Migraine with aura

disease
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Summary

Migraine with aura (MONDO:0005475) is a disease with 3 cohort genes (13 GWAS associations across 12 studies) and 84 clinical trials. Top therapeutic interventions include dihydroergotamine, sumatriptan, and amitriptyline.

At a glance

  • Cohort genes: 3
  • GWAS associations: 13
  • ClinVar variants: 7
  • Clinical trials: 84

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namemigraine with aura
Mondo IDMONDO:0005475
MeSHD020325
DOIDDOID:10024
ICD-10-CMG43.1
ICD-11525744634
NCITC117005
SNOMED CT4473006
UMLSC0154723
MedGen57822
Is cancer (heuristic)no

Data availability: 7 ClinVar variants · 13 GWAS associations (12 studies) · 1 HPO phenotype.

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 disordermigraine with aura

Related subtypes (1): migraine without aura

Subtypes (2): familial or sporadic hemiplegic migraine, migraine with brainstem aura

Genetics & variants

GWAS landscape

13 GWAS associations across 12 studies. Top hits map to 9 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs29838963e-26FHL5?
rs20526921e-24IRAG1?
rs37982931e-12FHL5?
rs111721132e-10LRP1?
rs776309417e-10CUX1?28.37
rs1467788551e-08CDH18?20.63
rs1124331201e-08IGKV3OR2-268 - LINC01943?
rs1176087152e-08NOL3?22.74
rs1505923099e-08ZNF511-PRAP1?21.72
rs13644024e-06CHRM2?1.19
rs20760548e-06BPIFCC1.12

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST011059Guo Y202059,674316,078A genome-wide cross-phenotype meta-analysis of the association of blood pressure with migraine.
GCST011060Guo Y202059,674316,078A genome-wide cross-phenotype meta-analysis of the association of blood pressure with migraine.
GCST011061Guo Y202059,674316,078A genome-wide cross-phenotype meta-analysis of the association of blood pressure with migraine.
GCST003722Gormley P20166,332144,883Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine.
GCST002080Anttila V20135,11874,239Genome-wide meta-analysis identifies new susceptibility loci for migraine.
GCST90477543Verma A20244,445441,492Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90477542Verma A20241,484118,840Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90481049Verma A20241,484118,840Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90477541Verma A202489558,139Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90651463Liu TY2025283220,421Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding0
Tier 2: splice/UTR0
Tier 3: regulatory0
Tier 4: intronic/intergenic11

MAF distribution

BucketVariants
common (>=0.05)7
low_freq (0.01-0.05)0
rare (<0.01)0
unknown4

Functional consequences

ConsequenceCount
intron_variant9
intergenic_variant2

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs2983896696581995G>A0.05intron_variantFHL53e-26Tier 4: intronic/intergenic
rs20526921110646094A>C,G0.05intron_variantIRAG11e-24Tier 4: intronic/intergenic
rs3798293696585494A>G0.05intron_variantFHL51e-12Tier 4: intronic/intergenic
rs111721131257133500T>C,G0.05intron_variantLRP12e-10Tier 4: intronic/intergenic
rs776309417102217020T>Cintron_variantCUX17e-10Tier 4: intronic/intergenic
rs146778855520412078C>Tintergenic_variantCDH181e-08Tier 4: intronic/intergenic
rs112433120287402135T>A,C0.05intergenic_variantIGKV3OR2-268 - LINC019431e-08Tier 4: intronic/intergenic
rs1176087151667172270C>G,Tintron_variantNOL32e-08Tier 4: intronic/intergenic
rs15059230910133346685G>Aintron_variantZNF511-PRAP19e-08Tier 4: intronic/intergenic
rs13644027136899616T>C0.09intron_variantCHRM24e-06Tier 4: intronic/intergenic
rs20760542232436887C>T0.26intron_variantBPIFC8e-06Tier 4: intronic/intergenic

ClinVar germline variants

7 retrieved; paginated sample, class counts are floors:

