicing variant; functional studies in oocytes demonstrate that the beta1B subunit increases the ionic current when coexpressed with the tetrodotoxin sensitive channel, NaV1.2 (PMID:14622265)
  • Although data suggest that SCN1B 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)
  • Use of these Na+ channel models in simple neuron models revealed that both mutations(R85C, R85H) cause an increase in excitability but the R85H mutation was more excitable. (PMID:17604911)
  • In summary, the mutant beta1 subunits essentially fail to modulate alpha subunits which could increase neuronal excitability and underlie GEFS+ pathogenesis. (PMID:17629415)
  • This suggests that mutations in the SCN1B gene is not a prevalent cause of familial cases of FS and epilepsy or GEFS+ in Scandinavia. (PMID:17927801)
  • SCN1B mutations were not found to directly cause long QT syndrome. (PMID:18052691)
  • In patient with epilepsy were carried the mutation (C121W) of SCN1B. (PMID:18093548)
  • Febrile Seizure is not related to the most common mutations of SCN1B in two Tunisian families (PMID:18175077)
  • SCN1B may have a role in human arrhythmia susceptibility (PMID:18464934)
  • The data of this study suggested that SCN1B p.R125C is an autosomal recessive cause of Dravet syndrome through functional gene inactivation. (PMID:19710327)
  • Loss of function mutations in sodium channel beta-subunits were identified in patients with atrial fibrillation and were associated with a distinctive ECG phenotype (PMID:19808477)
  • Enhanced tubulin polymerization reduces sarcolemmal Na(v)1.5 expression and I(Na) amplitude in a beta1-subunit-independent fashion and causes I(Na) fast and slow inactivation impairment in a beta1-subunit-dependent way (PMID:19861310)
  • The IVS3+ 2996(TTA)8 allele in SCN1B commonly seen in Japanese would not be pathogenic itself but may render male, middle-aged Japanese more susceptible to Brugada syndrome (PMID:20137763)
  • SCN1B is the gene responsible in one out of six Tunisian families with febrile seizures (FS) that may contribute susceptibility for the five others. (PMID:21040232)
  • This study demonstrated that SCN1B may not be related to the occurrence of benign partial epilepsy in infancy or convulsions with gastroenteritis. (PMID:21882141)
  • The results suggested that beta1B p.G257R may contribute to epilepsy through a mechanism that includes intracellular retention resulting in aberrant neuronal pathfinding. (PMID:21994374)
  • Mutation analysis of the SCN1B, SCN1A and GABRG2 genes in children affected by Genetic (Generalised) Epilepsy with Febrile Seizures plus was performed (PMID:22011963)
  • results suggest that R214Q variation in SCN1Bb is a functional polymorphism that may serve as a modifier of the substrate responsible for Brugada syndrome or SIDS phenotypes (PMID:22155597)
  • Our study supports the association of SCN1Bb with BrS. (PMID:22284586)
  • A novel seizure-causing mechanism is suggested for NaV1.2beta1 in patients harboring mutant C121W subunit: increased channel excitability at elevated temperature. (PMID:22292491)
  • SCN1B mutation is not a common cause of Dravet syndrome. (PMID:23182416)
  • sodium channel polymorphisms are associated with epilepsy (PMID:24337656)
  • experimental data indicate that sodium channel voltage-gated type I beta subunit (Navbeta1b)/H162P results in reduced sodium channel activity functionally affecting the ventricular action potential. (PMID:24561865)
  • Hippocampal networks of a NaV beta1 transgenic mouse model of genetic epilepsy show enhanced excitability. (PMID:24605816)
  • data revealed SCN1Bb as a susceptibility gene responsible for LQTS (PMID:24662403)
  • High SCN1B expression is associated with increased tumour growth and metastasis in breast cancer. (PMID:24729314)
  • Study showed that the human SCN1B C121W epilepsy mutation leads to decreased axon initial segments expression of SCN1B in heterozygous CW mice and a complete lack of SCN1B in homozygous WW mice (PMID:25421039)
  • In a nonreferred nationwide Danish cohort of SIDS cases, up to 5/66 (7.5%) of SIDS cases can be explained by genetic variants in the sodium channel complex genes. (PMID:25757662)
  • SCN1B gene mutations that reduce sodium channel current may provide a mechanistic link between Atrioventricular nodal reentrant tachycardia and Brugada syndrome and predispose to expression of both phenotypes. (PMID:25998140)
  • We also identified an SCN1B T189M variant in 2 probands with lone AF and in 1 of 250 control subjects. (PMID:26129877)
  • Contribution of Cardiac Sodium Channel beta-Subunit Variants to Brugada Syndrome. (PMID:26179811)
  • we confirm the recessive inheritance of 2 novel SCN1B mutations in 5 children from 3 families with developmental epileptic encephalopathy. The recessive inheritance and early death in these patients is consistent with the Dravet-like phenotype observed in Scn1b(-/-) mice. (PMID:28218389)
  • This report provides the first genetic evidence of SCN1B mutation causing the Benign Familial Infantile Epilepsy (BFIE) phenotype. (PMID:28566192)
  • Genetic analysis was suggestive of SCN1B gene mutation associated with Dravet syndrome (PMID:28681755)
  • results show that the primary defect of E87Q mutation of the beta1 subunit is to compromise the correct voltage gated sodium channel maturation and traffic (PMID:28878239)
  • The lack of genotype-phenotype concordance among families, combined with the high frequency of previously reported mutations in the Genome Aggregation Database browser, suggests that SCN1B is not a monogenic cause of BrS or SADS. (PMID:29758173)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioscn1baENSDARG00000060222
danio_reriosi:ch211-225p5.8ENSDARG00000070170
danio_rerioscn1bbENSDARG00000105003
mus_musculusScn1bENSMUSG00000019194
rattus_norvegicusScn1bENSRNOG00000021102

Paralogs (1): SCN3B (ENSG00000166257)

