Migraine disorder

disease
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Also known as migrainemigraine headache

Summary

Migraine disorder (MONDO:0005277) is a disease with 75 cohort genes (826 GWAS associations across 74 studies) and 1,313 clinical trials. Top therapeutic interventions include sumatriptan, topiramate, and erenumab.

At a glance

  • Cohort genes: 75
  • GWAS associations: 826
  • ClinVar variants: 17
  • Clinical trials: 1,313

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namemigraine disorder
Mondo IDMONDO:0005277
MeSHD008881
DOIDDOID:6364
ICD-10-CMG43
ICD-11669367341
NCITC89715
UMLSC0149931
MedGen57451
Is cancer (heuristic)no

Also known as: migraine · migraine headache

Data availability: 17 ClinVar variants · 826 GWAS associations (74 studies) · 25 cell lines.

Disease family

An umbrella term covering 2 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › nervous system disordercentral nervous system disorderbrain disordermigraine disorder

Related subtypes (70): leukoencephalopathy, megalencephalic, encephalopathy, acute, infection-induced, diabetic encephalopathy, complex cortical dysplasia with other brain malformations, hydrocephalus, brain compression, cerebral sarcoidosis, hepatic encephalopathy, visual pathway disorder, central nervous system origin vertigo, cerebellar disorder, cerebritis, olfactory nerve disorder, thalamic disorder, pituitary gland disorder, disorder of optic chiasm, basal ganglia disorder, epilepsy, mental disorder, central nervous system cyst, multiple sclerosis, prion disease, carbon monoxide-induced delayed encephalopathy, cerebral malaria, akinetic mutism, bulbar polio, Reye syndrome, brain edema, encephalomalacia, intracranial hypertension, intracranial hypotension, Wernicke encephalopathy, encephalopathy, recurrent, of childhood, XK aprosencephaly, progressive bulbar palsy, cerebrovascular disorder, glycine encephalopathy, autosomal recessive frontotemporal pachygyria, occipital pachygyria and polymicrogyria, insomnia, narcolepsy-cataplexy syndrome, megalencephaly, meningoencephalocele, cerebral cortical dysplasia, encephaloclastic disorder, bilirubin encephalopathy, autoimmune encephalopathy with parasomnia and obstructive sleep apnea, narcolepsy without cataplexy, hypothalamic hamartomas with gelastic seizures, encephalitis, cerebral lipidosis with dementia, brain neoplasm, colpocephaly, corpus callosum agenesis of blepharophimosis robin type, corpus callosum dysgenesis X-linked recessive, corpus callosum dysgenesis cleft spasm, corpus callosum dysgenesis hypopituitarism, cerebral degeneration, acute bilirubin encephalopathy, chronic bilirubin encephalopathy, atelencephaly, aprosencephaly, brain injury, traumatic encephalopathy, cluster headache syndrome, cerebral cortex disorder, midbrain disorder, encephalopathy due to mitochondrial and peroxisomal fission defect, brain malformations with or without urinary tract defects, encephalopathy, acute transient

Subtypes (2): migraine with aura, migraine without aura

Genetics & variants

GWAS landscape

826 GWAS associations across 74 studies. Top hits map to 21 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs111721131e-90LRP1T1.11
rs578667677e-71PLCE1?
rs102184527e-71PRDM16G1.12
rs111530827e-54FHL5G1.09
rs60353559e-54SLC24A3?
rs101669429e-51MSL3B - TRPM8T1.1
rs93493791e-47PHACTR1A1.08
rs30014264e-42STAT6?
rs20783716e-42LINC01765 - NGF-AS1C1.11
rs48884081e-41CFDP1?
rs171717103e-41SUGCT?
rs22743193e-41MEF2DT1.08
rs94867157e-39FHL5?
rs29838962e-37FHL5?
rs79687199e-37LRP1, LRP1-AS?
rs21608753e-36FGF23 - FGF6C1.07
rs121344936e-36LINC01765 - NGF-AS1A1.11
rs29716032e-35FHL5?
rs621557505e-34LINC00342?
rs13328443e-33PHACTR1?
rs20526925e-31IRAG1?
rs19259503e-30MEF2DA0.94
chr12:571328633e-30A0.11
rs48148641e-28SLC24A3C1.07
chr1:31559181e-28A0.12
rs10755502e-28FGF23 - FGF6T0.94
rs102346364e-28SUGCTT1.09
rs10484835e-28SMG6, HIC1?
rs20759689e-28PRDM16?1.1
rs673382272e-27FHL5T1.09

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90281112Islam MR2023102,084771,257Cross-trait analyses identify shared genetics between migraine, headache, and glycemic traits, and a causal relationship with fasting proinsulin.
GCST90281113Islam MR2023102,084771,257Cross-trait analyses identify shared genetics between migraine, headache, and glycemic traits, and a causal relationship with fasting proinsulin.
GCST90281114Islam MR2023102,084771,257Cross-trait analyses identify shared genetics between migraine, headache, and glycemic traits, and a causal relationship with fasting proinsulin.
GCST90281115Islam MR2023102,084771,257Cross-trait analyses identify shared genetics between migraine, headache, and glycemic traits, and a causal relationship with fasting proinsulin.
GCST90281116Islam MR2023102,084771,257Cross-trait analyses identify shared genetics between migraine, headache, and glycemic traits, and a causal relationship with fasting proinsulin.
GCST90281117Islam MR2023102,084771,257Cross-trait analyses identify shared genetics between migraine, headache, and glycemic traits, and a causal relationship with fasting proinsulin.
GCST90281118Islam MR2023102,084771,257Cross-trait analyses identify shared genetics between migraine, headache, and glycemic traits, and a causal relationship with fasting proinsulin.
GCST90102553Hautakangas H2022102,084771,257Genome-wide analysis of 102,084 migraine cases identifies 123 risk loci and subtype-specific risk alleles.
GCST90429186Choquet H202185,726803,292New and sex-specific migraine susceptibility loci identified from a multiethnic genome-wide meta-analysis.
GCST90244660Islam MR202274,1241,595,263Genetic Overlap Analysis Identifies a Shared Etiology between Migraine and Headache with Type 2 Diabetes.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding2
Tier 2: splice/UTR2
Tier 3: regulatory1
Tier 4: intronic/intergenic45