3 pathogenic, 2 uncertain significance, 2 likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
523300GRCh37/hg19 Xq28(chrX:153575976-153586768)FLNAPathogeniccriteria provided, single submitter
523301GRCh37/hg19 Xq28(chrX:153588672-153609996)FLNAPathogeniccriteria provided, single submitter
812745NM_000435.3(NOTCH3):c.634T>C (p.Cys212Arg)NOTCH3Pathogenicno assertion criteria provided
812743NM_000435.3(NOTCH3):c.1162T>C (p.Cys388Arg)NOTCH3Likely pathogenicno assertion criteria provided
812744NM_000435.3(NOTCH3):c.1136G>C (p.Cys379Ser)NOTCH3Likely pathogeniccriteria provided, single submitter
523553NM_080916.3(DGUOK):c.278G>A (p.Gly93Glu)DGUOKUncertain significancecriteria provided, single submitter
523554NM_080916.3(DGUOK):c.65C>T (p.Pro22Leu)DGUOKUncertain significancecriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 16 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
DGUOKOrphanet:279934Mitochondrial DNA depletion syndrome, hepatocerebral form due to DGUOK deficiency
DGUOKOrphanet:329314Adult-onset multiple mitochondrial DNA deletion syndrome due to DGUOK deficiency
FLNAOrphanet:1826Frontometaphyseal dysplasia
FLNAOrphanet:2301Congenital short bowel syndrome
FLNAOrphanet:2484Melnick-Needles syndrome
FLNAOrphanet:482606X-linked keloid scarring-reduced joint mobility-increased optic cup-to-disc ratio syndrome
FLNAOrphanet:555877FLNA-related X-linked myxomatous valvular dysplasia
FLNAOrphanet:75497X-linked Ehlers-Danlos syndrome
FLNAOrphanet:88630Terminal osseous dysplasia-pigmentary defects syndrome
FLNAOrphanet:90650Otopalatodigital syndrome type 1
FLNAOrphanet:90652Otopalatodigital syndrome type 2
FLNAOrphanet:98892Periventricular nodular heterotopia
FLNAOrphanet:99811Neuronal intestinal pseudoobstruction
NOTCH3Orphanet:136Cerebral autosomal dominant arteriopathy-subcortical infarcts-leukoencephalopathy
NOTCH3Orphanet:2591Infantile myofibromatosis
NOTCH3Orphanet:2789Lateral meningocele syndrome

Cohort genes → proteins

3 cohort genes, 3 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence3

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
DGUOKHGNC:2858ENSG00000114956Q16854Deoxyguanosine kinase, mitochondrialclinvar
FLNAHGNC:3754ENSG00000196924P21333Filamin-Aclinvar
NOTCH3HGNC:7883ENSG00000074181Q9UM47Neurogenic locus notch homolog protein 3clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
DGUOKDeoxyguanosine kinase, mitochondrialPhosphorylates deoxyguanosine and deoxyadenosine in the mitochondrial matrix, with the highest efficiency for deoxyguanosine.
FLNAFilamin-APromotes orthogonal branching of actin filaments and links actin filaments to membrane glycoproteins.
NOTCH3Neurogenic locus notch homolog protein 3Functions as a receptor for membrane-bound ligands Jagged1, Jagged2 and Delta1 to regulate cell-fate determination.

Protein-family classification

Druggable: 2 · Difficult: 1 · Unknown: 0 · Druggable fraction: 0.67

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
Antibody/Immunoglobulin19.7×0.157
Kinase19.2×0.157
Scaffold/PPI15.8×0.164

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
DGUOKKinaseyes2.7.1.113DCK/DGK, P-loop_NTPase, DNK_dom
FLNAAntibody/ImmunoglobulinyesFilamin/ABP280_rpt, Actinin_actin-bd_CS, CH_dom
NOTCH3Scaffold/PPInoEGF-type_Asp/Asn_hydroxyl_site, EGF, Notch_dom

Expression context

Cohort genes with no expression data: 0.