Protein

Protein identifiers

Sodium channel regulatory subunit beta-1Q07699 (reviewed: Q07699)

All UniProt accessions (6): Q07699, A0A1W2PR05, A0A1W2PS68, A0A6Q8PGS1, A0A6Q8PHF7, B4DI92

UniProt curated annotations — full annotation on UniProt →

Function. Regulatory subunit of multiple voltage-gated sodium (Nav) channels directly mediating the depolarization of excitable membranes. Navs, also called VGSCs (voltage-gated sodium channels) or VDSCs (voltage-dependent sodium channels), operate by switching between closed and open conformations depending on the voltage difference across the membrane. In the open conformation they allow Na(+) ions to selectively pass through the pore, along their electrochemical gradient. The influx of Na+ ions provokes membrane depolarization, initiating the propagation of electrical signals throughout cells and tissues. The accessory beta subunits participate in localization and functional modulation of the Nav channels. Modulates the activity of SCN1A/Nav1.1, SCN2A/Nav1.2, SCN3A/Nav1.3, SCN4A/Nav1.4, SCN5A/Nav1.5, SCN8A/Nav1.6, SCN9A/Nav1.7 and SCN10A/Nav1.8. Cell adhesion molecule that plays a critical role in neuronal migration and pathfinding during brain development. Stimulates neurite outgrowth. Has no regulatory function on the SCN2A sodium channel complex.

Subunit / interactions. Voltage-gated sodium (Nav) channel consists of an ion-conducting pore-forming alpha subunit functional on its own that is regulated by one or more beta subunits. Interacts with SCN1A; regulatory subunit of SCN1A/Nav1.1. Interacts with SCN3A; regulatory subunit of SCN3A/Nav1.3. Interacts with SCN4A; regulatory subunit of SCN4A/Nav1.4. Interacts with SCN5A; regulatory subunit of SCN5A/Nav1.5. Interacts with SCN8A; regulatory subunit of SCN8A/Nav1.6. Interacts with SCN9A; regulatory subunit of SCN9A/Nav1.7. Interacts with SCN10A; regulatory subunit of SCN10A/Nav1.8. Interacts with NFASC. Interacts with TMEM65.

Subcellular location. Cell membrane. Perikaryon. Cell projection. Axon Perikaryon. Secreted.

Tissue specificity. The overall expression of isoform 1 and isoform 2 is very similar. Isoform 1 is abundantly expressed in skeletal muscle, heart and brain. Isoform 2 is highly expressed in brain and skeletal muscle and present at a very low level in heart, placenta, lung, liver, kidney and pancreas. In brain, isoform 2 is most abundant in the cerebellum, followed by the cerebral cortex and occipital lobe, while isoform 1 levels are higher in the cortex compared to the cerebellum. Isoform 2 is expressed in many regions of the brain, including cerebellar Purkinje cells, cortex pyramidal neurons and many of the neuronal fibers throughout the brain (at protein level). Also detected in dorsal root ganglion, in fibers of the spinal nerve and in cortical neurons and their processes (at protein level).

Disease relevance. Generalized epilepsy with febrile seizures plus 1 (GEFSP1) [MIM:604233] A rare autosomal dominant, familial condition with incomplete penetrance and large intrafamilial variability. Patients display febrile seizures persisting sometimes beyond the age of 6 years and/or a variety of afebrile seizure types. This disease combines febrile seizures, generalized seizures often precipitated by fever at age 6 years or more, and partial seizures, with a variable degree of severity. The disease is caused by variants affecting the gene represented in this entry. Brugada syndrome 5 (BRGDA5) [MIM:612838] A tachyarrhythmia characterized by right bundle branch block and ST segment elevation on an electrocardiogram (ECG). It can cause the ventricles to beat so fast that the blood is prevented from circulating efficiently in the body. When this situation occurs, the individual will faint and may die in a few minutes if the heart is not reset. The gene represented in this entry may be involved in disease pathogenesis. Atrial fibrillation, familial, 13 (ATFB13) [MIM:615377] A familial form of atrial fibrillation, a common sustained cardiac rhythm disturbance. Atrial fibrillation is characterized by disorganized atrial electrical activity and ineffective atrial contraction promoting blood stasis in the atria and reduces ventricular filling. It can result in palpitations, syncope, thromboembolic stroke, and congestive heart failure. The disease is caused by variants affecting the gene represented in this entry. Developmental and epileptic encephalopathy 52 (DEE52) [MIM:617350] A form of epileptic encephalopathy, a heterogeneous group of severe early-onset epilepsies characterized by refractory seizures, neurodevelopmental impairment, and poor prognosis. Development is normal prior to seizure onset, after which cognitive and motor delays become apparent. DEE52 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry.

Miscellaneous. Due to intron 3 retention.

Similarity. Belongs to the sodium channel auxiliary subunit SCN1B (TC 8.A.17) family.

Isoforms (2)

UniProt IDNamesCanonical?
Q07699-11, Beta-1yes
Q07699-22, Beta-1B, beta1A, beta1B

RefSeq proteins (3): NP_001028, NP_001308534, NP_950238 (=MANE)

Domains & families (InterPro)

IDNameType
IPR013106Ig_V-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR027098Na_channel_b1/b3Family
IPR036179Ig-like_dom_sfHomologous_superfamily

Pfam: PF07686

UniProt features (42 total): strand 13, sequence variant 12, glycosylation site 4, helix 3, disulfide bond 2, topological domain 2, signal peptide 1, chain 1, splice variant 1, transmembrane region 1, turn 1, domain 1

Structure

Experimental structures (PDB)

39 structures, top 30 by resolution.

