Colitis

disease
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Also known as colitis (disease)colon inflammationinflammation of colon

Summary

Colitis (MONDO:0005292) is a disease (an umbrella term covering 9 Mondo subtypes) with 2 cohort genes (1 GWAS associations across 13 studies) and 46 clinical trials. Top therapeutic interventions include infliximab, loperamide, and ganciclovir.

At a glance

  • Umbrella term: 9 Mondo subtypes
  • Cohort genes: 2
  • GWAS associations: 1
  • ClinVar variants: 6
  • Clinical trials: 46

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namecolitis
Mondo IDMONDO:0005292
EFOEFO:0003872
MeSHD003092
DOIDDOID:0060180
ICD-111870792958
NCITC26723
SNOMED CT64226004
UMLSC0009319
MedGen40385
Is cancer (heuristic)no

Also known as: colitis · colitis (disease) · colon inflammation · inflammation of colon

Data availability: 6 ClinVar variants · 1 GWAS association (13 studies) · 1 HPO phenotype.

Disease family

An umbrella term covering 9 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › digestive system disorderintestinal disordergastroenteritiscolitis

Related subtypes (8): inflammatory diarrhea, intestinal infectious disease, intestinal tuberculosis, appendicitis, campylobacteriosis, Salmonella gastroenteritis, eosinophilic gastroenteritis, enteritis

Subtypes (9): ischemic colitis, microscopic colitis, chemical colitis, diversion colitis, ulcerative colitis, ileocolitis, indeterminate colitis, infectious colitis, proctocolitis

Genetics & variants

GWAS landscape

1 GWAS associations across 13 studies. Top hits map to 2 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs1153788186e-15TSBP1, TSBP1-AS1?2.43

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90080237Backman JD202119,104362,399Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90084223Backman JD202119,104362,399Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90080236Backman JD202117,883365,747Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90084222Backman JD202117,883365,747Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90726997Kim HI20262,03341,993Exome sequencing and analysis of 44,028 British South Asians enriched for high autozygosity.
GCST90077865Backman JD20211,203330,551Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90081851Backman JD20211,203330,551Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90077866Backman JD20211,104327,948Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90081852Backman JD20211,104327,948Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90080235Backman JD2021650387,279Exome sequencing and analysis of 454,787 UK Biobank participants.

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/intergenic1

MAF distribution

BucketVariants
common (>=0.05)0
low_freq (0.01-0.05)0
rare (<0.01)0
unknown1

Functional consequences

ConsequenceCount
intron_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs115378818632333650C>Tintron_variantTSBP1, TSBP1-AS16e-15Tier 4: intronic/intergenic

ClinVar germline variants

6 retrieved; paginated sample, class counts are floors:

2 uncertain significance, 2 likely pathogenic, 1 conflicting classifications of pathogenicity, 1 pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
989389NM_003177.7(SYK):c.1649C>A (p.Ser550Tyr)SYKPathogeniccriteria provided, single submitter
989237NM_003177.7(SYK):c.1350G>A (p.Met450Ile)SYKLikely pathogeniccriteria provided, single submitter
989387NM_003177.7(SYK):c.1024C>A (p.Pro342Thr)SYKLikely pathogeniccriteria provided, single submitter
989386NM_003177.7(SYK):c.1649C>T (p.Ser550Phe)SYKConflicting classifications of pathogenicitycriteria provided, conflicting classifications
2571633NM_015695.3(BRPF3):c.1978C>T (p.Leu660Phe)BRPF3Uncertain significancecriteria provided, single submitter
989236NM_003177.7(SYK):c.1057G>A (p.Ala353Thr)SYKUncertain significancecriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

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

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SYKOrphanet:695807Immunodeficiency-systemic inflammation-lymphoma predisposition syndrome

Cohort genes → proteins

2 cohort genes, 2 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence2

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SYKHGNC:11491ENSG00000165025P43405Tyrosine-protein kinase SYKclinvar
BRPF3HGNC:14256ENSG00000096070Q9ULD4Bromodomain and PHD finger-containing protein 3clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SYKTyrosine-protein kinase SYKNon-receptor tyrosine kinase which mediates signal transduction downstream of a variety of transmembrane receptors including classical immunoreceptors like the B-cell receptor (BCR).
BRPF3Bromodomain and PHD finger-containing protein 3Scaffold subunit of various histone acetyltransferase (HAT) complexes, such as the MOZ/MORF and HBO1 complexes, which have a histone H3 acetyltransferase activity.