3 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)3
unknown0

Top tissues across cohort

TissueCohort genes
popliteal artery2
right coronary artery2
tibial artery2
adenohypophysis1
olfactory segment of nasal mucosa1
pituitary gland1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
DGUOK297ubiquitousmarkeradenohypophysis, olfactory segment of nasal mucosa, pituitary gland
FLNA285ubiquitousmarkerright coronary artery, popliteal artery, tibial artery
NOTCH3273ubiquitousmarkerpopliteal artery, tibial artery, right coronary artery

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
FLNA5,321
NOTCH34,403
DGUOK201

Structural data

PDB: 3 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
FLNAP2133326
NOTCH3Q9UM476
DGUOKQ168541

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 14. Enrichment computed across 3 evidence-associated genes (3 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 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Defective LFNG causes SCDO31761.3×0.008NOTCH3
Pre-NOTCH Processing in the Endoplasmic Reticulum1634.4×0.008NOTCH3
Noncanonical activation of NOTCH31475.8×0.008NOTCH3
OAS antiviral response1423.0×0.008FLNA
GP1b-IX-V activation signalling1317.2×0.008FLNA
Purine salvage1292.8×0.008DGUOK
Cell-extracellular matrix interactions1223.9×0.008FLNA
Pre-NOTCH Processing in Golgi1211.5×0.008NOTCH3
RHO GTPases activate PAKs1181.3×0.009FLNA
NOTCH3 Activation and Transmission of Signal to the Nucleus1158.6×0.009NOTCH3
NOTCH3 Intracellular Domain Regulates Transcription1146.4×0.009NOTCH3
Notch-HLH transcription pathway1135.9×0.009NOTCH3
Pre-NOTCH Transcription and Translation140.9×0.026NOTCH3
Platelet degranulation129.3×0.034FLNA

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
guanosine metabolic process15617.3×0.002DGUOK
dGTP metabolic process15617.3×0.002DGUOK
purine deoxyribonucleoside metabolic process15617.3×0.002DGUOK
regulation of membrane repolarization during atrial cardiac muscle cell action potential15617.3×0.002FLNA
regulation of membrane repolarization during cardiac muscle cell action potential15617.3×0.002FLNA
glomerular capillary formation11872.4×0.004NOTCH3
tubulin deacetylation11872.4×0.004FLNA
dAMP salvage11872.4×0.004DGUOK
formation of radial glial scaffolds11404.3×0.004FLNA
adenylate cyclase-inhibiting dopamine receptor signaling pathway11123.5×0.005FLNA
establishment of Sertoli cell barrier11123.5×0.005FLNA
protein localization to bicellular tight junction1936.2×0.005FLNA
negative regulation of transcription by RNA polymerase I1802.5×0.005FLNA
blood coagulation, intrinsic pathway1702.2×0.005FLNA
neuroblast differentiation1702.2×0.005NOTCH3
mitochondrial ATP synthesis coupled electron transport1624.1×0.006DGUOK
positive regulation of platelet activation1432.1×0.007FLNA
positive regulation of integrin-mediated signaling pathway1432.1×0.007FLNA
positive regulation of actin filament bundle assembly1401.2×0.007FLNA
actin crosslink formation1401.2×0.007FLNA
wound healing, spreading of cells1374.5×0.007FLNA
positive regulation of potassium ion transmembrane transport1330.4×0.007FLNA
positive regulation of neuron migration1330.4×0.007FLNA
neuron fate commitment1267.5×0.009NOTCH3
positive regulation of neural precursor cell proliferation1255.3×0.009FLNA
obsolete negative regulation of DNA-binding transcription factor activity1244.2×0.009FLNA
megakaryocyte development1234.1×0.009FLNA
artery morphogenesis1224.7×0.009NOTCH3
receptor clustering1208.1×0.009FLNA
protein localization to cell surface1165.2×0.011FLNA

Therapeutics

Drugs indicated or in trials for this disease

No drug has an approved disease-direct ChEMBL indication for this disease.

