Prion disease

disease
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Also known as spongiform encephalopathy

Summary

Prion disease (MONDO:0005429) is a disease (an umbrella term covering 10 Mondo subtypes) with 10 cohort genes (18 GWAS associations across 4 studies) and 6 clinical trials. Top therapeutic interventions include quinacrine.

At a glance

  • Umbrella term: 10 Mondo subtypes
  • Cohort genes: 10
  • GWAS associations: 18
  • Clinical trials: 6

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameprion disease
Mondo IDMONDO:0005429
EFOEFO:0004720
MeSHD017096
DOIDDOID:649
NCITC128346
SNOMED CT230284004
UMLSC0162534
MedGen56445
GARD0024183
Is cancer (heuristic)no

Also known as: spongiform encephalopathy

Data availability: 18 GWAS associations (4 studies).

Disease family

An umbrella term covering 10 Mondo subtypes.

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

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, migraine disorder, multiple sclerosis, 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 (10): Creutzfeldt Jacob disease, kuru, scrapie, Gerstmann-Straussler-Scheinker syndrome, fatal familial insomnia, Huntington disease-like 1, spongiform encephalopathy with neuropsychiatric features, familial Alzheimer-like prion disease, PrP systemic amyloidosis, sporadic fatal insomnia

Genetics & variants

GWAS landscape

18 GWAS associations across 4 studies. Top hits map to 12 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs17999907e-07PRNP?1.3
rs105091251e-06ANK3?2.09
rs98572752e-06PXYLP1, ZBTB38?1.28
rs77898502e-06AGK?4.6
rs4883333e-06SEMA3A?1.27
rs10555693e-06HCP5?2.36
rs125709474e-06LINC01435?1.45
rs127891454e-06PIWIL4-AS1?
rs5614375e-06COL4A1?2.04
rs29036986e-06LINC02483 - RCHY1?1.25
rs127612246e-06ADAMTS14 - TBATA?1.39
rs68678206e-06MGC32805 - LINC02201?2.24
rs71519686e-06LINC00648 - RNU6-297P?2.12
rs177633737e-06CPEB4?1.51
rs7305667e-06TMA7 - ATRIP?1.27
rs101089547e-06MFHAS1?1.74
rs81058158e-06CYP2T3P - RPL36P16?1.39
rs20715989e-06RIDA - POP1?1.26

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST001366Mead S20111,2816,015Genome-wide association study in multiple human prion diseases suggests genetic risk factors additional to PRNP.
GCST002862Thompson AG20151705,200Genome-wide association study of behavioural and psychiatric features in human prion disease.
GCST002866Thompson AG20151705,200Genome-wide association study of behavioural and psychiatric features in human prion disease.
GCST002871Thompson AG20151705,200Genome-wide association study of behavioural and psychiatric features in human prion disease.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding1
Tier 2: splice/UTR0
Tier 3: regulatory1
Tier 4: intronic/intergenic16

MAF distribution

BucketVariants
common (>=0.05)17
low_freq (0.01-0.05)1
rare (<0.01)0
unknown0

Functional consequences

ConsequenceCount
intron_variant14
intergenic_variant2
missense_variant1
regulatory_region_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs1799990204699605A>G0.05missense_variantPRNP7e-07Tier 1: coding
rs105091251060167108C>A0.402intron_variantANK31e-06Tier 4: intronic/intergenic
rs98572753141359346C>A0.05intron_variantPXYLP1, ZBTB382e-06Tier 4: intronic/intergenic
rs77898507141600811T>C0.026intron_variantAGK2e-06Tier 4: intronic/intergenic
rs488333784281955G>A,C0.05intron_variantSEMA3A3e-06Tier 4: intronic/intergenic
rs1055569631472305C>G,T0.291intron_variantHCP53e-06Tier 4: intronic/intergenic
rs1257094710107810092T>A,C0.05intron_variantLINC014354e-06Tier 4: intronic/intergenic
rs127891451194674570T>C,G0.084intron_variantPIWIL4-AS14e-06Tier 4: intronic/intergenic
rs56143713110283880T>C0.499intron_variantCOL4A15e-06Tier 4: intronic/intergenic
rs2903698475407765A>G,T0.05intron_variantLINC02483 - RCHY16e-06Tier 4: intronic/intergenic
rs127612241070767761G>T0.05intergenic_variantADAMTS14 - TBATA6e-06Tier 4: intronic/intergenic
rs68678205122518830C>T0.224intron_variantMGC32805 - LINC022016e-06Tier 4: intronic/intergenic
rs71519681448132233G>A,C,T0.205intergenic_variantLINC00648 - RNU6-297P6e-06Tier 4: intronic/intergenic
rs177633735173932328A>G0.05intron_variantCPEB47e-06Tier 4: intronic/intergenic
rs730566348445644C>A,G,T0.05intron_variantTMA7 - ATRIP7e-06Tier 4: intronic/intergenic
rs1010895488864868C>T0.05intron_variantMFHAS17e-06Tier 4: intronic/intergenic
rs81058151941167943G>A,T0.05intron_variantCYP2T3P - RPL36P168e-06Tier 4: intronic/intergenic
rs2071598898117279G>A,C,T0.05regulatory_region_variantRIDA - POP19e-06Tier 3: regulatory