Protein-family classification

Druggable: 1 · Difficult: 1 · Unknown: 0 · Druggable fraction: 0.5

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
Kinase113.9×0.142
Transcription factor14.1×0.228

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SYKKinaseyes2.7.10.2Prot_kinase_dom, SH2, Ser-Thr/Tyr_kinase_cat_dom
BRPF3Transcription factornoPWWP_dom, Bromodomain, Znf_PHD

Expression context

Cohort genes with no expression data: 0.

2 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)2
unknown0

Top tissues across cohort

TissueCohort genes
leukocyte1
monocyte1
mononuclear cell1
ganglionic eminence1
sural nerve1
ventricular zone1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SYK239broadmarkermonocyte, mononuclear cell, leukocyte
BRPF3209ubiquitousmarkerganglionic eminence, ventricular zone, sural nerve

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
SYK5,172
BRPF31,462

Structural data

PDB: 2 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
SYKP4340593
BRPF3Q9ULD41

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 58. Enrichment computed across 2 evidence-associated genes (2 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 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Platelet activation, signaling and aggregation2105.7×0.005SYK, BRPF3
FLT3 signaling through SRC family kinases1815.7×0.013SYK
Interleukin-2 signaling1475.8×0.013SYK
FCGR activation1439.2×0.013SYK
Interleukin-2 family signaling1317.2×0.013SYK
Role of LAT2/NTAL/LAB on calcium mobilization1300.5×0.013SYK
Signaling by CSF3 (G-CSF)1285.5×0.013SYK
Regulation of signaling by CBL1248.3×0.013SYK
DAP12 interactions1237.9×0.013SYK
Role of phospholipids in phagocytosis1228.4×0.013SYK
Regulation of TP53 Activity through Acetylation1228.4×0.013BRPF3
Platelet Aggregation (Plug Formation)1219.6×0.013SYK
Inactivation of CSF3 (G-CSF) signaling1219.6×0.013SYK
Integrin signaling1211.5×0.013SYK
Dectin-2 family1211.5×0.013SYK
Anti-inflammatory response favouring Leishmania parasite infection1196.9×0.013SYK
Leishmania parasite growth and survival1196.9×0.013SYK
DAP12 signaling1184.2×0.013SYK
FCERI mediated Ca+2 mobilization1178.4×0.013SYK
Antigen activates B Cell Receptor (BCR) leading to generation of second messengers1178.4×0.013SYK
FCERI mediated MAPK activation1173.0×0.013SYK
FLT3 Signaling1173.0×0.013SYK
Parasite infection1173.0×0.013SYK
Leishmania phagocytosis1173.0×0.013SYK
Signaling by the B Cell Receptor (BCR)1173.0×0.013SYK
Hemostasis236.0×0.013SYK, BRPF3
Interleukin-3, Interleukin-5 and GM-CSF signaling1158.6×0.013SYK
GPVI-mediated activation cascade1154.3×0.013SYK
FCGR3A-mediated IL10 synthesis1146.4×0.014SYK
Fcgamma receptor (FCGR) dependent phagocytosis1139.3×0.014SYK