MAF distribution

BucketVariants
common (>=0.05)48
low_freq (0.01-0.05)0
rare (<0.01)0
unknown2

Functional consequences

ConsequenceCount
intron_variant37
intergenic_variant5
missense_variant2
unknown2
regulatory_region_variant1
3_prime_UTR_variant1
splice_polypyrimidine_tract_variant1
non_coding_transcript_exon_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs111721131257133500T>C,G0.415intron_variantLRP11e-90Tier 4: intronic/intergenic
rs578667671094263320T>C,G0.05intron_variantPLCE17e-71Tier 4: intronic/intergenic
rs1021845213159033A>G0.229intron_variantPRDM167e-71Tier 4: intronic/intergenic
rs11153082696611790A>C,G0.331intron_variantFHL57e-54Tier 4: intronic/intergenic
rs60353552019484445T>A,C0.05intron_variantSLC24A39e-54Tier 4: intronic/intergenic
rs101669422233916448T>A,C0.195intergenic_variantMSL3B - TRPM89e-51Tier 4: intronic/intergenic
rs9349379612903725A>C,G,T0.41intron_variantPHACTR11e-47Tier 4: intronic/intergenic
rs30014261257115272T>C0.05intergenic_variantSTAT64e-42Tier 4: intronic/intergenic
rs20783711115134562T>A,C,G0.117intergenic_variantLINC01765 - NGF-AS16e-42Tier 4: intronic/intergenic
rs48884081675398926G>A,C,T0.05intron_variantCFDP11e-41Tier 4: intronic/intergenic
rs17171710740400634C>T0.05intron_variantSUGCT3e-41Tier 4: intronic/intergenic
rs22743191156481081T>C0.347intron_variantMEF2D3e-41Tier 4: intronic/intergenic
rs9486715696611893A>C,T0.05intron_variantFHL57e-39Tier 4: intronic/intergenic
rs2983896696581995G>A0.05intron_variantFHL52e-37Tier 4: intronic/intergenic
rs79687191257146968C>G0.05intron_variantLRP1, LRP1-AS9e-37Tier 4: intronic/intergenic
rs2160875124418156C>T0.477intron_variantFGF23 - FGF63e-36Tier 4: intronic/intergenic
rs121344931115135325C>A0.12regulatory_region_variantLINC01765 - NGF-AS16e-36Tier 3: regulatory
rs2971603696587542C>G,T0.05intron_variantFHL52e-35Tier 4: intronic/intergenic
rs62155750295825708A>G0.05intron_variantLINC003425e-34Tier 4: intronic/intergenic
rs1332844612888772C>T0.05intron_variantPHACTR13e-33Tier 4: intronic/intergenic
rs20526921110646094A>C,G0.05intron_variantIRAG15e-31Tier 4: intronic/intergenic
rs19259501156480948G>A,C0.35missense_variantMEF2D3e-30Tier 1: coding
chr12:571328633e-30Tier 4: intronic/intergenic
rs48148642019489173G>A,C,T0.254intron_variantSLC24A31e-28Tier 4: intronic/intergenic
chr1:31559181e-28Tier 4: intronic/intergenic
rs1075550124417341C>A,T0.48intron_variantFGF23 - FGF62e-28Tier 4: intronic/intergenic
rs10234636740388018T>C,G0.111intron_variantSUGCT4e-28Tier 4: intronic/intergenic
rs1048483172063163C>T0.053_prime_UTR_variantSMG6, HIC15e-28Tier 2: splice/UTR
rs207596813164677C>T0.05intron_variantPRDM169e-28Tier 4: intronic/intergenic
rs67338227696594271A>C,G,T0.23intron_variantFHL52e-27Tier 4: intronic/intergenic

ClinVar germline variants

17 retrieved; paginated sample, class counts are floors:

5 uncertain significance, 4 pathogenic, 3 conflicting classifications of pathogenicity, 3 pathogenic/likely pathogenic, 2 likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
195935NM_001127222.2(CACNA1A):c.4174G>A (p.Val1392Met)CACNA1APathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
17621NM_000070.3(CAPN3):c.550del (p.Thr184fs)CAPN3Pathogenicreviewed by expert panel
92408NM_000070.3(CAPN3):c.1746-20C>GCAPN3Pathogenicreviewed by expert panel
17542NM_000083.3(CLCN1):c.950G>A (p.Arg317Gln)CLCN1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
373443NM_001292034.3(TAB2):c.1039C>T (p.Arg347Ter)LOC126859827Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
812745NM_000435.3(NOTCH3):c.634T>C (p.Cys212Arg)NOTCH3Pathogenicno assertion criteria provided
523355NM_001122764.3(PPOX):c.1353T>G (p.Tyr451Ter)PPOXPathogeniccriteria provided, single submitter
9733NC_012920.1(MT-ND1):m.3697G>AMT-ND1Likely pathogenicreviewed by expert panel
523370NM_000435.3(NOTCH3):c.1450T>G (p.Cys484Gly)NOTCH3Likely pathogeniccriteria provided, single submitter
44926NM_004415.4(DSP):c.5218G>A (p.Glu1740Lys)DSPConflicting classifications of pathogenicitycriteria provided, conflicting classifications
14149NM_002471.4(MYH6):c.3195G>C (p.Gln1065His)MYH6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
239175NM_002471.4(MYH6):c.4594C>T (p.Arg1532Cys)MYH6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
983126NM_138420.4(AHNAK2):c.6406_6408delinsGAC (p.Gln2136Asp)AHNAK2Uncertain significancecriteria provided, single submitter
523536NM_030662.4(MAP2K2):c.514A>G (p.Lys172Glu)MAP2K2Uncertain significancecriteria provided, multiple submitters, no conflicts
9387NM_000335.5(SCN5A):c.892G>A (p.Gly298Ser)SCN5AUncertain significancecriteria provided, multiple submitters, no conflicts
374095NM_006516.4(SLC2A1):c.1407G>C (p.Gln469His)SLC2A1Uncertain significancecriteria provided, multiple submitters, no conflicts
523431NM_001382567.1(STIM1):c.1627T>A (p.Ser543Thr)STIM1Uncertain significancecriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 93 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SCN5AOrphanet:101016Romano-Ward syndrome
SCN5AOrphanet:130Brugada syndrome
SCN5AOrphanet:1344Isolated atrial standstill
SCN5AOrphanet:154Familial isolated dilated cardiomyopathy
SCN5AOrphanet:166282Hereditary sick sinus syndrome
SCN5AOrphanet:228140Idiopathic ventricular fibrillation
SCN5AOrphanet:334Hereditary atrial fibrillation
SCN5AOrphanet:871Hereditary progressive cardiac conduction defect
SLC2A1Orphanet:168577Hereditary cryohydrocytosis with reduced stomatin
SLC2A1Orphanet:1942Epilepsy with myoclonic-atonic seizures
SLC2A1Orphanet:2131Alternating hemiplegia of childhood
SLC2A1Orphanet:53583Paroxysmal dystonic choreathetosis with episodic ataxia and spasticity
SLC2A1Orphanet:71277Classic glucose transporter type 1 deficiency syndrome
SLC2A1Orphanet:86911Epilepsy with myoclonic absences
SLC2A1Orphanet:98811Paroxysmal exertion-induced dyskinesia
SPINK2Orphanet:399805Male infertility with azoospermia or oligozoospermia due to single gene mutation
STAT6Orphanet:2126Solitary fibrous tumor
STIM1Orphanet:2593Tubular aggregate myopathy
STIM1Orphanet:317430Combined immunodeficiency due to STIM1 deficiency
STIM1Orphanet:3204Stormorken-Sjaastad-Langslet syndrome
TGFBR2Orphanet:144Lynch syndrome
TGFBR2Orphanet:284973Marfan syndrome type 2
TGFBR2Orphanet:60030Loeys-Dietz syndrome
TGFBR2Orphanet:91387Familial thoracic aortic aneurysm and aortic dissection
TGFBR2Orphanet:99977Squamous cell carcinoma of the esophagus
TSC1Orphanet:210159Adult hepatocellular carcinoma
TSC1Orphanet:269008Isolated focal cortical dysplasia type IIb
TSC1Orphanet:538Lymphangioleiomyomatosis
TSC1Orphanet:805Tuberous sclerosis complex
USP9XOrphanet:480880X-linked female restricted facial dysmorphism-short stature-choanal atresia-intellectual disability
USP9XOrphanet:777X-linked non-syndromic intellectual disability
CACNA1AOrphanet:2131Alternating hemiplegia of childhood
CACNA1AOrphanet:2382Lennox-Gastaut syndrome
CACNA1AOrphanet:442835Non-specific early-onset epileptic encephalopathy
CACNA1AOrphanet:569Familial or sporadic hemiplegic migraine
CACNA1AOrphanet:71518Benign paroxysmal torticollis of infancy
CACNA1AOrphanet:97Familial paroxysmal ataxia
CACNA1AOrphanet:98758Spinocerebellar ataxia type 6
PRDM16Orphanet:154Familial isolated dilated cardiomyopathy
PRDM16Orphanet:16061p36 deletion syndrome
PRDM16Orphanet:54260Left ventricular noncompaction
JPH3Orphanet:98934Huntington disease-like 2
NLRP1Orphanet:352662Corneal intraepithelial dyskeratosis-palmoplantar hyperkeratosis-laryngeal dyskeratosis syndrome
RNF213Orphanet:2573Moyamoya disease
CAPN3Orphanet:267Calpain-3-related limb-girdle muscular dystrophy R1
CAPN3Orphanet:565909Calpain-3-related limb-girdle muscular dystrophy D4
SUGCTOrphanet:35706Glutaric acidemia type 3
YAP1Orphanet:1473Uveal coloboma-cleft lip and palate-intellectual disability
YAP1Orphanet:157791Epithelioid hemangioendothelioma
CTR9Orphanet:528084Non-specific syndromic intellectual disability