PDBMethodResolution (Å)
7W9KELECTRON MICROSCOPY2.2
25IIELECTRON MICROSCOPY2.5
8I5YELECTRON MICROSCOPY2.6
21TQELECTRON MICROSCOPY2.7
7XVEELECTRON MICROSCOPY2.7
8I5BELECTRON MICROSCOPY2.7
8I5GELECTRON MICROSCOPY2.7
8THHELECTRON MICROSCOPY2.7
25IHELECTRON MICROSCOPY2.8
7XVFELECTRON MICROSCOPY2.8
8G1AELECTRON MICROSCOPY2.8
8XMMELECTRON MICROSCOPY2.89
7W9PELECTRON MICROSCOPY2.9
8I5XELECTRON MICROSCOPY2.9
8S9BELECTRON MICROSCOPY2.9
8THGELECTRON MICROSCOPY2.9
9DK5ELECTRON MICROSCOPY2.9
21TPELECTRON MICROSCOPY3
7W9MELECTRON MICROSCOPY3
7W9TELECTRON MICROSCOPY3
8J4FELECTRON MICROSCOPY3
7XMFELECTRON MICROSCOPY3.07
7XMGELECTRON MICROSCOPY3.09
25IJELECTRON MICROSCOPY3.1
8FHDELECTRON MICROSCOPY3.1
6AGFELECTRON MICROSCOPY3.2
6J8GELECTRON MICROSCOPY3.2
6J8HELECTRON MICROSCOPY3.2
6J8IELECTRON MICROSCOPY3.2
6J8JELECTRON MICROSCOPY3.2

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q07699-F187.900.68

Functional residue map

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

Disulfide bonds (2): 21–43, 40–121

Glycosylation sites (4): 93, 110, 114, 135

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: 531 (showing top): GOBP_MEMBRANE_DEPOLARIZATION, MODULE_274, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOBP_POSITIVE_REGULATION_OF_CATION_CHANNEL_ACTIVITY, GOBP_SODIUM_ION_TRANSMEMBRANE_TRANSPORT, GOBP_MEMBRANE_DEPOLARIZATION_DURING_ACTION_POTENTIAL, GOBP_POSITIVE_REGULATION_OF_TRANSPORTER_ACTIVITY, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_UP, GOBP_NEUROGENESIS, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, TAL1ALPHAE47_01

GO Biological Process (25): cell adhesion (GO:0007155), axon guidance (GO:0007411), positive regulation of sodium ion transport (GO:0010765), positive regulation of neuron projection development (GO:0010976), neuronal action potential propagation (GO:0019227), corticospinal neuron axon guidance (GO:0021966), sodium ion transmembrane transport (GO:0035725), locomotion (GO:0040011), membrane depolarization (GO:0051899), cardiac muscle contraction (GO:0060048), regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307), regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371), cardiac conduction (GO:0061337), cardiac muscle cell action potential involved in contraction (GO:0086002), membrane depolarization during action potential (GO:0086010), membrane depolarization during cardiac muscle cell action potential (GO:0086012), membrane depolarization during Purkinje myocyte cell action potential (GO:0086047), regulation of heart rate by cardiac conduction (GO:0086091), regulation of sodium ion transmembrane transport (GO:1902305), positive regulation of voltage-gated sodium channel activity (GO:1905152), regulation of sodium ion transport (GO:0002028), monoatomic ion transport (GO:0006811), sodium ion transport (GO:0006814), neuron projection development (GO:0031175), monoatomic ion transmembrane transport (GO:0034220)

GO Molecular Function (4): sodium channel regulator activity (GO:0017080), sodium channel inhibitor activity (GO:0019871), transmembrane transporter binding (GO:0044325), protein binding (GO:0005515)

GO Cellular Component (11): voltage-gated sodium channel complex (GO:0001518), extracellular region (GO:0005576), plasma membrane (GO:0005886), intercalated disc (GO:0014704), T-tubule (GO:0030315), node of Ranvier (GO:0033268), perikaryon (GO:0043204), membrane (GO:0016020), axon (GO:0030424), sodium channel complex (GO:0034706), cell projection (GO:0042995)

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
cellular anatomical structure6
regulation of sodium ion transport2
sodium ion transport2
cardiac muscle cell action potential2
sodium channel activity2
cellular process1
axonogenesis1
neuron projection guidance1
positive regulation of monoatomic ion transport1
regulation of neuron projection development1
neuron projection development1
positive regulation of cell projection organization1
transmission of nerve impulse1
nervous system process1
action potential propagation1
axon guidance1
corticospinal tract morphogenesis1
monoatomic cation transmembrane transport1
biological_process1
regulation of membrane potential1
striated muscle contraction1
heart contraction1
regulation of cardiac muscle cell membrane repolarization1
ventricular cardiac muscle cell membrane repolarization1
regulation of membrane depolarization1
regulation of heart contraction1
cardiac muscle cell contraction1
action potential1
membrane depolarization1
membrane depolarization during action potential1
membrane depolarization during cardiac muscle cell action potential1
Purkinje myocyte action potential1
regulation of heart rate1
cardiac conduction1
sodium ion transmembrane transport1
regulation of monoatomic cation transmembrane transport1
voltage-gated sodium channel activity1
regulation of voltage-gated sodium channel activity1
positive regulation of sodium ion transmembrane transporter activity1
positive regulation of cation channel activity1

Protein interactions and networks

STRING

1306 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SCN1BSCN2BO60939986
SCN1BSCN1AP35498980
SCN1BSCN4BQ8IWT1973
SCN1BSCN5AQ14524967
SCN1BGABRG2P18507943
SCN1BSCN9AQ15858935
SCN1BSCN2AQ99250930
SCN1BGPD1LQ8N335894
SCN1BSCN3AQ9NY46889
SCN1BKCNE3Q9Y6H6885
SCN1BSCN8AQ9UQD0876
SCN1BKCND3Q9UK17837
SCN1BHCN4Q9Y3Q4826
SCN1BCACNB2Q08289825
SCN1BSCN4AP35499795

IntAct

6 interactions, top by confidence:

ABTypeScore
SCN1BGET4psi-mi:“MI:0915”(physical association)0.400
SCN1BADRA1Apsi-mi:“MI:0915”(physical association)0.370
SCN1BC5AR2psi-mi:“MI:0915”(physical association)0.370
SCN1BF2RL1psi-mi:“MI:0915”(physical association)0.370
SCN1BUBBpsi-mi:“MI:0914”(association)0.350