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
positive regulation of interleukin-3 production18426.0×0.003SYK
regulation of superoxide anion generation18426.0×0.003SYK
regulation of arachidonate secretion18426.0×0.003SYK
regulation of neutrophil degranulation14213.0×0.004SYK
cellular response to lectin14213.0×0.004SYK
leukocyte activation involved in immune response12808.7×0.004SYK
serotonin secretion by platelet12808.7×0.004SYK
beta selection12808.7×0.004SYK
cellular response to molecule of fungal origin12106.5×0.004SYK
positive regulation of mast cell cytokine production11685.2×0.004SYK
regulation of platelet activation11404.3×0.004SYK
positive regulation of alpha-beta T cell proliferation11404.3×0.004SYK
interleukin-3-mediated signaling pathway11203.7×0.004SYK
regulation of developmental process11203.7×0.004BRPF3
regulation of platelet aggregation11203.7×0.004SYK
gamma-delta T cell differentiation11053.2×0.004SYK
lymph vessel development1936.2×0.004SYK
neutrophil activation involved in immune response1936.2×0.004SYK
positive regulation of gamma-delta T cell differentiation1936.2×0.004SYK
cell activation1842.6×0.004SYK
positive regulation of alpha-beta T cell differentiation1842.6×0.004SYK
regulation of phagocytosis1842.6×0.004SYK
positive regulation of mast cell degranulation1766.0×0.004SYK
obsolete regulation of DNA-binding transcription factor activity1766.0×0.004SYK
regulation of hemopoiesis1766.0×0.004BRPF3
cell surface pattern recognition receptor signaling pathway1702.2×0.004SYK
leukotriene biosynthetic process1648.1×0.005SYK
collagen-activated tyrosine kinase receptor signaling pathway1648.1×0.005SYK
positive regulation of monocyte chemotactic protein-1 production1601.9×0.005SYK
macrophage activation involved in immune response1561.7×0.005SYK

Therapeutics

Drugs indicated for this disease

0 approved, 4 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
InfliximabPhase 3 (in late-stage trials)
MethylprednisolonePhase 3 (in late-stage trials)
PrednisolonePhase 3 (in late-stage trials)
UstekinumabPhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Adalimumab, Mesalamine, Tacrolimus Anhydrous, Tofacitinib, Vedolizumab.

Drug target analysis

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

Druggability breadth: 2 of 2 evidence-associated genes (100%) 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
SYKFEDRATINIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
SYK544
BRPF300

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
FEDRATINIB4SYK
NERATINIB4SYK
INFIGRATINIB PHOSPHATE4SYK
INFIGRATINIB4SYK
ENTRECTINIB4SYK
FOSTAMATINIB4SYK
CERITINIB4SYK
BOSUTINIB4SYK
GILTERITINIB4SYK
FOSTAMATINIB DISODIUM4SYK
PAZOPANIB4SYK
DASATINIB4SYK
ERLOTINIB4SYK
CRIZOTINIB4SYK
MIDOSTAURIN4SYK
IMATINIB4SYK
ENTOSPLETINIB3SYK
CEDIRANIB3SYK
QUERCETIN3SYK
LESTAURTINIB3SYK
FORETINIB2SYK
LUTEOLIN2SYK
REBASTINIB2SYK
APITOLISIB2SYK
CENISERTIB2SYK
ADAVOSERTIB2SYK
ILORASERTIB2SYK
R-3432SYK
FISETIN2SYK
TOP-12882SYK

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
SYK873Binding:863, Functional:10
BRPF389Binding:88, Functional:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
SYK2.7.10.2, 2.7.12.1non-specific protein-tyrosine kinase, dual-specificity kinase