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 20 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 1

Dual-evidence genes (GWAS + Mendelian — highest-confidence targets)

GeneHGNCEvidence routes
PRNPPRNPGWAS, Orphanet

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SEMA3AOrphanet:130Brugada syndrome
SEMA3AOrphanet:478Kallmann syndrome
AGKOrphanet:1369Congenital cataract-hypertrophic cardiomyopathy-mitochondrial myopathy syndrome
AGKOrphanet:98994Total early-onset cataract
COL4A1Orphanet:36383COL4A1/2-related familial vascular leukoencephalopathy
COL4A1Orphanet:477749Pontine autosomal dominant microangiopathy with leukoencephalopathy
COL4A1Orphanet:481986Familial schizencephaly
COL4A1Orphanet:73229HANAC syndrome
COL4A1Orphanet:75326Familial isolated retinal arteriolar tortuosity
COL4A1Orphanet:899Walker-Warburg syndrome
COL4A1Orphanet:99810Familial porencephaly
ANK3Orphanet:356996ANK3-related intellectual disability-sleep disturbance syndrome
PRNPOrphanet:157941Huntington disease-like 1
PRNPOrphanet:280397Familial Alzheimer-like prion disease
PRNPOrphanet:282166Inherited Creutzfeldt-Jakob disease
PRNPOrphanet:356Gerstmann-Straussler-Scheinker syndrome
PRNPOrphanet:397606PrP systemic amyloidosis
PRNPOrphanet:454745Kuru
PRNPOrphanet:466Fatal familial insomnia
RASA2Orphanet:648Noonan syndrome

Cohort genes → proteins

10 cohort genes, 9 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only10

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SEMA3AHGNC:10723ENSG00000075213Q14563Semaphorin-3Agwas
SNCAIPHGNC:11139ENSG00000064692Q9Y6H5Synphilin-1gwas
PIWIL4HGNC:18444ENSG00000134627Q7Z3Z4Piwi-like protein 4gwas
AGKHGNC:21869ENSG00000006530Q53H12Acylglycerol kinase, mitochondrialgwas
COL4A1HGNC:2202ENSG00000187498P02462Collagen alpha-1(IV) chaingwas
ZBTB38HGNC:26636ENSG00000177311Q8NAP3Zinc finger and BTB domain-containing protein 38gwas
HCG26HGNC:29671HLA complex group 26gwas
ANK3HGNC:494ENSG00000151150Q12955Ankyrin-3gwas
PRNPHGNC:9449ENSG00000171867F7VJQ1Alternative prion proteingwas
RASA2HGNC:9872ENSG00000155903Q15283Ras GTPase-activating protein 2gwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SEMA3ASemaphorin-3AInvolved in the development of the olfactory system and in neuronal control of puberty.
SNCAIPSynphilin-1Isoform 2 inhibits the ubiquitin ligase activity of SIAH1 and inhibits proteasomal degradation of target proteins.
PIWIL4Piwi-like protein 4Plays a central role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for the germline integrity.
AGKAcylglycerol kinase, mitochondrialLipid kinase that can phosphorylate both monoacylglycerol and diacylglycerol to form lysophosphatidic acid (LPA) and phosphatidic acid (PA), respectively.
COL4A1Collagen alpha-1(IV) chainType IV collagen is the major structural component of glomerular basement membranes (GBM), forming a ‘chicken-wire’ meshwork together with laminins, proteoglycans and entactin/nidogen.
ZBTB38Zinc finger and BTB domain-containing protein 38Transcriptional regulator with bimodal DNA-binding specificity.
ANK3Ankyrin-3Membrane-cytoskeleton linker.
RASA2Ras GTPase-activating protein 2Inhibitory regulator of the Ras-cyclic AMP pathway.