12 drugs in clinical trials for this disease (phase 2–3, investigational): efficacy not established — a trial record, not an indication.

DrugHighest phase
Anisodine HydrobromidePhase 3
CaffeinePhase 3
DihydroergotaminePhase 3
EletriptanPhase 3
PromethazinePhase 3
RizatriptanPhase 3
SumatriptanPhase 3
AmiloridePhase 2
CandesartanPhase 2
DronabinolPhase 2
PropranololPhase 2
RamelteonPhase 2

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 2 · Undrugged: 1

Druggability breadth: 3 of 3 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
FLNA12
NOTCH312
DGUOK00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
MOLIBRESIB2FLNA
VAREGACESTAT2NOTCH3

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
FLNA7Binding:7
NOTCH33Binding:3
DGUOK1Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
DGUOK2.7.1.113deoxyguanosine kinase

Pharmacogenomics

Cohort genes with a PharmGKB record: 3; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

2 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)
MOLIBRESIB2FLNA
VAREGACESTAT2NOTCH3

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved2FLNA, NOTCH3
CDruggable family + PDB, no drug1DGUOK
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug0

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
DGUOK1

Clinical trials & evidence

Clinical trials

Clinical trials: 84.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified52
PHASE311
PHASE211
PHASE45
EARLY_PHASE12
PHASE12
PHASE2/PHASE31