BioGRID (16): ANK3 (Affinity Capture-Western), CNTN1 (Affinity Capture-Western), SCN1B (Affinity Capture-Western), SCN1B (Affinity Capture-Western), SCN4B (Affinity Capture-Western), SCN1B (Two-hybrid), SCN1B (Two-hybrid), SCN1B (Two-hybrid), TTC1 (Affinity Capture-MS), RNF126 (Affinity Capture-MS), UBB (Affinity Capture-MS), RNF115 (Affinity Capture-MS), DHRS7 (Affinity Capture-MS), AMFR (Affinity Capture-MS), GET4 (Affinity Capture-MS)

ESM2 similar proteins: A3KPA0, A5A6L6, A5D7C3, O60487, O70255, O88792, P01865, P01903, P01904, P01910, P04224, P04228, P14434, P14439, P14778, P15980, P22646, P23150, P53788, P57087, P59822, P97952, Q00954, Q02955, Q07699, Q17QN4, Q1WIM2, Q28740, Q2WGK2, Q30631, Q3TEW6, Q3V3F6, Q4PPC4, Q5EAB0, Q5R804, Q61730, Q62929, Q63621, Q66KX2, Q68FQ2

Diamond homologs: A5A6L6, P53788, P97952, Q00954, Q07699, Q17QN4, Q2KI11, Q4PPC4, Q8BHK2, Q8HXJ7, Q9JK00, Q9NY72, O70255, Q5EAB0, Q6WEB5

SIGNOR signaling

2 interactions.

AEffectBMechanism
SCN1B“form complex”“Nax cation channel complex, SCN1B-SCN4B variant”binding
SCN1B“form complex”“Nax cation channel complex, SCN1B-SCN2B variant”binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic27
Likely pathogenic5
Uncertain significance369
Likely benign164
Benign35

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1376394NM_001037.5(SCN1B):c.219T>G (p.Tyr73Ter)Pathogenic
1449534NM_001037.5(SCN1B):c.304C>T (p.Gln102Ter)Pathogenic
190871NM_001037.5(SCN1B):c.449-1G>APathogenic
2014378NM_001037.5(SCN1B):c.312_315del (p.Ile106fs)Pathogenic
2031780NM_001037.5(SCN1B):c.518G>A (p.Trp173Ter)Pathogenic
2035464NM_001037.5(SCN1B):c.447del (p.Ala150fs)Pathogenic
2123799NM_001037.5(SCN1B):c.448+10delPathogenic
2709805NM_001037.5(SCN1B):c.178dup (p.Arg60fs)Pathogenic
2728379NM_001037.5(SCN1B):c.59dup (p.Cys21fs)Pathogenic
2728854NM_001037.5(SCN1B):c.105del (p.Phe36fs)Pathogenic
2762136NM_001037.5(SCN1B):c.94_95insC (p.Tyr32fs)Pathogenic
2891167NM_001037.5(SCN1B):c.3G>A (p.Met1Ile)Pathogenic
3644786NM_001037.5(SCN1B):c.20del (p.Ala6_Leu7insTer)Pathogenic
3672329NM_001037.5(SCN1B):c.166G>T (p.Glu56Ter)Pathogenic
3726861NM_001037.5(SCN1B):c.24_25insT (p.Val9fs)Pathogenic
3730944NM_001037.5(SCN1B):c.40+1G>APathogenic
375404NM_001037.5(SCN1B):c.308A>T (p.Asp103Val)Pathogenic
375687NM_001037.5(SCN1B):c.316A>T (p.Ile106Phe)Pathogenic
4720677NM_001037.5(SCN1B):c.77C>A (p.Ser26Ter)Pathogenic
4726829NM_001037.5(SCN1B):c.357C>A (p.Tyr119Ter)Pathogenic
4728335NM_001037.5(SCN1B):c.178del (p.Arg60fs)Pathogenic
4796654NM_001037.5(SCN1B):c.40+1G>TPathogenic
694617NM_001037.5(SCN1B):c.449-2A>GPathogenic
694618NM_001037.5(SCN1B):c.355T>G (p.Tyr119Asp)Pathogenic
855779NM_001037.5(SCN1B):c.207+1G>APathogenic
9253NM_001037.5(SCN1B):c.208-2A>CPathogenic
9256NM_001037.5(SCN1B):c.448+89G>APathogenic
1677458NM_001037.5(SCN1B):c.41-1G>TLikely pathogenic
2146865NM_001037.5(SCN1B):c.449-1G>TLikely pathogenic
3065198NM_001037.5(SCN1B):c.448+349delLikely pathogenic

SpliceAI

1090 predictions. Top by Δscore:

VariantEffectΔscore
19:35032526:A:AGacceptor_gain1.0000
19:35032526:AGT:Aacceptor_gain1.0000
19:35032527:G:GTacceptor_gain1.0000
19:35032527:GT:Gacceptor_gain1.0000
19:35032527:GTG:Gacceptor_gain1.0000
19:35032527:GTGT:Gacceptor_gain1.0000
19:35032527:GTGTC:Gacceptor_gain1.0000
19:35032674:GGCAC:Gdonor_gain1.0000
19:35032682:G:GTdonor_gain1.0000
19:35032690:TCAAG:Tdonor_loss1.0000
19:35032694:GG:Gdonor_loss1.0000
19:35033486:T:Aacceptor_gain1.0000
19:35033492:C:Gacceptor_gain1.0000
19:35033495:CTAG:Cacceptor_loss1.0000
19:35033496:TA:Tacceptor_loss1.0000
19:35033497:A:AGacceptor_gain1.0000
19:35033497:AGAT:Aacceptor_loss1.0000
19:35033498:G:GCacceptor_gain1.0000
19:35033498:GA:Gacceptor_gain1.0000
19:35033498:GAT:Gacceptor_gain1.0000
19:35033498:GATC:Gacceptor_gain1.0000
19:35033498:GATCC:Gacceptor_gain1.0000
19:35033740:G:Cdonor_loss1.0000
19:35033741:T:Adonor_loss1.0000
19:35039171:T:TAacceptor_gain1.0000
19:35039251:GAGAA:Gdonor_gain1.0000
19:35039255:ATGC:Adonor_gain1.0000
19:35039256:TGC:Tdonor_gain1.0000
19:35039256:TGCG:Tdonor_loss1.0000
19:35039257:GC:Gdonor_gain1.0000