Cohort genes → proteins

75 cohort genes, 75 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only66
multi_evidence9

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SCN5AHGNC:10593ENSG00000183873Q14524Sodium channel protein type 5 subunit alphaclinvar
SLC24A3HGNC:10977ENSG00000185052Q9HC58Sodium/potassium/calcium exchanger 3gwas
SLC2A1HGNC:11005ENSG00000117394P11166Solute carrier family 2, facilitated glucose transporter member 1clinvar
SPINK2HGNC:11245ENSG00000128040P20155Serine protease inhibitor Kazal-type 2gwas
STAT6HGNC:11368ENSG00000166888P42226Signal transducer and activator of transcription 6gwas
STIM1HGNC:11386ENSG00000167323Q13586Stromal interaction molecule 1clinvar
TGFBR2HGNC:11773ENSG00000163513P37173TGF-beta receptor type-2gwas
MPPED2HGNC:1180ENSG00000066382Q15777Metallophosphoesterase MPPED2gwas
TSC1HGNC:12362ENSG00000165699Q92574Hamartingwas
USP9XHGNC:12632ENSG00000124486Q93008Ubiquitin carboxyl-terminal hydrolase 9Xgwas
CACNA1AHGNC:1388ENSG00000141837O00555Voltage-dependent P/Q-type calcium channel subunit alpha-1Aclinvar
PRDM16HGNC:14000ENSG00000142611Q9HAZ2Histone-lysine N-methyltransferase PRDM16gwas
JPH3HGNC:14203ENSG00000154118Q8WXH2Junctophilin-3gwas
NLRP1HGNC:14374ENSG00000091592Q9C000NACHT, LRR and PYD domains-containing protein 1gwas
CARFHGNC:14435ENSG00000138380Q8N187Calcium-responsive transcription factorgwas
RNF213HGNC:14539ENSG00000173821Q63HN8E3 ubiquitin-protein ligase RNF213gwas
IMMP2LHGNC:14598ENSG00000184903Q96T52Mitochondrial inner membrane protease subunit 2gwas
CAPN3HGNC:1480ENSG00000092529P20807Calpain-3clinvar
SUGCTHGNC:16001ENSG00000175600Q9HAC7Succinyl-CoA:glutarate CoA-transferasegwas
CCM2LHGNC:16153ENSG00000101331Q9NUG4Cerebral cavernous malformations 2 protein-likegwas
YAP1HGNC:16262ENSG00000137693P46937Transcriptional coactivator YAP1gwas
MOAP1HGNC:16658ENSG00000165943Q96BY2Modulator of apoptosis 1gwas
CTR9HGNC:16850ENSG00000198730Q6PD62RNA polymerase-associated protein CTR9 homologgwas
CPQHGNC:16910ENSG00000104324Q9Y646Carboxypeptidase Qgwas
ASTN2HGNC:17021ENSG00000148219O75129Astrotactin-2gwas
PLCE1HGNC:17175ENSG00000138193Q9P2121-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1gwas
FHL5HGNC:17371ENSG00000112214Q5TD97Four and a half LIM domains protein 5gwas
MSL3BHGNC:17837ENSG00000224287P0C860MSL complex subunit 3Bgwas
TRPM8HGNC:17961ENSG00000144481Q7Z2W7Transient receptor potential cation channel subfamily M member 8gwas
HPSE2HGNC:18374ENSG00000172987Q8WWQ2Inactive heparanase-2gwas
NAXEHGNC:18453ENSG00000163382Q8NCW5NAD(P)H-hydrate epimerasegwas
CFDP1HGNC:1873ENSG00000153774Q9UEE9Heterochromatin-stabilizing protein CFDP1gwas
DOCK4HGNC:19192ENSG00000128512Q8N1I0Dedicator of cytokinesis protein 4gwas
ADAMTSL4HGNC:19706ENSG00000143382Q6UY14ADAMTS-like protein 4gwas
AHNAK2HGNC:20125ENSG00000185567Q8IVF2Protein AHNAK2clinvar
CLCN1HGNC:2019ENSG00000188037P35523Chloride channel protein 1clinvar
TSPAN2HGNC:20659ENSG00000134198O60636Tetraspanin-2gwas
PHACTR1HGNC:20990ENSG00000112137Q9C0D0Phosphatase and actin regulator 1gwas
TBC1D7HGNC:21066ENSG00000145979Q9P0N9TBC1 domain family member 7gwas
NCOA7HGNC:21081ENSG00000111912Q8NI08Nuclear receptor coactivator 7gwas
LINGO2HGNC:21207ENSG00000174482Q7L985Leucine-rich repeat and immunoglobulin-like domain-containing nogo receptor-interacting protein 2gwas
UFL1HGNC:23039ENSG00000014123O94874E3 UFM1-protein ligase 1gwas
GPR149HGNC:23627ENSG00000174948Q86SP6Probable G-protein coupled receptor 149gwas
MED14HGNC:2370ENSG00000180182O60244Mediator of RNA polymerase II transcription subunit 14gwas
ZCCHC14HGNC:24134ENSG00000140948Q8WYQ9Zinc finger CCHC domain-containing protein 14gwas
CDKN2AIPHGNC:24325ENSG00000168564Q9NXV6CDKN2A-interacting proteingwas
HJURPHGNC:25444ENSG00000123485Q8NCD3Holliday junction recognition proteingwas
AGBL1HGNC:26504ENSG00000273540Q96MI9Cytosolic carboxypeptidase 4gwas
LRRIQ3HGNC:28318ENSG00000162620A6PVS8Leucine-rich repeat and IQ domain-containing protein 3gwas
WSCD1HGNC:29060ENSG00000179314Q658N2Sialate:O-sulfotransferase 1gwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SCN5ASodium channel protein type 5 subunit alphaPore-forming subunit of Nav1.5, a voltage-gated sodium (Nav) channel that directly mediates the depolarizing phase of action potentials in excitable membranes.
SLC24A3Sodium/potassium/calcium exchanger 3Calcium, potassium:sodium antiporter that transports 1 Ca(2+) and 1 K(+) in exchange for 4 Na(+).
SLC2A1Solute carrier family 2, facilitated glucose transporter member 1Facilitative glucose transporter, which is responsible for constitutive or basal glucose uptake.
SPINK2Serine protease inhibitor Kazal-type 2As a strong inhibitor of acrosin, it is required for normal spermiogenesis.
STAT6Signal transducer and activator of transcription 6Carries out a dual function: signal transduction and activation of transcription.
STIM1Stromal interaction molecule 1Acts as a Ca(2+) sensor that gates two major inward rectifying Ca(2+) channels at the plasma membrane: Ca(2+) release-activated Ca(2+) (CRAC) channels and arachidonate-regulated Ca(2+)-selective (ARC) channels.
TGFBR2TGF-beta receptor type-2Transmembrane serine/threonine kinase forming with the TGF-beta type I serine/threonine kinase receptor, TGFBR1, the non-promiscuous receptor for the TGF-beta cytokines TGFB1, TGFB2 and TGFB3.
MPPED2Metallophosphoesterase MPPED2Displays low metallophosphoesterase activity (in vitro).
TSC1HamartinNon-catalytic component of the TSC-TBC complex, a multiprotein complex that acts as a negative regulator of the canonical mTORC1 complex, an evolutionarily conserved central nutrient sensor that stimulates anabolic reactions and macromolec…
USP9XUbiquitin carboxyl-terminal hydrolase 9XDeubiquitinase involved both in the processing of ubiquitin precursors and of ubiquitinated proteins.
CACNA1AVoltage-dependent P/Q-type calcium channel subunit alpha-1AVoltage-sensitive calcium channels (VSCC) mediate the entry of calcium ions into excitable cells and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene exp…
