Encephalitis

Summary

Encephalitis (MONDO:0019956) is a disease (an umbrella term covering 7 Mondo subtypes) with 1 cohort gene (1 GWAS associations across 3 studies) and 53 clinical trials. Top therapeutic interventions include inebilizumab, valacyclovir, and mgawn1.

At a glance

• Umbrella term: 7 Mondo subtypes
• Cohort genes: 1
• GWAS associations: 1
• ClinVar variants: 1
• Clinical trials: 53

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	encephalitis
Mondo ID	MONDO:0019956
MeSH	D004660
Orphanet	97275
DOID	DOID:9588
ICD-10-CM	A85
NCIT	C26760
SNOMED CT	45170000
UMLS	C0014038
MedGen	4027
MedDRA	10014581
Is cancer (heuristic)	no

Also known as: brain inflammation

Data availability: 1 ClinVar variant · 1 GWAS association (3 studies).

Disease family

An umbrella term covering 7 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › nervous system disorder › central nervous system disorder › encephalomyelitis › encephalitis

Related subtypes (6): myelitis, cerebritis, optic neuritis, Venezuelan equine encephalitis, meningitis, hypophysitis

Subtypes (7): post-vaccinal encephalitis, meningoencephalitis, limbic encephalitis, infectious encephalitis, autoimmune encephalitis, anti-NMDA receptor encephalitis, paraneoplastic isolated brainstem encephalitis

Genetics & variants

GWAS landscape

1 GWAS associations across 3 studies. Top hits map to 1 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs147363369	5e-08	EZR	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90481853	Verma A	2024	560	450,196	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90435895	Zhou W	2018	345	407,888	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90651719	Liu TY	2025	260	235,960	Diversity 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)

Tier	Variants
Tier 1: coding	0
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	1

MAF distribution

Bucket	Variants
common (>=0.05)	0
low_freq (0.01-0.05)	0
rare (<0.01)	0
unknown	1

Functional consequences

Consequence	Count
intron_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs147363369	6	158811021	A>T		intron_variant	EZR	5e-08	Tier 4: intronic/intergenic

ClinVar germline variants

1 retrieved; paginated sample, class counts are floors:

1 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
523312	NM_000033.4(ABCD1):c.1866-1G>C	PLXNB3-AS1	Likely pathogenic	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

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

Cohort genes → proteins

1 cohort genes, 0 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
PLXNB3-AS1	HGNC:40454	ENSG00000232725		PLXNB3 antisense RNA 1	clinvar

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.0

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.

Family	Genes	Fold	FDR
Other/Unknown	1	1.8×	0.558

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
PLXNB3-AS1	Other/Unknown	no

Expression context

Cohort genes with no expression data: 0.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
muscle layer of sigmoid colon	1
primordial germ cell in gonad	1
sural nerve	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
PLXNB3-AS1	133		yes	sural nerve, primordial germ cell in gonad, muscle layer of sigmoid colon

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
PLXNB3-AS1	0

Structural data

PDB: 0 · AlphaFold-only: 0 · No structure: 1

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 1 evidence-associated genes (0 with Reactome annotation).

Therapeutics

Drugs indicated for this disease

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

Drug	Development status
Human Immunoglobulin G	Phase 3 (in late-stage trials)
Sodium Chloride	Phase 3 (in late-stage trials)
Valacyclovir	Phase 3 (in late-stage trials)

Drug target analysis

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

Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
PLXNB3-AS1	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 0; 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):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	PLXNB3-AS1