AlphaMissense

1434 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:35032605:T:AC40S1.000
19:35032605:T:CC40R1.000
19:35032606:G:AC40Y1.000
19:35032606:G:CC40S1.000
19:35032607:C:GC40W1.000
19:35032614:T:AC43S1.000
19:35032615:G:AC43Y1.000
19:35032615:G:CC43S1.000
19:35032616:C:GC43W1.000
19:35032656:T:AW57R1.000
19:35032656:T:CW57R1.000
19:35032657:G:CW57S1.000
19:35032658:G:CW57C1.000
19:35032658:G:TW57C1.000
19:35032662:T:CF59L1.000
19:35032664:C:AF59L1.000
19:35032664:C:GF59L1.000
19:35033565:T:AW92R1.000
19:35033565:T:CW92R1.000
19:35033567:G:CW92C1.000
19:35033567:G:TW92C1.000
19:35033652:T:AC121S1.000
19:35033652:T:CC121R1.000
19:35033653:G:CC121S1.000
19:35033654:C:GC121W1.000
19:35033665:G:CR125P1.000
19:35032606:G:TC40F0.999
19:35032614:T:CC43R0.999
19:35032615:G:TC43F0.999
19:35032619:G:CK44N0.999

dbSNP variants (sampled 300 via entrez): RS1000092363 (19:35036127 G>GT), RS1000117221 (19:35040367 G>A), RS1001222519 (19:35035645 T>C), RS1002043027 (19:35038064 G>A,C,T), RS1002137782 (19:35030952 C>G), RS1002200861 (19:35029966 C>T), RS1002487178 (19:35030697 G>A), RS1003177665 (19:35029137 C>A,T), RS1003567394 (19:35034250 G>A,C), RS1003784441 (19:35039970 C>T), RS1003906744 (19:35030893 G>A,T), RS1004045980 (19:35038790 G>A), RS1004092373 (19:35032236 C>T), RS1004104847 (19:35030677 C>A), RS1005229466 (19:35030109 G>A)

Disease associations

OMIM: gene MIM:600235 | disease phenotypes: MIM:612838, MIM:604233, MIM:615377, MIM:617350, MIM:601144, MIM:308350, MIM:117100, MIM:600131, MIM:608583

GenCC curated gene-disease

DiseaseClassificationInheritance
genetic developmental and epileptic encephalopathyDefinitiveAutosomal recessive
generalized epilepsy with febrile seizures plus, type 1DefinitiveAutosomal dominant
developmental and epileptic encephalopathy, 52DefinitiveAutosomal recessive
Brugada syndrome 5ModerateAutosomal dominant
Dravet syndromeSupportiveAutosomal dominant
generalized epilepsy with febrile seizures plusSupportiveAutosomal dominant
progressive familial heart blockSupportiveAutosomal dominant
atrial fibrillation, familial, 13LimitedUnknown
Brugada syndrome 1Disputed EvidenceAutosomal dominant

ClinGen Gene-Disease Validity (3)

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

DiseaseClassificationInheritance
generalized epilepsy with febrile seizures plusDefinitiveAD
genetic developmental and epileptic encephalopathyDefinitiveAR
Brugada syndrome 1DisputedAD

Mondo (21): Brugada syndrome 5 (MONDO:0013015), Dravet syndrome (MONDO:0100135), generalized epilepsy with febrile seizures plus, type 1 (MONDO:0011416), atrial fibrillation, familial, 13 (MONDO:0014155), developmental and epileptic encephalopathy, 52 (MONDO:0033361), Brugada syndrome 1 (MONDO:0011001), long QT syndrome (MONDO:0002442), ventricular fibrillation (MONDO:0000190), cardiac rhythm disease (MONDO:0007263), cardiomyopathy (MONDO:0004994), developmental and epileptic encephalopathy, 1 (MONDO:0010632), self-limited epilepsy with centrotemporal spikes (MONDO:0007295), Brugada syndrome (MONDO:0015263), undetermined early-onset epileptic encephalopathy (MONDO:0018614), childhood absence epilepsy (MONDO:0010826)

Orphanet (8): Brugada syndrome (Orphanet:130), Hereditary progressive cardiac conduction defect (Orphanet:871), Dravet syndrome (Orphanet:33069), Genetic epilepsy with febrile seizure plus (Orphanet:36387), Rare cardiomyopathy (Orphanet:167848), Self-limited epilepsy with centrotemporal spikes (Orphanet:1945), Non-specific early-onset epileptic encephalopathy (Orphanet:442835), Childhood absence epilepsy (Orphanet:64280)

HPO phenotypes

148 total (30 of 148 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000007Autosomal recessive inheritance
HP:0000054Micropenis
HP:0000070Ureterocele
HP:0000110Renal dysplasia
HP:0000175Cleft palate
HP:0000252Microcephaly
HP:0000340Sloping forehead
HP:0000463Anteverted nares
HP:0000466Limited neck range of motion
HP:0000486Strabismus
HP:0000729Autistic behavior
HP:0000736Short attention span
HP:0000739Anxiety
HP:0000752Hyperactivity
HP:0000826Precocious puberty
HP:0000980Pallor
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001251Ataxia
HP:0001252Hypotonia
HP:0001254Lethargy
HP:0001257Spasticity
HP:0001263Global developmental delay
HP:0001266Choreoathetosis
HP:0001272Cerebellar atrophy
HP:0001279Syncope
HP:0001290Generalized hypotonia
HP:0001300Parkinsonism
HP:0001302Pachygyria