PRDM16Histone-lysine N-methyltransferase PRDM16Transcription regulator that acts both as a histone methyltransferase or chromatin adapter, depending on the context.
JPH3Junctophilin-3Junctophilins contribute to the formation of junctional membrane complexes (JMCs) which link the plasma membrane with the endoplasmic or sarcoplasmic reticulum in excitable cells.
NLRP1NACHT, LRR and PYD domains-containing protein 1Acts as the sensor component of the NLRP1 inflammasome, which mediates inflammasome activation in response to various pathogen-associated signals, leading to subsequent pyroptosis.
CARFCalcium-responsive transcription factorActs as a transcriptional activator that mediates the calcium- and neuron-selective induction of BDNF exon III transcription.
RNF213E3 ubiquitin-protein ligase RNF213Atypical E3 ubiquitin ligase that can catalyze ubiquitination of both proteins and lipids, and which is involved in various processes, such as lipid metabolism, angiogenesis and cell-autonomous immunity.
IMMP2LMitochondrial inner membrane protease subunit 2Catalyzes the removal of transit peptides required for the targeting of proteins from the mitochondrial matrix, across the inner membrane, into the inter-membrane space.
CAPN3Calpain-3Calcium-regulated non-lysosomal thiol-protease.
SUGCTSuccinyl-CoA:glutarate CoA-transferaseCoenzyme A (CoA) transferase that reversibly catalyzes the transfer of a CoA moiety from a dicarboxyl-CoA to a dicarboxylate in a metabolite recycling process.
YAP1Transcriptional coactivator YAP1Transcriptional regulator with dual roles as a coactivator and corepressor.
MOAP1Modulator of apoptosis 1Retrotransposon-derived protein that forms virion-like capsids.
CTR9RNA polymerase-associated protein CTR9 homologComponent of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency.
CPQCarboxypeptidase QCarboxypeptidase that may play an important role in the hydrolysis of circulating peptides.
ASTN2Astrotactin-2Mediates recycling of the neuronal cell adhesion molecule ASTN1 to the anterior pole of the cell membrane in migrating neurons.
PLCE11-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes.
FHL5Four and a half LIM domains protein 5May be involved in the regulation of spermatogenesis.
MSL3BMSL complex subunit 3BProbable non-catalytic component of the MSL histone acetyltransferase complex, a multiprotein complex that mediates the majority of histone H4 acetylation at ‘Lys-16’ (H4K16ac), an epigenetic mark that prevents chromatin compaction.
TRPM8Transient receptor potential cation channel subfamily M member 8Non-selective ion channel permeable to monovalent and divalent cations, including Na(+), K(+), and Ca(2+), with higher permeability for Ca(2+).
HPSE2Inactive heparanase-2Binds heparin and heparan sulfate with high affinity, but lacks heparanase activity.
NAXENAD(P)H-hydrate epimeraseCatalyzes the epimerization of the S- and R-forms of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration.
CFDP1Heterochromatin-stabilizing protein CFDP1Required for the structural stability of pericentromeric heterochromatin.
DOCK4Dedicator of cytokinesis protein 4Functions as a guanine nucleotide exchange factor (GEF) that promotes the exchange of GDP to GTP, converting inactive GDP-bound small GTPases into their active GTP-bound form.
ADAMTSL4ADAMTS-like protein 4Positive regulation of apoptosis.
CLCN1Chloride channel protein 1Voltage-gated chloride channel involved in skeletal muscle excitability.
TSPAN2Tetraspanin-2May play a role in signalling in oligodendrocytes in the early stages of their terminal differentiation into myelin-forming glia and may also function in stabilizing the mature sheath.
PHACTR1Phosphatase and actin regulator 1Binds actin monomers (G actin) and plays a role in multiple processes including the regulation of actin cytoskeleton dynamics, actin stress fibers formation, cell motility and survival, formation of tubules by endothelial cells, and regula…
TBC1D7TBC1 domain family member 7Non-catalytic component of the TSC-TBC complex, a multiprotein complex that acts as a negative regulator of the canonical mTORC1 complex, an evolutionarily conserved central nutrient sensor that stimulates anabolic reactions and macromolec…
NCOA7Nuclear receptor coactivator 7Enhances the transcriptional activities of several nuclear receptors.
UFL1E3 UFM1-protein ligase 1E3 protein ligase that mediates ufmylation, the covalent attachment of the ubiquitin-like modifier UFM1 to lysine residues on target proteins, and which plays a key role in various processes, such as ribosome recycling, response to DNA dam…
GPR149Probable G-protein coupled receptor 149Orphan receptor.
MED14Mediator of RNA polymerase II transcription subunit 14Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes.
CDKN2AIPCDKN2A-interacting proteinRegulates DNA damage response in a dose-dependent manner through a number of signaling pathways involved in cell proliferation, apoptosis and senescence.
HJURPHolliday junction recognition proteinCentromeric protein that plays a central role in the incorporation and maintenance of histone H3-like variant CENPA at centromeres.
AGBL1Cytosolic carboxypeptidase 4Metallocarboxypeptidase that mediates deglutamylation of tubulin and non-tubulin target proteins.
WSCD1Sialate:O-sulfotransferase 1Sialate:O-sulfotransferase which catalyzes 8-O-sulfation at the Sia-glycan level using 3’-phosphoadenosine 5’-phosphosulfate (PAPS) as a donor, forming 8-O-sulfated Sia (Sia8S)-glycans.
MARCHF4E3 ubiquitin-protein ligase MARCHF4E3 ubiquitin-protein ligase that may mediate ubiquitination of MHC-I and CD4, and promote their subsequent endocytosis and sorting to lysosomes via multivesicular bodies.
MTDHProtein LYRICDown-regulates SLC1A2/EAAT2 promoter activity when expressed ectopically.
SDR9C7Short-chain dehydrogenase/reductase family 9C member 7Plays a crucial role in the formation of the epidermal permeability barrier.
DSPDesmoplakinA component of desmosome cell-cell junctions which are required for positive regulation of cellular adhesion.
AJAP1Adherens junction-associated protein 1Plays a role in cell adhesion and cell migration.