Cohort genes with high screening signal

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

SymbolChEMBL assays
SYK873

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; 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)
FEDRATINIB4SYK
NERATINIB4SYK
INFIGRATINIB PHOSPHATE4SYK
INFIGRATINIB4SYK
ENTRECTINIB4SYK
FOSTAMATINIB4SYK
CERITINIB4SYK
BOSUTINIB4SYK
GILTERITINIB4SYK
FOSTAMATINIB DISODIUM4SYK
PAZOPANIB4SYK
DASATINIB4SYK
ERLOTINIB4SYK
CRIZOTINIB4SYK
MIDOSTAURIN4SYK
IMATINIB4SYK
ENTOSPLETINIB3SYK
CEDIRANIB3SYK
QUERCETIN3SYK
LESTAURTINIB3SYK
FORETINIB2SYK
LUTEOLIN2SYK
REBASTINIB2SYK
APITOLISIB2SYK
CENISERTIB2SYK
ADAVOSERTIB2SYK
ILORASERTIB2SYK
R-3432SYK
FISETIN2SYK
TOP-12882SYK

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1SYK
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug1BRPF3

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
BRPF389

Clinical trials & evidence

Clinical trials

Clinical trials: 46.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified27
PHASE26
PHASE16
PHASE34
PHASE41
PHASE2/PHASE31
PHASE1/PHASE21