GWAS associations

4 associations (top):

StudyTraitp-value
GCST001699_14Serum albumin levels2.000000e-13
GCST001699_5Serum albumin levels4.000000e-18
GCST001699_8Serum albumin levels3.000000e-15
GCST009391_1239Metabolite levels6.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0010422triacylglycerol 54:4 measurement

MeSH disease descriptors (7)

DescriptorNameTree numbers
D053840Brugada SyndromeC14.280.067.322; C14.280.123.250; C16.320.100
D009202CardiomyopathiesC14.280.238
D008133Long QT SyndromeC14.280.067.565; C14.280.123.625; C16.131.240.400.715; C23.550.073.547
D014693Ventricular FibrillationC14.280.067.922; C23.550.073.922
C538261Atrial fibrillation, familial 1 (supp.)
C565809Generalized Epilepsy With Febrile Seizures Plus, Type 1 (supp.)
C565808Generalized Epilepsy with Febrile Seizures Plus (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (10): CHEMBL4523668 (PROTEIN COMPLEX), CHEMBL4523669 (PROTEIN COMPLEX), CHEMBL4523670 (PROTEIN COMPLEX), CHEMBL4523671 (PROTEIN COMPLEX), CHEMBL4523672 (PROTEIN COMPLEX), CHEMBL4630760 (PROTEIN COMPLEX), CHEMBL4630762 (PROTEIN COMPLEX), CHEMBL4630763 (PROTEIN COMPLEX), CHEMBL4630765 (PROTEIN COMPLEX), CHEMBL5487 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

2 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 236 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL4633566DS-1971217
CHEMBL2325014PF-050897712219

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

ChEMBL bioactivities

85 potent at pChembl≥5 of 125 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
9.40IC500.4nMCHEMBL3657855
9.22IC500.6nMCHEMBL5094715
8.72IC501.9nMCHEMBL2325622
7.97IC5010.6nMCHEMBL3657855
7.92IC5012nMCHEMBL4642571
7.89IC5013nMCHEMBL4580996
7.89IC5013nMPF-05089771
7.85IC5014nMCHEMBL5288162
7.82IC5015nMCHEMBL5286433
7.77IC5017nMCHEMBL4632675
7.72IC5019nMCHEMBL5276801
7.70IC5020nMCHEMBL4468899
7.70IC5020nMCHEMBL4435054
7.66IC5021.7nMDS-1971
7.62IC5024nMCHEMBL4637488
7.61IC5024.5nMDS-1971
7.55IC5028nMCHEMBL4633573
7.55IC5028nMCHEMBL4642940
7.52IC5030nMCHEMBL4444000
7.52IC5030nMCHEMBL4648397
7.51IC5031nMCHEMBL4460028
7.51IC5031nMCHEMBL4639987
7.50IC5032nMCHEMBL5286829
7.47IC5034nMCHEMBL5270366
7.42IC5038nMCHEMBL5280425
7.40IC5040nMCHEMBL4530743
7.40IC5040nMCHEMBL4544968
7.40IC5040nMCHEMBL4471825
7.40IC5040nMCHEMBL5284082
7.35IC5045nMCHEMBL4637909
7.33IC5047nMCHEMBL4466858
7.30IC5050nMCHEMBL4580815
7.29IC5051nMCHEMBL3657855
7.28IC5052nMCHEMBL5286125
7.24IC5058nMCHEMBL5285313
7.23IC5059nMCHEMBL5287784
7.22IC5060nMCHEMBL4466858
7.22IC5060nMCHEMBL4460028
7.22IC5060nMCHEMBL4645788
7.18IC5066nMCHEMBL4435054
7.16IC5070nMCHEMBL4529272
7.10IC5080nMCHEMBL4457973
7.07IC5085nMCHEMBL5267728
7.06IC5087nMCHEMBL5269981
7.00IC50100nMCHEMBL4462046
6.96IC50110nMCHEMBL4445144
6.95IC50113nMCHEMBL4640756
6.92IC50119nMCHEMBL4580996
6.92IC50120nMCHEMBL4558113
6.90IC50125nMCHEMBL4471825