Protein-family classification

Druggable: 25 · Difficult: 11 · Unknown: 39 · Druggable fraction: 0.33

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Ion channel46.0×0.051
Protease52.4×0.298
Complement13.6×0.786
Kinase41.5×0.786
Antibody/Immunoglobulin31.2×0.876
Transporter11.0×0.876
Enzyme (other)61.0×0.876
Scaffold/PPI40.9×0.876
Other/Unknown390.9×0.901
Transcription factor70.8×0.901
GPCR10.3×0.960

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SCN5AIon channelyesNa_channel_asu, Ion_trans_dom, Na_channel_a5su
SLC24A3Other/UnknownnoK/Na/Ca-exchanger, NaCa_Exmemb, NCX_ion-bd_dom_sf
SLC2A1TransporteryesGlu_transpt_1, Sugar/inositol_transpt, MFS_sugar_transport-like
SPINK2Other/UnknownnoKazal_dom, Kazal_dom_sf, SPINK2
STAT6Transcription factornoSH2, STAT, p53-like_TF_DNA-bd_sf
STIM1Other/UnknownnoSAM, SAM/pointed_sf, SOAR_STIM1/2
TGFBR2Kinaseyes2.7.10.2TGFB_receptor, Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom
MPPED2Other/UnknownnoCalcineurin-like_PHP, Calcineurin-like_Pesterase, Metallo-depent_PP-like
TSC1Other/UnknownnoHamartin
USP9XProteaseyesPeptidase_C19_UCH, ARM-type_fold, USP_CS
CACNA1AIon channelyesVDCCAlpha1, CACNA1A, Ion_trans_dom
PRDM16Transcription factorno2.1.1.367SET_dom, Znf_C2H2_type, Znf_C2H2_sf
JPH3Other/UnknownnoMORN, Junctophilin
NLRP1Other/UnknownnoCARD, Leu-rich_rpt, DAPIN
CARFOther/UnknownnoCaRF
RNF213Transcription factornoZnf_RING, AAA+_ATPase, Znf_RING/FYVE/PHD
IMMP2LProteaseyesPept_S26A_signal_pept_1, Peptidase_S26, Pept_S26A_signal_pept_1_CS
CAPN3Proteaseyes3.4.22.54Pept_cys_AS, Peptidase_C2_calpain_cat, EF_hand_dom
SUGCTEnzyme (other)yes2.8.3.13CoA-Trfase_fam_III, CoA-Trfase_III_dom_1_sf, CoA-Trfase_III_dom3_sf
CCM2LOther/UnknownnoPH-like_dom_sf, Malcavernin, CCM2_C
YAP1Scaffold/PPInoWW_dom, WW_dom_sf, YAP1
MOAP1Other/UnknownnoPNMA, PNMA_C, PNMA_N
CTR9Other/UnknownnoTPR-like_helical_dom_sf, TPR_rpt, Ctr9
CPQProteaseyesPeptidase_M28, CPQ
ASTN2ComplementyesMACPF, Astrotactin, FN3_sf
PLCE1Enzyme (other)yes3.1.4.11C2_dom, RA_dom, PLipase_C_PInositol-sp_X_dom
FHL5Transcription factornoZnf_LIM, FHL5_LIM2, LIM_FHL1/2/3/5_N
MSL3BOther/UnknownnoMRG, MRG_dom, MRG_C_sf
TRPM8Ion channelyesIon_trans_dom, TRPM_SLOG, TRPM
HPSE2Other/UnknownnoGlyco_hydro_79, GH_hydrolase_sf
NAXEEnzyme (other)yes5.1.99.6YjeF_N_dom, YJEFN_prot_NAXE-like, YjeF_N_dom_sf
CFDP1Other/UnknownnoBCNT-C, Swc5/CFDP1/2
DOCK4Scaffold/PPInoSH3_domain, DOCK, C2_DOCK-type_domain
ADAMTSL4Other/UnknownnoTSP1_rpt, ADAMTS_spacer1, PLAC
AHNAK2Scaffold/PPInoPDZ, PDZ_sf, Myelin_sheath_structural
CLCN1Other/UnknownnoClC, Cl_channel-1, Cl-channel_core
TSPAN2Other/UnknownnoTetraspanin_animals, Tetraspanin_EC2_sf, Tetraspanin/Peripherin
PHACTR1Other/UnknownnoRPEL_repeat
TBC1D7Other/UnknownnoRab-GAP-TBC_dom, Rab-GAP_TBC_sf, TBC1D7
NCOA7Other/UnknownnoTLDc_dom, LysM, LysM_dom_sf
LINGO2Antibody/ImmunoglobulinyesLRRNT, Leu-rich_rpt, Leu-rich_rpt_typical-subtyp
UFL1Other/UnknownnoUfl1, Ufl1_N, Ufl1_dom
GPR149GPCRyesGPCR_Rhodpsn_7TM
MED14Other/UnknownnoMediator_Med14, Med14_RM8, Med14_RM2
ZCCHC14Transcription factornoSAM, Znf_CCHC, SAM/pointed_sf
CDKN2AIPOther/UnknownnodsRBD_dom, XTBD, DSRM_CARF/NKRF
HJURPOther/UnknownnoScm3/HJURP, HJURP_central_dom, HJURP_C
AGBL1ProteaseyesPeptidase_M14, ARM-like, ARM-type_fold
LRRIQ3Other/UnknownnoLeu-rich_rpt, LRR_dom_sf, LRR-IQ_domain_protein
WSCD1Other/UnknownnoSulfotransferase_dom, WSC_carb-bd, P-loop_NTPase

Expression context

Cohort genes with no expression data: 0.

63 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)75
unknown0

Top tissues across cohort

TissueCohort genes
secondary oocyte8
cortical plate6
calcaneal tendon6
male germ line stem cell (sensu Vertebrata) in testis6
oocyte6
hindlimb stylopod muscle5
primordial germ cell in gonad5
ganglionic eminence4
ventricular zone4
apex of heart3
lateral nuclear group of thalamus3
saphenous vein3
sural nerve3
corpus epididymis3
granulocyte3
lateral globus pallidus3
popliteal artery3
upper leg skin3
hair follicle3
skin of abdomen2

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SCN5A161broadyesapex of heart, heart left ventricle, cardiac ventricle
SLC24A3272broadmarkerlateral nuclear group of thalamus, tongue squamous epithelium, saphenous vein
SLC2A1250ubiquitousmarkertibial nerve, sural nerve, skin of abdomen
SPINK2177broadmarkercorpus epididymis, cauda epididymis, seminal vesicle
STAT6292ubiquitousmarkergranulocyte, right ovary, left ovary
STIM1237ubiquitousmarkergastrocnemius, muscle of leg, hindlimb stylopod muscle
TGFBR2289ubiquitousmarkerpericardium, tibia, parietal pleura
MPPED2255broadmarkerventricular zone, ganglionic eminence, cortical plate
TSC1297ubiquitousmarkersubstantia nigra pars compacta, gluteal muscle, lateral globus pallidus
USP9X295ubiquitousmarkermiddle frontal gyrus, endometrium epithelium, secondary oocyte
CACNA1A237broadmarkercerebellar hemisphere, right hemisphere of cerebellum, cerebellar cortex
PRDM16202broadmarkersural nerve, pigmented layer of retina, ascending aorta
JPH3166broadyesright frontal lobe, postcentral gyrus, parietal lobe
NLRP1203ubiquitousmarkergranulocyte, monocyte, mononuclear cell
CARF215ubiquitousyescalcaneal tendon, male germ line stem cell (sensu Vertebrata) in testis, primordial germ cell in gonad
RNF213252ubiquitousmarkergranulocyte, metanephros cortex, pancreatic ductal cell
IMMP2L223ubiquitousmarkertibialis anterior, deltoid, calcaneal tendon
CAPN3134broadmarkerhindlimb stylopod muscle, skeletal muscle tissue, C1 segment of cervical spinal cord
SUGCT191ubiquitousmarkerright adrenal gland cortex, oocyte, right coronary artery
CCM2L207broadmarkerspleen, apex of heart, oocyte
YAP1279ubiquitousmarkersaphenous vein, germinal epithelium of ovary, cauda epididymis
MOAP1142ubiquitousmarkersuperior frontal gyrus, prefrontal cortex, frontal cortex
CTR9292ubiquitousmarkercorpus epididymis, epithelium of nasopharynx, palpebral conjunctiva
CPQ293ubiquitousmarkerleft lobe of thyroid gland, thyroid gland, right lobe of thyroid gland
ASTN2236ubiquitousmarkerbuccal mucosa cell, trigeminal ganglion, dorsal root ganglion
PLCE1271broadmarkerrenal glomerulus, metanephric glomerulus, ventricular zone
FHL5210tissue_specificmarkerpopliteal artery, tibial artery, right coronary artery
MSL3B130ubiquitousyesmale germ line stem cell (sensu Vertebrata) in testis, primordial germ cell in gonad, testis
TRPM8122tissue_specificmarkerright lobe of liver, liver, prostate gland
HPSE2153tissue_specificmarkercalcaneal tendon, lower esophagus muscularis layer, lower esophagus

Protein interactions among cohort

Intra-cohort edges: 26.

Hub genes (top 10 by interactor count)

SymbolInteractor count
YAP16,742
TGFBR25,777
SLC2A15,711
TSC15,445
MED145,271
GJA14,942
DOCK44,803
JAG14,405
CTR94,367
UFL13,840

Intra-cohort edges

ABSources
ADAMTSL4SPINK2biogrid_interaction, intact
AHNAK2CAPN3string_interaction
AHNAK2DOCK4intact
AJAP1MPPED2string_interaction
AJAP1TSPAN2string_interaction
ASTN2TRPM8string_interaction
ASTN2TSPAN2string_interaction
CCM2LZCCHC14string_interaction
CPQMTDHstring_interaction
DOCK4IMMP2Lstring_interaction
FHL5HEY2intact
FHL5SUGCTstring_interaction
FHL5UFL1string_interaction
FSHBMPPED2string_interaction
GJA1SCN5Astring_interaction
GPR149MPPED2string_interaction
HEY2JAG1string_interaction
IGSF9BYAP1intact
KCNK5SLC24A3string_interaction
LINGO2WSCD1string_interaction
MOAP1YAP1string_interaction
PHACTR1TRPM8string_interaction
PHACTR1TSPAN2string_interaction
SUGCTTSPAN2string_interaction
TBC1D7TSC1biogrid_interaction, intact, string_interaction
USP9XYAP1biogrid_interaction