Top trials by phase / activity

NCTPhaseStatusTitle
NCT01319825PHASE4UNKNOWNPreventive Treatment of Episodic and Chronic Migraine
NCT01596166PHASE4COMPLETEDIntravenous Ketorolac and Metoclopramide for Pediatric Migraine in the Emergency Department
NCT05211154PHASE4TERMINATEDEvaluation of the Efficacy of Diclofenac Potassium and Rimegepant for the Acute Treatment of Migraine
NCT05214001PHASE4TERMINATEDEvaluation of the Efficacy of Almotriptan and Ubrogepant for the Acute Treatment of Migraine
NCT06244823PHASE4UNKNOWNThe FreMRI Study: Advanced MRI on Migraine Patients Treated With Fremanezumab
NCT05484349PHASE3RECRUITINGTIzanidine for the Preventive Treatment of Episodic MigrainE (TIME)
NCT00334178PHASE3COMPLETEDEvaluation of the Efficacy and Safety of Laxymig® as Prophylactic Treatment in Patients With Migraine
NCT00449540PHASE3COMPLETEDEfficacy and Safety of TMS for the Preemptive Treatment of Migraine With Aura
NCT00471952PHASE3COMPLETEDMaxalt 10mg Plus Caffeine 75mg in the Acute Treatment of Migraine Headache
NCT00884663PHASE2/PHASE3COMPLETEDCandesartan Versus Propranolol for Migraine Prevention
NCT01814189PHASE3COMPLETEDEfficacy and Safety of Oral Sumatriptan Plus Oral Promethazine in Migraine Treatment
NCT01859481PHASE3COMPLETEDEletriptan Provides Consistent Migraine Relief: Results Of A Within-Patient Multiple-Dose Study
NCT03901482PHASE3COMPLETEDA Randomized, Double-Blind, Placebo-Controlled Study to Evaluate STS101 in the Acute Treatment of Migraine
NCT04406649PHASE3COMPLETEDA Study to Evaluate the Safety of STS101 in the Acute Treatment of Migraine
NCT04726592PHASE3TERMINATEDEfficacy of CLORazepate for the Treatment of MIGraine Attack in the Emergency Room
NCT04940390PHASE3COMPLETEDA Randomized, Double-Blind, Parallel Group, Placebo-Controlled Study to Assess STS101 in the Acute Treatment of Migraine
NCT05416476PHASE3UNKNOWNAnisodine Hydrobromide For The Preventive Treatment Of Episodic Migraine
NCT04063540PHASE2RECRUITINGAcid-Sensing Ion Channel and Migraine Disease Proof of Concept Study on the Efficacy of Amiloride in the Prophylaxis of Migraine Aura
NCT00123201PHASE2COMPLETEDStudy to Evaluate the Efficacy and Safety of Dronabinol Metered Dose Inhaler (MDI) in Acute Treatment of Migraine Headache
NCT00285402PHASE2UNKNOWNEfficacy and Safety Clinical Trial of Intranasal AST-726 for the Prevention of Migraine
NCT00311662PHASE2COMPLETEDEfficacy and Tolerability of Tonabersat in the Prophylaxis of Migraine Headache
NCT00332007PHASE2COMPLETEDTonabersat in the Prophylaxis of Migraine With Aura
NCT00505570PHASE2TERMINATEDPRIMA PFO Migraine Trial
NCT00534560PHASE2COMPLETEDDose Ranging Study of the Efficacy and Tolerability of Tonabersat in the Prophylaxis of Migraine Headache
NCT00739024PHASE2TERMINATEDA Study of a Melatonin Receptor Agonist to Prevent Migraine
NCT00877838PHASE2UNKNOWNStudy of the Safety and Effectiveness of NXN-188 for the Acute Treatment of Migraine Attacks With Aura
NCT00920686PHASE2COMPLETEDStudy of NXN 188 for the Treatment of Migraine With Aura
NCT03472378PHASE2COMPLETEDCan DFN-15 Terminate Migraine With Allodynia?
NCT03874832PHASE1COMPLETEDA Phase I Study to Study the PK and Safety of Single Doses of STS101, DHE Injection and Nasal Spray in Healthy Subjects
NCT05337254PHASE1COMPLETEDA Study of the PK and Safety of Single Doses of STS101, DHE Injection and Nasal Spray in Healthy Subjects
NCT02253004EARLY_PHASE1COMPLETEDInduction of Migraine Aura With Cilostazol
NCT02795351EARLY_PHASE1COMPLETEDInduction of Migraine Aura With Sildenafil
NCT03301441Not specifiedACTIVE_NOT_RECRUITINGSensitivity to Acute Cerebral Ischemia in Migrainers
NCT04715685Not specifiedRECRUITINGMind Body Balance for Pediatric Migraine
NCT05889624Not specifiedRECRUITINGResponding With Evidence and Access for Childhood Headaches
NCT05903027Not specifiedRECRUITINGGepant treAtments: EffectIveNess and tolERability (GAINER)
NCT06409832Not specifiedRECRUITINGRimegepAnt effectIvenesS and tolErability as Migraine Preventive Treatment
NCT06409845Not specifiedRECRUITINGEffectiveness and Tolerability of Eptinezumab
NCT06414044Not specifiedACTIVE_NOT_RECRUITINGItalian Real-life obServational Study on the effecTiveness, sAfety and Tolerability of Atogepant in Migraine Patients
NCT06459635Not specifiedRECRUITINGMigraine Attack Pain Phase Prediction Study

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
DIHYDROERGOTAMINE415
SUMATRIPTAN44
AMITRIPTYLINE43
PROPRANOLOL43
ERENUMAB42
METOCLOPRAMIDE42
RIMEGEPANT42
TIZANIDINE42
AMILORIDE41
ATOGEPANT41
CILOSTAZOL41
CLORAZEPATE DIPOTASSIUM41
DICLOFENAC41
ELETRIPTAN HYDROBROMIDE41
FREMANEZUMAB41
GALCANEZUMAB41
KETOPROFEN41
KETOROLAC TROMETHAMINE41
LASMIDITAN41
MILNACIPRAN41
RAMELTEON41
ANISODINE HYDROBROMIDE31
CANDESARTAN31
TONABERSAT23
DEXPROPRANOLOL21
ENDOTHELIN21
LEVCROMAKALIM21
CHEMBL458597805
CHEMBL507282801
CHEMBL377523401