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
PLXNB3-AS1	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 53.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	36
PHASE3	8
PHASE2	4
PHASE1/PHASE2	2
PHASE1	2
PHASE4	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT02526550	PHASE4	COMPLETED	Immunogenicity of a Live Attenuated Chimeric JE Vaccine (IMOJEV) as a Booster Dose in Thai Children Primed With CD.JEVAX
NCT00031486	PHASE3	COMPLETED	Long Term Treatment of Herpes Simplex Encephalitis (HSE) With Valacyclovir
NCT00314132	PHASE3	COMPLETED	Safety Study of ChimeriVax™-JE Vaccine to Prevent Japanese Encephalitis.
NCT01001988	PHASE3	COMPLETED	Long-term Follow-up of Immunogenicity of a Single Dose of Japanese Encephalitis Chimeric Virus Vaccine (JE-CV) in Toddlers
NCT01041573	PHASE3	COMPLETED	Safety and Immunogenicity of the Japanese Encephalitis Vaccine IC51 (IXIARO®) in a Pediatric Population
NCT01047839	PHASE3	COMPLETED	Immunogenicity and Safety of the Japanese Encephalitis Vaccine IC51 (IXIARO®, JESPECT®) in a Pediatric Population in Non-endemic Countries
NCT01092507	PHASE3	COMPLETED	A Study of Japanese Encephalitis Chimeric Virus Vaccine Compared With SA14-14-2 Vaccine in Infants and Toddlers
NCT02308982	PHASE3	COMPLETED	Investigating the Role of Early Intravenous Immunoglobulin Treatment for Children With Encephalitis
NCT02367664	PHASE3	COMPLETED	A Clinical Trial for Inactivated Japanese Encephalitis Vaccine in Healthy Chinese Infants
NCT04372615	PHASE2	RECRUITING	The ExTINGUISH Trial of Inebilizumab in NMDAR Encephalitis
NCT06899802	PHASE2	ACTIVE_NOT_RECRUITING	A Phase 2 Trial in Healthy Adult Participants of the Recombinant MVA-BN-WEV Vaccine
NCT00927953	PHASE2	TERMINATED	Treatment of West Nile Virus With MGAWN1
NCT00981175	PHASE2	COMPLETED	A Study of ChimeriVax™-JE Live Attenuated Vaccine in Healthy Adults
NCT02714959	PHASE1/PHASE2	COMPLETED	IL-2 in Refractory Autoimmune Encephalitis
NCT04080921	PHASE1/PHASE2	COMPLETED	Stem Cell Transplantation In-patient With Neurological Sequelae Due to Encephalitis or Meningitis
NCT00381433	PHASE1	COMPLETED	Pharmacokinetic Study of a Single Dose of AVI-4065 in Cerebral Spinal Fluid
NCT03776994	PHASE1	UNKNOWN	Venezuelan Equine Encephalitis Monovalent Virus-Like Particle Vaccine
NCT02979951	Not specified	RECRUITING	Fosfomycin I.v. for Treatment of Severely Infected Patients
NCT03418441	Not specified	RECRUITING	Central Nervous System Infections in Denmark
NCT05413733	Not specified	ACTIVE_NOT_RECRUITING	Neuropsychological Rehabilitation Over the Internet
NCT06368648	Not specified	RECRUITING	CoMind Early Feasibility Study
NCT06584045	Not specified	RECRUITING	Efficacy and Safety of Calculus Bovis Sativus (CBS) for Adult Encephalitis (CBSinEncephalitis)
NCT06849011	Not specified	NOT_YET_RECRUITING	Inflammatory and Metabolic Prognostic Assessment in Critically Ill Neurological Patients
NCT07186881	Not specified	ENROLLING_BY_INVITATION	Evolving Diagnostic Approaches to Undocumented Lymphocytic Meningitis and Meningoencephalitis
NCT07200687	Not specified	ACTIVE_NOT_RECRUITING	Effects of Combined Music Therapy and Occupational Therapy on Motor and Physiological Parameters in Children With Neurological Impairments: A Non-Randomized Controlled Trial
NCT07241858	Not specified	NOT_YET_RECRUITING	Clinicolaboratory Predictors of Outcome in Children With Encephalitis
NCT07251049	Not specified	RECRUITING	Acute Infectious Encephalitis and Myelitis in Guadeloupe by New Generation Sequencing
NCT07432113	Not specified	NOT_YET_RECRUITING	Prediction of Infectious Agents in the Biofire® FilmArray bioMérieux Meningitis/Encephalitis Panel Based on Clinical Syndrome and Cerebrospinal Fluid Parameters: a Diagnostic Stewardship Proposal.
NCT00001648	Not specified	COMPLETED	Structure of the Herpes Simplex Virus Receptor
NCT00069303	Not specified	COMPLETED	Natural History of West Nile Virus Infection
NCT01694524	Not specified	COMPLETED	Nervous System Infections Among Patients With Febrile Seizure
NCT02538094	Not specified	COMPLETED	tDCS and Cognition in Adults With Multiple Sclerosis or Encephalitis
NCT02856451	Not specified	COMPLETED	Risk Factors and Outcomes of Immune-Mediated Encephalitis Following Exposure to Nivolumab
NCT02906631	Not specified	COMPLETED	Epidemiology and Prognosis of Encephalitis in Intensive Care
NCT02910037	Not specified	COMPLETED	Precision Diagnosis of Acute Infectious Diseases; Neuroinflammatory Cohort
NCT03144570	Not specified	COMPLETED	EURopean Study on Encephalitis in Intensive CAre
NCT03206541	Not specified	COMPLETED	Neurologic Manifestations of the Arbovirus Infection in Colombia
NCT03710278	Not specified	COMPLETED	The Effectiveness and Safety of Human Lumbar Puncture Assist Device (LPat)
NCT03826056	Not specified	COMPLETED	Neurology Inpatient Clinical Education Trial
NCT04001270	Not specified	UNKNOWN	Core Cerebrospinal Fluid Biomarker Profile in Anti-Leucine Rich Glioma Inactivated 1 (Anti-LGI1) Encephalitis

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
INEBILIZUMAB	4	1
VALACYCLOVIR	4	1
MGAWN1	2	1