Structural data

PDB: 43 · AlphaFold-only: 32 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
YAP1P4693741
HCKP0863140
FECHP2283025
TGFBR2P3717322
CTR9Q6PD6221
GJA1P1730219
SCN5AQ1452416
NLRP1Q9C00012
MED14O6024411
CLCN1P355239
UFL1O948749
FUT9Q9Y2318
STAT6P422267
JAG1P785047
LRP1Q079547
STIM1Q135866
TRPM8Q7Z2W76
PHACTR1Q9C0D06
TBC1D7Q9P0N96
FGF23Q9GZV96
FSHBP012256
SLC2A1P111665
TSC1Q925745
CAPN3P208075
GFRA2O004515
USP9XQ930084
CACNA1AO005554
RNF213Q63HN84
DSPP159244
ITPK1Q135724

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
MPPED2Q1577795.43
CPQQ9Y64693.81
SDR9C7Q8NEX993.41
INPP5AQ1464291.81
IMMP2LQ96T5287.66
TSPAN2O6063687.26
NAXEQ8NCW586.71
LINGO2Q7L98585.02
HPSE2Q8WWQ282.90
FGF6P1076779.20
AGBL1Q96MI978.53
WSCD1Q658N277.87
DOCK4Q8N1I076.47
INAQ1635275.42
SLC24A3Q9HC5870.31
LRRIQ3A6PVS870.18
KCNK5O9527969.94
ECM1Q1661069.05
MSL3BP0C86068.69
HEY2Q9UBP565.56
ADAMTSL4Q6UY1465.18
CFDP1Q9UEE964.86
CDKN2AIPQ9NXV663.54
IGSF9BQ9UPX062.71
MARCHF4Q9P2E862.42
JPH3Q8WXH261.52
CCM2LQ9NUG459.84
ARMS2P0C7Q258.14
CARFQ8N18756.59
GPR149Q86SP654.04

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 352. Enrichment computed across 92 evidence-associated genes (61 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 61 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Defective LFNG causes SCDO3274.9×0.073NOTCH3, NOTCH4
Pre-NOTCH Processing in the Endoplasmic Reticulum262.4×0.073NOTCH3, NOTCH4
NOTCH4 Activation and Transmission of Signal to the Nucleus234.0×0.090JAG1, NOTCH4
Frs2-mediated activation231.2×0.090MAP2K2, NGF
Signaling by activated point mutants of FGFR1231.2×0.090FGF23, FGF6
FGFR2c ligand binding and activation228.8×0.090FGF23, FGF6
FGFR4 ligand binding and activation226.7×0.090FGF23, FGF6
Heme biosynthesis225.0×0.090FECH, PPOX
FGFR1c ligand binding and activation225.0×0.090FGF23, FGF6
Phospholipase C-mediated cascade; FGFR4225.0×0.090FGF23, FGF6
Degradation of the extracellular matrix47.7×0.090CAPN3, MMP16, MMP17, HTRA1
Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1)1187.2×0.092SLC2A1
Activated point mutants of FGFR2222.0×0.092FGF23, FGF6
Phospholipase C-mediated cascade: FGFR1222.0×0.092FGF23, FGF6
Pre-NOTCH Processing in Golgi220.8×0.092NOTCH3, NOTCH4
Phospholipase C-mediated cascade; FGFR2220.8×0.092FGF23, FGF6
PI-3K cascade:FGFR4218.7×0.092FGF23, FGF6
NOTCH4 Intracellular Domain Regulates Transcription218.7×0.092HEY2, NOTCH4
Downstream signaling of activated FGFR1217.8×0.092FGF23, FGF6
SHC-mediated cascade:FGFR4217.8×0.092FGF23, FGF6
Signal transduction by L1217.0×0.092MAP2K2, NRP1
PI-3K cascade:FGFR1217.0×0.092FGF23, FGF6
SHC-mediated cascade:FGFR1216.3×0.092FGF23, FGF6
PI-3K cascade:FGFR2216.3×0.092FGF23, FGF6
FRS-mediated FGFR4 signaling216.3×0.092FGF23, FGF6
SHC-mediated cascade:FGFR2215.6×0.092FGF23, FGF6
NOTCH3 Activation and Transmission of Signal to the Nucleus215.6×0.092JAG1, NOTCH3
FRS-mediated FGFR1 signaling215.0×0.092FGF23, FGF6
RUNX2 regulates osteoblast differentiation215.0×0.092YAP1, HEY2
FRS-mediated FGFR2 signaling214.4×0.092FGF23, FGF6

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 86 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
mammary gland morphogenesis2195.9×0.023STAT6, TGFBR2
cardiac conduction system development336.7×0.030SCN5A, GJA1, HEY2
aorta morphogenesis330.9×0.035TGFBR2, JAG1, LRP1
tricuspid valve morphogenesis278.4×0.040TGFBR2, HEY2
negative regulation of endothelial cell differentiation278.4×0.040JAG1, NOTCH4
artery morphogenesis323.5×0.040TGFBR2, NOTCH3, NRP1
pulmonary artery morphogenesis265.3×0.042HEY2, JAG1
vasculogenesis411.9×0.042TGFBR2, YAP1, HEY2, NRP1
trachea formation256.0×0.046TGFBR2, MAP2K2
branching involved in blood vessel morphogenesis318.4×0.046TGFBR2, NOTCH4, NRP1
positive regulation of transcription by RNA polymerase II152.6×0.046STAT6, YAP1, CTR9, FHL5, NCOA7, MED14, FSHB, HEY2 (+7 more)
sprouting angiogenesis316.8×0.055RNF213, NAXE, NRP1
heme B biosynthetic process239.2×0.058FECH, PPOX
atrial cardiac muscle cell action potential239.2×0.058SCN5A, GJA1
epithelial cell development235.6×0.058ADAMTSL4, ONECUT2
cardiac left ventricle morphogenesis235.6×0.058TGFBR2, HEY2
heme A biosynthetic process235.6×0.058FECH, PPOX
self proteolysis235.6×0.058NLRP1, CAPN3
aortic valve morphogenesis315.1×0.058TGFBR2, HEY2, JAG1
cellular response to amyloid-beta313.7×0.058CACNA1A, GJA1, LRP1
positive regulation of angiogenesis56.7×0.058STIM1, TGFBR2, MTDH, ECM1, NRP1
positive regulation of tolerance induction to self antigen1195.9×0.060TGFBR2
positive regulation of B cell tolerance induction1195.9×0.060TGFBR2
innate immune response-activating signaling pathway1195.9×0.060HCK
regulation of type 2 immune response1195.9×0.060ECM1
visceral muscle development1195.9×0.060MYH6
detection of UV1195.9×0.060FECH
obsolete positive regulation of vitamin D 24-hydroxylase activity1195.9×0.060FGF23
regulation of polarized epithelial cell differentiation1195.9×0.060AJAP1
leukocyte degranulation1195.9×0.060HCK