PubChem BioAssay actives

85 with measured affinity, of 184 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
4-(1-adamantylmethoxy)-N-(azetidin-1-ylsulfonyl)-5-cyclopropyl-2-fluorobenzamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0004uM
5-cyclopropyl-4-[[1-[(1S)-1-(3,5-dichlorophenyl)ethyl]piperidin-4-yl]methoxy]-2-fluoro-N-methylsulfonylbenzamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0006uM
4-[4-chloro-2-[2-(1-methylazetidin-3-yl)pyrazol-3-yl]phenoxy]-2,5-difluoro-N-(1,2,4-thiadiazol-5-yl)benzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0019uM
2,5-difluoro-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cyclohexyl]oxy-N-(1,2,4-thiadiazol-5-yl)benzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0120uM
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
4-[2-(5-amino-1H-pyrazol-4-yl)-4-chlorophenoxy]-5-chloro-2-fluoro-N-(1,3-thiazol-4-yl)benzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0130uM
6-fluoro-1-(3-fluorophenyl)-3-methyl-N-methylsulfonylindole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0140uM
N-cyclopropylsulfonyl-3-methyl-1-[5-(trifluoromethyl)-3-pyridinyl]indole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0150uM
2,5-difluoro-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cyclopentyl]oxy-N-(1,2,4-thiadiazol-5-yl)benzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0170uM
6-fluoro-3-methyl-N-methylsulfonyl-1-[3-(trifluoromethyl)phenyl]indole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0190uM
2,6-difluoro-4-[[2-fluoro-6-[[methyl(propan-2-yl)amino]methyl]phenyl]methylamino]-N-(1,3-thiazol-4-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0200uM
5-chloro-2-fluoro-4-[[(1S)-1-phenylethyl]amino]-N-(1,3-thiazol-2-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0200uM
5-chloro-2-fluoro-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cyclohexyl]oxy-N-pyrimidin-4-ylbenzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0217uM
2-fluoro-5-methyl-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cyclopentyl]oxy-N-pyrimidin-4-ylbenzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0240uM
2,5-difluoro-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cyclopentyl]oxy-N-(1,3-thiazol-2-yl)benzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0280uM
2,6-difluoro-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cycloheptyl]oxy-N-pyrimidin-4-ylbenzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0280uM
4-[[2-(azetidin-1-ylmethyl)-6-fluorophenyl]methylamino]-5-chloro-2-fluoro-N-(1,3-thiazol-4-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0300uM
2,6-difluoro-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cyclohexyl]oxy-N-pyrimidin-4-ylbenzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0300uM
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
2-fluoro-5-methyl-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cyclohexyl]oxy-N-pyrimidin-4-ylbenzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0310uM
N-cyclopropylsulfonyl-1-(3-fluorophenyl)-3-methylindole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0320uM
3-methyl-N-methylsulfonyl-1-[3-(trifluoromethyl)phenyl]indole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0340uM
1-(3-fluorophenyl)-3-methyl-N-methylsulfonylindole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0380uM
5-chloro-2-fluoro-4-[[(1R)-2-methoxy-1-phenylethyl]amino]-N-(1,3-thiazol-2-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0400uM
5-chloro-4-[[(1S)-1-(2,4-difluorophenyl)ethyl]amino]-2-fluoro-N-(1,3-thiazol-2-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0400uM
4-[[2-[[tert-butyl(methyl)amino]methyl]-6-fluorophenyl]methylamino]-2,6-difluoro-N-(1,3-thiazol-4-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0400uM
N-cyclopropylsulfonyl-6-fluoro-3-methyl-1-[5-(trifluoromethyl)-3-pyridinyl]indole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0400uM
5-chloro-2-fluoro-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cyclopentyl]oxy-N-pyrimidin-4-ylbenzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0450uM
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
3-chloro-4-(1-phenylpropylamino)-N-(1,3-thiazol-2-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0500uM
5-chloro-4-[(5-chloro-6-cyclopropyl-3-pyridinyl)oxy]-2-fluoro-N-methylsulfonylbenzamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0520uM
3-methyl-1-(3-methylphenyl)-N-methylsulfonylindole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0580uM
N-cyclopropylsulfonyl-3-methyl-1-[6-(trifluoromethyl)-3-pyridinyl]indole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0590uM
2,6-difluoro-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cyclopentyl]oxy-N-pyrimidin-4-ylbenzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.0600uM
2,6-difluoro-4-[[(1S)-1-(2-fluoro-5-methoxyphenyl)ethyl]amino]-N-(1,3-thiazol-4-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0700uM
5-chloro-2-fluoro-4-[[(1S)-1-pyridin-3-ylethyl]amino]-N-(1,3-thiazol-2-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.0800uM
1-(5-chloro-3-pyridinyl)-N-cyclopropylsulfonyl-3-methylindole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0850uM
1-(3-chlorophenyl)-3-methyl-N-methylsulfonylindole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.0870uM
3-chloro-4-(1-phenylethylamino)-N-(1,3-thiazol-2-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.1000uM
5-chloro-2-fluoro-4-[[(1S)-1-(2-fluoro-5-methoxyphenyl)ethyl]amino]-N-(1,3-thiazol-4-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.1100uM
2,5-difluoro-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cyclohexyl]oxy-N-pyrimidin-4-ylbenzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.1130uM
4-[[(1S)-1-[5-(azetidin-1-ylmethyl)-2-fluorophenyl]ethyl]amino]-5-chloro-2-fluoro-N-(1,3-thiazol-4-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.1200uM
3-chloro-4-[[(1S)-1-phenylethyl]amino]-N-(1,3-thiazol-2-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.1300uM
4-[[(1S)-1-(5-cyano-2-fluorophenyl)ethyl]amino]-2,6-difluoro-N-(1,3-thiazol-4-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.1400uM
2,5-difluoro-4-[(1S,2R)-2-(2-methylpyrazol-3-yl)cyclopentyl]oxy-N-pyrimidin-4-ylbenzenesulfonamide1662959: Inhibition of human NaV1.7/beta1/beta2 expressed in HEK293A cells by Ionworks high-throughput electrophysiology methodic500.1800uM
1-(3-methoxyphenyl)-3-methyl-N-methylsulfonylindole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.1900uM
1-(4-fluorophenyl)-3-methyl-N-methylsulfonylindole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.1900uM
5-chloro-2-fluoro-4-[[(1S)-1-(4-fluorophenyl)ethyl]amino]-N-(1,3-thiazol-2-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.2300uM
5-chloro-4-[[2-[(2,2-dimethylazetidin-1-yl)methyl]-6-fluorophenyl]methylamino]-2-fluoro-N-(1,3-thiazol-4-yl)benzenesulfonamide1616304: Inhibition of recombinant human full length Nav1.6 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayic500.2300uM
1-(4-chlorophenyl)-3-methyl-N-methylsulfonylindole-5-carboxamide1948697: Inhibition of human Nav1.7/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisic500.2600uM