Top trials by phase / activity

NCTPhaseStatusTitle
NCT02687724PHASE4UNKNOWNGolimumab (GLM) Dose Optimisation to Adequate Levels to Achieve Response in Colitis
NCT05947669PHASE3RECRUITINGEfficacy and Safety of Infliximab for Immune Checkpoint Inhibitor Induced Colitis
NCT07047339PHASE2/PHASE3RECRUITINGEvaluate the Efficacy and Safety of Probiotic 6600 as an Adjuvant Therapy for Colitis
NCT01369329PHASE3COMPLETEDA Study to Evaluate the Safety and Efficacy of Ustekinumab in Patients With Moderately to Severely Active Crohn’s Disease Who Have Failed or Are Intolerant to Tumor Necrosis Factor (TNF) Antagonist Therapy (UNITI-1)
NCT01369342PHASE3COMPLETEDA Study to Evaluate the Safety and Efficacy of Ustekinumab Induction Therapy in Patients With Moderately to Severely Active Crohn’s Disease (UNITI-2)
NCT01369355PHASE3COMPLETEDA Study to Evaluate the Safety and Efficacy of Ustekinumab Maintenance Therapy in Patients With Moderately to Severely Active Crohn’s Disease (IM-UNITI)
NCT04407247PHASE1/PHASE2ACTIVE_NOT_RECRUITINGInfliximab or Vedolizumab in Treating Immune Checkpoint Inhibitor-Related Colitis in Patients With Genitourinary Cancer or Melanoma
NCT07012395PHASE2RECRUITINGA Study of Long-acting Antibodies Alone and in Combinations for Moderate to Severe Ulcerative Colitis
NCT00072943PHASE2COMPLETEDA Humanized Anti-Interferon-γ Monoclonal Antibody (HuZAF) for Moderate to Severe Crohn’s Disease
NCT00514982PHASE2WITHDRAWNMedical Treatment of Colitis in Patients With Hermansky-Pudlak Syndrome
NCT00533078PHASE2COMPLETEDLipid Use, Nutrition, and Colitis in Patients With Hematological Malignancies
NCT02647866PHASE2COMPLETEDStudy of a Monoclonal Antibody KHK4083 in Moderate Ulcerative Colitis
NCT05726396PHASE2WITHDRAWNA Pilot Study Testing the Safety and Feasibility of Restorative Microbiota Therapy (RMT) in Patients With Refractory Immune-checkpoint Inhibitor-related Colitis
NCT03819296PHASE1RECRUITINGRole of Gut Microbiome and Fecal Transplant on Medication-Induced GI Complications in Patients With Cancer
NCT04038619PHASE1RECRUITINGFecal Microbiota Transplantation in Treating Immune-Checkpoint Inhibitor Induced-Diarrhea or Colitis in Genitourinary Cancer Patients
NCT07196410PHASE1RECRUITINGKAN-004 for Immune-Related Diarrhea or Colitis
NCT00000768PHASE1COMPLETEDA Randomized Comparative Pharmacokinetic Study of Oral Ganciclovir After Treatment With Intravenous Ganciclovir for Cytomegalovirus Gastrointestinal Disease in AIDS Patients
NCT00325013PHASE1COMPLETEDEvaluation of DHA for the Treatment of PSC
NCT03378167PHASE1COMPLETEDPediCRaFT: Pediatric Crohn’s Disease Fecal Transplant Trial
NCT06206707Not specifiedRECRUITINGFMT in Checkpoint Inhibitor-mediated Diarrhea and Colitis
NCT06424769Not specifiedENROLLING_BY_INVITATIONImproving Outcomes and Reducing Disparities for Patients With Inflammatory Bowel Disease Through Epidemiology and Enhanced Disease Management
NCT07541261Not specifiedNOT_YET_RECRUITINGA Real-World Study of Guselkumab in Ulcerative Colitis and Crohn’s Disease in Saudi Arabia
NCT00002273Not specifiedCOMPLETEDA Study of Ganciclovir in the Treatment of Cytomegalovirus of the Large Intestine in Patients With AIDS
NCT00184171Not specifiedTERMINATEDTreatment of Microscopic Colitis
NCT00272818Not specifiedCOMPLETEDStudy to Identify Non-Invasive Markers of Gastrointestinal Allergy
NCT00518349Not specifiedCOMPLETEDColonoscope Passive Bending Function
NCT00936585Not specifiedTERMINATEDNIH Substudy of AIN457 (Anti-IL-17 Monoclonal Antibody) for Treatment of Moderate to Severe Crohn’s Disease
NCT01326013Not specifiedCOMPLETEDA Two-Arm, Multi-Centre Clinical Evaluation of the xTAG Gastrointestinal Pathogen Panel
NCT01346059Not specifiedTERMINATEDIntracolonic Vancomycin Therapy in Severe C. Diff Colitis
NCT02063282Not specifiedCOMPLETEDThe Risk for Clostridium Difficile Colitis During Hospitalization in Asymptomatic Carriers
NCT02333526Not specifiedUNKNOWNSyndecan 1 as Biomarker for Inflammation
NCT02503514Not specifiedCOMPLETEDAutoimmune Paradoxical Reactions in IBD Longitudinal Cohort
NCT02569333Not specifiedCOMPLETEDPatient Centered Algorithms to Optimize the Inpatient Experience and Treatment of Ulcerative Colitis
NCT02600143Not specifiedCOMPLETEDIdentification of Predictive Parameters for Colitis in Melanoma Patients Treated With Immunotherapy.
NCT02709213Not specifiedCOMPLETEDDetermination of the Aetiologies of Acute Colitis and Early Identification of Patients Requiring Diagnostic Colonoscopy
NCT02768038Not specifiedWITHDRAWNIntestinal Microbiome and Chronic Inflammatory Bowel Disease
NCT03014284Not specifiedWITHDRAWNNovel Listeria Vectors Secreting Gut Flora-Altering Agents to Prevent Colon Cancer and Treat Colitis
NCT03548948Not specifiedCOMPLETEDObesity, Iron Regulation and Colorectal Cancer Risk
NCT03601611Not specifiedCOMPLETEDCheckpoint Inhibitor Induced Colitis and Arthritis -Immunomodulation With IL-6 Blockade and Exploration of Disease Mechanisms
NCT04272307Not specifiedUNKNOWNMIcroorganisms as Triggers in Acute Severe Ulcerative Colitis and Their Influence on Medical Therapy Efficacy: a Multi-omics Pilot Approach.

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
INFLIXIMAB44
LOPERAMIDE43
GANCICLOVIR42
VEDOLIZUMAB42
FISH OIL TRIGLYCERIDES41
GOLIMUMAB41
MESALAMINE41
ROCATINLIMAB31
GLUTAMIC ACID HYDROCHLORIDE11
CHEMBL392074101
CHEMBL313767301