Therapeutics

Drugs indicated for this disease

27 approved, 29 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
AcetaminophenApproved (phase 4)
AspirinApproved (phase 4)
AtogepantApproved (phase 4)
Botulinum Toxin Type AApproved (phase 4)
ButalbitalApproved (phase 4)
CaffeineApproved (phase 4)
CelecoxibApproved (phase 4)
ClonidineApproved (phase 4)
DiclofenacApproved (phase 4)
DihydroergotamineApproved (phase 4)
EletriptanApproved (phase 4)
EptinezumabApproved (phase 4)
ErenumabApproved (phase 4)
ErgotamineApproved (phase 4)
FremanezumabApproved (phase 4)
FrovatriptanApproved (phase 4)
GalcanezumabApproved (phase 4)
IbuprofenApproved (phase 4)
LasmiditanApproved (phase 4)
LisurideApproved (phase 4)
MethysergideApproved (phase 4)
NaratriptanApproved (phase 4)
RizatriptanApproved (phase 4)
SumatriptanApproved (phase 4)
TopiramateApproved (phase 4)
UbrogepantApproved (phase 4)
ZolmitriptanApproved (phase 4)
AmitriptylinePhase 3 (in late-stage trials)
BupivacainePhase 3 (in late-stage trials)
DexamethasonePhase 3 (in late-stage trials)
DiphenhydraminePhase 3 (in late-stage trials)
Ethinyl EstradiolPhase 3 (in late-stage trials)
FentanylPhase 3 (in late-stage trials)
KetoprofenPhase 3 (in late-stage trials)
KetorolacPhase 3 (in late-stage trials)
LacosamidePhase 3 (in late-stage trials)
LevonorgestrelPhase 3 (in late-stage trials)
LidocainePhase 3 (in late-stage trials)
MelatoninPhase 3 (in late-stage trials)
MeloxicamPhase 3 (in late-stage trials)
MemantinePhase 3 (in late-stage trials)
MetforminPhase 3 (in late-stage trials)
MetoclopramidePhase 3 (in late-stage trials)
NaproxenPhase 3 (in late-stage trials)
OnabotulinumtoxinaPhase 3 (in late-stage trials)
PalmidrolPhase 3 (in late-stage trials)
PregabalinPhase 3 (in late-stage trials)
ProchlorperazinePhase 3 (in late-stage trials)
PropranololPhase 3 (in late-stage trials)
RimegepantPhase 3 (in late-stage trials)
Sodium ChloridePhase 3 (in late-stage trials)
TelcagepantPhase 3 (in late-stage trials)
Valproic AcidPhase 3 (in late-stage trials)
Vitamin EPhase 3 (in late-stage trials)
ZavegepantPhase 3 (in late-stage trials)
ZonisamidePhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Almotriptan, Atorvastatin, Candesartan, Cannabidiol, Carbon Dioxide, Carisbamate, Corticotropin, Ergocalciferol, Eslicarbazepine Acetate, Estradiol, Fospropofol, Gabapentin Enacarbil, Lactose, Anhydrous, Lornoxicam, Loxapine, Methylprednisolone, Naltrexone, Niacin, Oxygen, Perampanel, Prabotulinumtoxin A, Propofol, Quinidine, Simvastatin, Timolol, Tricaprilin.

Drug target analysis

Approved (phase 4): 12 · Phase ≥3: 12 · Phased (≥1): 14 · Undrugged: 61

Druggability breadth: 43 of 92 evidence-associated genes (47%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
SCN5ABEPRIDIL
SLC2A1EMETINE
STAT6THIORIDAZINE HYDROCHLORIDE
STIM1TERIFLUNOMIDE
TGFBR2PONATINIB
CACNA1ANIMODIPINE
NLRP1PERHEXILINE MALEATE
TRPM8CLOTRIMAZOLE
FECHVEMURAFENIB
GJA1KANAMYCIN
HCKPONATINIB
MAP2K2VEMURAFENIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
SCN5A1084
HCK614
MAP2K2524
FECH344
TGFBR2224
TRPM8154
STAT6114
SLC2A174
STIM124
CACNA1A24

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
BEPRIDIL4SCN5A
CANDESARTAN CILEXETIL4SCN5A
TELMISARTAN4SCN5A
CARBAMAZEPINE4SCN5A
DIBUCAINE4SCN5A
IMIPRAMINE4SCN5A
DROPERIDOL4SCN5A
PONATINIB4HCK, SCN5A, TGFBR2
DULOXETINE4SCN5A
PALONOSETRON4SCN5A
VILANTEROL4SCN5A
MEXILETINE HYDROCHLORIDE4SCN5A
UNOPROSTONE ISOPROPYL4SCN5A
LURASIDONE4SCN5A
LETERMOVIR4SCN5A
SERTINDOLE4SCN5A
FEDRATINIB4HCK, MAP2K2, SCN5A, TGFBR2
QUINIDINE4SCN5A
DARUNAVIR4SCN5A
DARIFENACIN4SCN5A
BENZONATATE4SCN5A
TOLTERODINE4SCN5A
RANOLAZINE4SCN5A
PIMOZIDE4SCN5A
NIMODIPINE4CACNA1A, SCN5A
FELODIPINE4SCN5A
NICARDIPINE4SCN5A
AMLODIPINE4SCN5A
PHENYTOIN4SCN5A
PALIPERIDONE4SCN5A

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 12.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
MAP2K2615Binding:581, Functional:33, ADMET:1
SCN5A594Binding:380, Functional:98, ADMET:72, Toxicity:43, Unclassified:1
HCK431Binding:429, Functional:1, ADMET:1
TGFBR2188Binding:188
TRPM8160Binding:148, Functional:12
SLC2A1158Binding:130, ADMET:24, Functional:4
YAP1135Binding:135
STAT681Binding:77, Functional:4
USP9X41Binding:41
STIM135Binding:33, Functional:1, ADMET:1
CACNA1A19Binding:18, Functional:1
FECH9Binding:9
CTR98Binding:8
INPP5A6Binding:6
ITPK16Binding:6
GJA14Binding:4
KCNK54Binding:4
PRDM162Binding:2
NLRP12Functional:1, Binding:1
GPR1492Binding:2
MTDH2Binding:2
DSP2Binding:2
FGF232Binding:2
GFRA22Binding:2
RNF2131Binding:1
UFL11Binding:1
FUT91Binding:1
INA1Binding:1
JAG11Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
TGFBR22.7.10.2non-specific protein-tyrosine kinase
PRDM162.1.1.367, 2.1.1.370[histone H3]-lysine9 N-methyltransferase, [histone H3]-lysine4 N-dimethyltransferase
CAPN33.4.22.54, 3.4.22.56calpain-3, caspase-3
SUGCT2.8.3.13succinate-hydroxymethylglutarate CoA-transferase
PLCE13.1.4.11phosphoinositide phospholipase C
NAXE5.1.99.6NAD(P)H-hydrate epimerase
FECH4.99.1.1protoporphyrin ferrochelatase
FUT92.4.1.1524-galactosyl-N-acetylglucosaminide 3-alpha-L-fucosyltransferase
HCK2.7.10.2non-specific protein-tyrosine kinase
INPP5A3.1.3.56inositol-polyphosphate 5-phosphatase
ITPK12.7.1.134, 2.7.1.159inositol-tetrakisphosphate 1-kinase, inositol-1,3,4-trisphosphate 5/6-kinase
MAP2K22.7.12.2mitogen-activated protein kinase kinase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
SCN5A594
SLC2A1158
TGFBR2188
YAP1135
TRPM8160
HCK431
MAP2K2615

Pharmacogenomics

Cohort genes with a PharmGKB record: 74; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

30 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
BEPRIDIL4SCN5A
CANDESARTAN CILEXETIL4SCN5A
TELMISARTAN4SCN5A
CARBAMAZEPINE4SCN5A
DIBUCAINE4SCN5A
IMIPRAMINE4SCN5A
DROPERIDOL4SCN5A
PONATINIB4HCK, SCN5A, TGFBR2
DULOXETINE4SCN5A
PALONOSETRON4SCN5A
VILANTEROL4SCN5A
MEXILETINE HYDROCHLORIDE4SCN5A
UNOPROSTONE ISOPROPYL4SCN5A
LURASIDONE4SCN5A
LETERMOVIR4SCN5A
SERTINDOLE4SCN5A
FEDRATINIB4HCK, MAP2K2, SCN5A, TGFBR2
QUINIDINE4SCN5A
DARUNAVIR4SCN5A
DARIFENACIN4SCN5A
BENZONATATE4SCN5A
TOLTERODINE4SCN5A
RANOLAZINE4SCN5A
PIMOZIDE4SCN5A
NIMODIPINE4CACNA1A, SCN5A
FELODIPINE4SCN5A
NICARDIPINE4SCN5A
AMLODIPINE4SCN5A
PHENYTOIN4SCN5A
PALIPERIDONE4SCN5A

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)12SCN5A, SLC2A1, STAT6, STIM1, TGFBR2, CACNA1A, NLRP1, TRPM8, FECH, GJA1 (+2 more)
BPhased (≥1) drug, not yet approved2USP9X, CTR9
CDruggable family + PDB, no drug7CAPN3, SUGCT, ASTN2, PLCE1, FUT9, IGLL1, ITPK1
DDruggable family + AlphaFold only, no drug9IMMP2L, CPQ, NAXE, LINGO2, GPR149, AGBL1, IGSF9B, INPP5A, KCNK5
EDifficult family or no structure, no drug45SLC24A3, SPINK2, MPPED2, TSC1, PRDM16, JPH3, CARF, RNF213, CCM2L, YAP1 (+35 more)