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
cobaltous chloridedecreases expression, increases expression2
S-(1,2-dichlorovinyl)cysteinedecreases reaction, increases expression, decreases expression2
Benzo(a)pyreneaffects methylation2
Particulate Matterdecreases expression, increases abundance2
tris(2-butoxyethyl) phosphateaffects expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arseniteaffects methylation1
CGP 52608affects binding, increases reaction1
2,3,5,6-tetrafluoro-4-methylbenzyl (Z)-(1RS)-cis-3-(2-chloro-3,3,3-trifluoroprop-1-enyl)-2,2-dimethylcyclopropanecarboxylateincreases transport, affects cotreatment, decreases reaction1
abrinedecreases expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arbutinincreases expression1
Aspirinincreases expression1
Calcitriolincreases expression, affects cotreatment1
Doxorubicindecreases expression1
Lipopolysaccharidesincreases expression, decreases reaction1
Phenytoinaffects binding, decreases activity, decreases response to substance1
Silicon Dioxidedecreases expression1
Smokedecreases expression1
Sodiumdecreases reaction, increases transport, affects cotreatment1
Testosteroneaffects cotreatment, increases expression1
Tobacco Smoke Pollutiondecreases expression1
Urethanedecreases expression1
Cyclosporinedecreases expression1
Okadaic Aciddecreases expression1
Acrylamideincreases expression1

ChEMBL screening assays

15 unique, capped per target: 7 binding, 6 admet, 2 toxicity

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4415855ADMETInhibition of recombinant human full length Nav1.1 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -45 mV holding potential by whole cell patch clamp assayIdentification of CNS-Penetrant Aryl Sulfonamides as Isoform-Selective NaV1.6 Inhibitors with Efficacy in Mouse Models of Epilepsy. — J Med Chem
CHEMBL4415863BindingInhibition of recombinant human full length Nav1.7 co-expressed with human SCN1B in HEK293 cells measured after 20 mins at -60 mV holding potential by whole cell patch clamp assayIdentification of CNS-Penetrant Aryl Sulfonamides as Isoform-Selective NaV1.6 Inhibitors with Efficacy in Mouse Models of Epilepsy. — J Med Chem
CHEMBL5252387ToxicityInhibition of human Nav1.1/beta1/2 transfected in HEK293-A cells assessed as inhibition of channel current incubated for 5.5 mins by high-throughput electrophysiology system analysisN-Aryl Indoles as a Novel Class of Potent NaV1.7 Inhibitors. — ACS Med Chem Lett

Cellosaurus cell lines

7 cell lines: 3 cancer cell line, 3 transformed cell line, 1 induced pluripotent stem cell

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

CellosaurusNameCategorySex
CVCL_A8HCBJTTHi001-A-2Induced pluripotent stem cellMale
CVCL_B2ESAbcam HeLa SCN1B KOCancer cell lineFemale
CVCL_D1KKPrecisION hNav1.8/beta1-HEKTransformed cell lineFemale
CVCL_TK15HAP1 SCN1B (-) 1Cancer cell lineMale
CVCL_TK16HAP1 SCN1B (-) 2Cancer cell lineMale
CVCL_WS18HEK293 SCN1A/SCN1B/SCN2BTransformed cell lineFemale
CVCL_YN15HEK-293 hNav1.9Transformed cell lineFemale

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
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
NCT02513940PHASE4COMPLETEDInfluence of Testosterone Administration on Drug-Induced QT Interval Prolongation and Torsades de Pointes
NCT03834883PHASE4COMPLETEDReducing the Risk of Drug-Induced QT Interval Lengthening in Women
NCT04169100PHASE4UNKNOWNNovel Form of Acquired Long QT Syndrome
NCT04675788PHASE4COMPLETEDNovel Approaches for Minimizing Drug-Induced QT Interval Lengthening
NCT00147277PHASE4COMPLETEDADVANCE-D: Antitachycardia Pacing (ATP) Delivery for Painless Implantable Cardioverter Defibrillator (ICD) Therapy
NCT00147290PHASE4COMPLETEDADVANCE CRT - D: Antitachycardia Pacing (ATP) Delivery for Painless Implantable Cardioverter Defibrillator (ICD) Therapy
NCT00180427PHASE4COMPLETEDVERRARI - Are Ventricular Arrhythmic Episodes Reduced by Rate Response in ICDs?
NCT00401466PHASE4COMPLETEDRemote Follow-up of Patients Receiving Implantable Cardioverter Defibrillator for Prophylactic Therapy
NCT00538356PHASE4COMPLETEDInfluence of Home Monitoring on the Clinical Status of Heart Failure Patients With an Impaired Left Ventricular Function
NCT00787800PHASE4COMPLETEDThe Use of Dual Chamber ICD With Special Programmed Features to Lower the Risk of Inappropriate Shock
NCT03826524PHASE4RECRUITINGEpinephrine Dose: Optimal Versus Standard Evaluation Trial
NCT03855826PHASE4UNKNOWNEvaluation of the Efficacy and Safety of Nifekalant Hydrochloride (NIF) Injection.
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)
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
NCT03936777PHASE3COMPLETEDA Study to Investigate the Long-Term Safety of ZX008 (Fenfluramine Hydrochloride) Oral Solution in Children and Adults With Epileptic Encephalopathy Including Dravet Syndrome and Lennox-Gastaut Syndrome
NCT04462770PHASE3RECRUITINGA Study of EPX-100 (Clemizole Hydrochloride) in Participants With Dravet Syndrome
NCT04611438PHASE3UNKNOWNResearch on Cognitive Effect of Cannabidiol on Dravet Syndrome and Lennox-Gastaut SyndromeGastaut Syndrome
NCT04940624PHASE3COMPLETEDA Study of Soticlestat as an Add-on Therapy in Children and Young Adults With Dravet Syndrome
NCT05163314PHASE3TERMINATEDA Study of Soticlestat as an Add-on Therapy in Children and Adults With Dravet Syndrome or Lennox-Gastaut Syndrome
NCT05560282PHASE3TERMINATEDFenfluramine for Adult Dravet Patients
NCT06118255PHASE3ACTIVE_NOT_RECRUITINGA Study to Evaluate Safety, Tolerability, and Pharmacokinetics of Fenfluramine (Hydrochloride) in Infants 1 Year to Less Than 2 Years of Age With Dravet Syndrome
NCT06422377PHASE3TERMINATEDA Study Evaluating Soticlestat in Participants With Dravet Syndrome or Lennox-Gastaut Syndrome Who Have Been Exposed to Fenfluramine