Protein-family classification

Druggable: 2 · Difficult: 4 · Unknown: 4 · Druggable fraction: 0.2

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
Scaffold/PPI23.5×0.433
Antibody/Immunoglobulin12.9×0.433
Kinase12.8×0.433
Transcription factor21.6×0.433
Other/Unknown40.7×0.907

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SEMA3AAntibody/ImmunoglobulinyesSemap_dom, Ig_sub, Ig-like_dom
SNCAIPScaffold/PPInoAnkyrin_rpt, SNCAIP_SNCA-bd, Ankyrin_rpt-contain_sf
PIWIL4Other/UnknownnoPAZ_dom, Piwi, RNaseH-like_sf
AGKKinaseyes2.7.1.94Diacylglycerol_kinase_cat_dom, NAD/diacylglycerol_kinase_sf, ATP-NAD_kinase_N
COL4A1Other/UnknownnoCollagen_IV_NC, Collagen, CTDL_fold
ZBTB38Transcription factornoBTB/POZ_dom, SKP1/BTB/POZ_sf, Znf_C2H2_type
HCG26Other/Unknownno
ANK3Scaffold/PPInoDeath_dom, ZU5_dom, Ankyrin_rpt
PRNPOther/UnknownnoPrion, Prion_copper_b_octapeptide, Prion/Doppel_prot_b-ribbon_dom
RASA2Transcription factornoC2_dom, Znf_Btk_motif, PH_domain

Expression context

Cohort genes with no expression data: 1.

9 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)9
unknown1

Top tissues across cohort

TissueCohort genes
pigmented layer of retina2
superficial temporal artery2
Brodmann (1909) area 232
colonic epithelium1
cortical plate1
stromal cell of endometrium1
ganglionic eminence1
germinal epithelium of ovary1
ventricular zone1
bone marrow1
male germ line stem cell (sensu Vertebrata) in testis1
primordial germ cell in gonad1
adrenal tissue1
cerebellar cortex1
cerebellar hemisphere1
placenta1
right coronary artery1
visceral pleura1
seminal vesicle1
dorsal motor nucleus of vagus nerve1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SEMA3A194ubiquitousmarkerstromal cell of endometrium, cortical plate, colonic epithelium
SNCAIP240broadmarkerventricular zone, ganglionic eminence, germinal epithelium of ovary
PIWIL4211tissue_specificmarkermale germ line stem cell (sensu Vertebrata) in testis, primordial germ cell in gonad, bone marrow
AGK161ubiquitousmarkeradrenal tissue, cerebellar hemisphere, cerebellar cortex
COL4A1283ubiquitousmarkervisceral pleura, placenta, right coronary artery
ZBTB38284ubiquitousmarkersuperficial temporal artery, seminal vesicle, pigmented layer of retina
HCG26
ANK3298ubiquitousmarkerendothelial cell, Brodmann (1909) area 23, dorsal motor nucleus of vagus nerve
PRNP294ubiquitousmarkerCA1 field of hippocampus, Brodmann (1909) area 23, pigmented layer of retina
RASA2269ubiquitousmarkerepithelium of nasopharynx, superficial temporal artery, trabecular bone tissue

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
ANK36,145
COL4A12,909
PRNP2,594
AGK2,341
PIWIL42,093
SEMA3A2,069
ZBTB381,498
SNCAIP1,456
RASA2844
HCG260

Intra-cohort edges

ABSources
RASA2ZBTB38string_interaction

Structural data

PDB: 6 · AlphaFold-only: 3 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
PRNPF7VJQ170
COL4A1P024624
ZBTB38Q8NAP32
SNCAIPQ9Y6H51
AGKQ53H121
ANK3Q129551

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
PIWIL4Q7Z3Z485.84
SEMA3AQ1456384.50
RASA2Q1528383.63