Undrugged target profiles

61 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
YAP1135
SLC24A30
SPINK20
MPPED20
TSC10
PRDM162
JPH30
CARF0
RNF2131
IMMP2L0
CAPN30
SUGCT0
CCM2L0
MOAP10
CPQ0
ASTN20
PLCE10
FHL50
MSL3B0
HPSE20
NAXE0
CFDP10
DOCK40
ADAMTSL40
AHNAK20
CLCN10
TSPAN20
PHACTR10
TBC1D70
NCOA70

Clinical trials & evidence

Clinical trials

Clinical trials: 1,313.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified522
PHASE3203
PHASE4148
PHASE2112
PHASE182
PHASE2/PHASE318
PHASE1/PHASE28
EARLY_PHASE17

Top trials by phase / activity

NCTPhaseStatusTitle
NCT02670161PHASE4ENROLLING_BY_INVITATIONQuality Improvement and Practice Based Research in Neurology Using the EMR
NCT04748601PHASE4RECRUITINGQudexy XR for the Prevention of Migraine in Children 6 to 11 Years Old
NCT04925414PHASE4RECRUITINGMigraine and High Flow Oxygenotherapy at the Emergency Department (MiOx)
NCT06173661PHASE4ACTIVE_NOT_RECRUITINGFremanezumab Treatment of Migraine in Women With Menstrual Migraine Ages 18-45
NCT06401642PHASE4RECRUITINGEffectiveness and Tolerability of Zavegepant for Acute Migraine Treatment Among Those Using CGRP Targeting Preventive Medications
NCT06432127PHASE4NOT_YET_RECRUITINGRole of Ultrasound Guide Greater Occipital Nerve Block at Second Cervical Vertebra in Migraine Headache Prophylaxis
NCT06473597PHASE4RECRUITINGA Comparison of Nurtec ODT to Maxalt MLT-ODT in Adult ED Patients With Migraine Headache
NCT06485726PHASE4RECRUITINGValproate Versus Propranolol in Migraine
NCT06499116PHASE4NOT_YET_RECRUITINGComparison of the Effectiveness of First-line Preventive Treatment of Migraine in Primary Care
NCT06509503PHASE4RECRUITINGImpact of Combined Oral Contraceptive Pills on Migraine
NCT06701526PHASE4ACTIVE_NOT_RECRUITINGA Trial of Eptinezumab in Participants With Migraine and Insufficient Response to Anti-CGRP Medications
NCT06786650PHASE4ACTIVE_NOT_RECRUITINGComparision of the Analgesic Effects of Intravenous Ibuprofen and Tenoxicam in Acute Migraine Attack
NCT06972056PHASE4RECRUITINGComparative Effectiveness of Migraine Preventive Medications: The APT Comparison Study
NCT07022496PHASE4RECRUITINGAssessment of Oral Caffeine Intake in Changing the Severity of Acute Migraine Attack Using VAS Score Among Patients Attending Headache and Neurology Outpatients Clinic of Ainshams University Hospitals
NCT07093138PHASE4RECRUITINGEvaluation of Efficacy and Safety of Topical Cannabidiol (Canvert-M Produced by Alasht Pharmed co. Iran) in the Treatment of Migraine Attacks
NCT07100496PHASE4ACTIVE_NOT_RECRUITINGEvaluation of MIG-SPRAY Treatment on Migraine
NCT07301008PHASE4RECRUITINGRimegepant as Preemptive Treatment for Predictable Trigger-Induced Migraine in Adult Patients in the US
NCT07336056PHASE4ACTIVE_NOT_RECRUITINGNerivio Efficacy Under High-Frequency Use
NCT00174395PHASE4COMPLETEDA Trial to Study of the Effects of Eletriptan 40mg on Mild vs Moderate to Severe Pain Intensity of Migraine
NCT00208065PHASE4COMPLETEDEvaluation of Histamine, CGRP and VIP as Markers for Activation of Trigeminal and Parasympathetic Nerve Fibers
NCT00210496PHASE4COMPLETEDPotential Impact (Benefit) of Preventative Treatment With Topamax on the Effectiveness of Axert in the Acute Treatment of Migraine
NCT00210509PHASE4COMPLETEDA Study of the Effectiveness and Safety of Almotriptan Versus Placebo in the Treatment of Migraine Headache
NCT00212810PHASE4COMPLETEDEvaluation of the Effectiveness of Topiramate in Preventing the Transformation From Episodic Migraine to Chronic Daily Headache.
NCT00212823PHASE4COMPLETEDThe Effectiveness of Almotriptan Malate (AXERT®) 12.5 Milligrams When Taken at the Onset of Migraine Pain
NCT00216736PHASE4COMPLETEDOral Dexamethasone for Treatment of Migraine
NCT00259636PHASE4WITHDRAWNZonisamide for Fibromyalgia & Migraine
NCT00259649PHASE4COMPLETEDProspective Survey of Menstrual Migraine & Prevention With Eletriptan
NCT00297375PHASE4COMPLETEDA Study Comparing the Effectiveness and Safety of ULTRACET® (Tramadol HCl/Acetaminophen) Versus Placebo for the Treatment of Acute Pain From a Migraine Headache
NCT00335777PHASE4COMPLETEDA Research Study Examining Migranal and Skin Sensitivity in Subjects With Migraine
NCT00363506PHASE4UNKNOWNAmerican Migraine Prevention Study
NCT00364806PHASE4COMPLETEDProchlorperazine vs Metoclopramide
NCT00391755PHASE4TERMINATEDA Double-Blind Placebo-Controlled Trial of Rozerem in Migraine Headaches
NCT00397254PHASE4COMPLETEDTwo Rizatriptan Prescribing Portions for Treatment of Migraine
NCT00443352PHASE4COMPLETEDA Research Study Examining The Use Of Duloxetine In The Prevention Of Migraine Headache
NCT00449787PHASE4COMPLETEDComparing Naproxen to Sumatriptan for Emergency Headache Patients
NCT00632385PHASE4COMPLETEDEfficacy and Safety of Eletriptan for the Treatment of Migraine in Patients Not Satisfied With Rizatriptan Therapy
NCT00634985PHASE4COMPLETEDSafety and Efficacy of Eletriptan for the Treatment of Migraine in Subjects Unsuccessfully Treated With Nonsteroidal Anti-inflammatory Drugs
NCT00637286PHASE4COMPLETEDZAP, US. Zomig for Appropriate for Primary Care
NCT00753311PHASE4COMPLETEDRizatriptan in Acute Treatment of Migraine in Patients With Unilateral Trigeminal-autonomic Symptoms.
NCT00792636PHASE4COMPLETEDA Study to Determine the Effect of Sumatriptan and Naproxen Sodium Combination Tablet, Sumatriptan Tablet, and Naproxen Sodium Tablet on Blood Pressure When Treating Migraine Headaches That Occur During a 6-month Period

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
SUMATRIPTAN4129
TOPIRAMATE443
ERENUMAB434
RIZATRIPTAN431
PROPRANOLOL425
AMITRIPTYLINE424
FREMANEZUMAB420
GALCANEZUMAB420
RIMEGEPANT420
EPTINEZUMAB419
LASMIDITAN416
ELETRIPTAN415
NAPROXEN415
PROCHLORPERAZINE415
DIHYDROERGOTAMINE414
METOCLOPRAMIDE413
KETOROLAC412
ATOGEPANT411
VALPROIC ACID411
FROVATRIPTAN410
UBROGEPANT410
NARATRIPTAN48
ONABOTULINUMTOXINA48
ZAVEGEPANT48
ZOLMITRIPTAN48
KETOPROFEN46
BOTULINUM TOXIN TYPE A45
CAFFEINE45
ZONISAMIDE45
ACETAMINOPHEN44