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 46. Enrichment computed across 10 evidence-associated genes (8 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 8 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
NCAM1 interactions262.1×0.020COL4A1, PRNP
Anchoring fibril formation195.2×0.060COL4A1
SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion195.2×0.060SEMA3A
Sema3A PAK dependent Axon repulsion184.0×0.060SEMA3A
CRMPs in Sema3A signaling179.3×0.060SEMA3A
Scavenging by Class A Receptors175.1×0.060COL4A1
Fibronectin matrix formation171.4×0.060COL4A1
Crosslinking of collagen fibrils171.4×0.060COL4A1
Attachment of bacteria to epithelial cells162.1×0.060COL4A1
Insertion of tail-anchored proteins into the endoplasmic reticulum membrane159.5×0.060PRNP
Semaphorin interactions149.2×0.060SEMA3A
PIWI-interacting RNA (piRNA) biogenesis149.2×0.060PIWIL4
Laminin interactions147.6×0.060COL4A1
Interaction between L1 and Ankyrins146.0×0.060ANK3
Glycerophospholipid biosynthesis142.0×0.060AGK
Regulation of CDH1 posttranslational processing and trafficking to plasma membrane142.0×0.060ANK3
Axon guidance211.3×0.060SEMA3A, ANK3
Nervous system development210.7×0.060SEMA3A, ANK3
Collagen chain trimerization132.4×0.070COL4A1
Signaling by PDGF131.7×0.070COL4A1
Oncogenic MAPK signaling131.0×0.070AGK
Phospholipid metabolism125.0×0.078AGK
Assembly of collagen fibrils and other multimeric structures125.0×0.078COL4A1
Regulation of RAS by GAPs124.2×0.078RASA2
Collagen degradation122.0×0.078COL4A1
Collagen biosynthesis and modifying enzymes121.3×0.078COL4A1
Signaling by BRAF and RAF1 fusions121.3×0.078AGK
Non-integrin membrane-ECM interactions119.3×0.083COL4A1
ECM proteoglycans118.8×0.083COL4A1
Integrin cell surface interactions116.8×0.087COL4A1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 9 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
positive regulation of protein targeting to membrane2124.8×0.007ANK3, PRNP
neuromuscular junction development2117.0×0.007COL4A1, ANK3
positive regulation of cell communication by electrical coupling1936.2×0.017ANK3
regulation of axon extension involved in axon guidance1936.2×0.017SEMA3A
maintenance of protein location in plasma membrane1936.2×0.017ANK3
regulation of inclusion body assembly1936.2×0.017SNCAIP
positive regulation of membrane depolarization during cardiac muscle cell action potential1936.2×0.017ANK3
sensory system development1624.1×0.017SEMA3A
secondary piRNA processing1624.1×0.017PIWIL4
basal dendrite arborization1624.1×0.017SEMA3A
renal tubule morphogenesis1468.1×0.017COL4A1
membrane assembly1468.1×0.017ANK3
sympathetic neuron projection guidance1468.1×0.017SEMA3A
protein localization to axon1374.5×0.017ANK3
regulation of glutamate receptor signaling pathway1374.5×0.017PRNP
negative regulation of amyloid precursor protein catabolic process1374.5×0.017PRNP
trigeminal nerve structural organization1312.1×0.017SEMA3A
positive regulation of membrane potential1312.1×0.017ANK3
sympathetic neuron projection extension1312.1×0.017SEMA3A
negative regulation of delayed rectifier potassium channel activity1312.1×0.017ANK3
negative regulation of dendritic spine maintenance1312.1×0.017PRNP
regulation of calcium ion import across plasma membrane1312.1×0.017PRNP
positive regulation of homotypic cell-cell adhesion1267.5×0.017ANK3
retinal blood vessel morphogenesis1267.5×0.017COL4A1
cellular response to magnesium ion1267.5×0.017ANK3
cell death1234.1×0.017SNCAIP
branchiomotor neuron axon guidance1234.1×0.017SEMA3A
glycerolipid metabolic process1234.1×0.017AGK
magnesium ion homeostasis1208.1×0.017ANK3
facial nerve structural organization1208.1×0.017SEMA3A

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 10

Druggability breadth: 4 of 10 evidence-associated genes (40%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
SEMA3A00
SNCAIP00
PIWIL400
AGK00
COL4A100
ZBTB3800
HCG2600
ANK300
PRNP00
RASA200

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
AGK19Binding:19
SNCAIP1Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
AGK2.7.1.94acylglycerol kinase

Pharmacogenomics

Cohort genes with a PharmGKB record: 10; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

0 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.

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1AGK
DDruggable family + AlphaFold only, no drug1SEMA3A
EDifficult family or no structure, no drug8SNCAIP, PIWIL4, COL4A1, ZBTB38, HCG26, ANK3, PRNP, RASA2

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
SEMA3A0
SNCAIP1
PIWIL40
AGK19
COL4A10
ZBTB380
HCG260
ANK30
PRNP0
RASA20

Clinical trials & evidence

Clinical trials

Clinical trials: 6.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified4
PHASE1/PHASE21
PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT06153966PHASE1/PHASE2RECRUITINGPrProfile: A Study to Assess the Safety, Tolerability, Pharmacokinetics and Pharmacodynamics of ION717
NCT07444580PHASE1RECRUITINGPrP-targeting siRNA Safety & Mechanism Study
NCT05124392Not specifiedRECRUITINGBiomarker Profiling in Individuals at Risk for Prion Disease
NCT00104663Not specifiedCOMPLETEDPRION-1: Quinacrine for Human Prion Disease
NCT02629640Not specifiedCOMPLETEDEnhanced CJD Surveillance in the Older Population
NCT02837705Not specifiedCOMPLETEDTherapeutic Antibodies Against Prion Diseases From PRNP Mutation Carriers

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
QUINACRINE41