Chronic pancreatitis

disease
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Also known as pancreatitis, chronic

Summary

Chronic pancreatitis (MONDO:0005003) is a disease with 3 cohort genes (9 GWAS associations across 10 studies) and 223 clinical trials. Top therapeutic interventions include pinaverium, secretin, and triamcinolone.

At a glance

  • Cohort genes: 3
  • GWAS associations: 9
  • ClinVar variants: 4
  • Clinical trials: 223

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namechronic pancreatitis
Mondo IDMONDO:0005003
EFOEFO:0000342
MeSHD050500
DOIDDOID:0051065
ICD-111758007371
NCITC84637
SNOMED CT235494005
UMLSC0149521
MedGen101753
Is cancer (heuristic)no

Also known as: pancreatitis, chronic

Data availability: 4 ClinVar variants · 9 GWAS associations (10 studies) · 15 cell lines.

Disease family

An umbrella term covering 3 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › digestive system disorderpancreas disorderpancreatitischronic pancreatitis

Related subtypes (4): alcoholic pancreatitis, thiopurine immunosuppressant-induced pancreatitis, acute pancreatitis, autoimmune pancreatitis

Subtypes (3): hereditary chronic pancreatitis, autoimmune pancreatitis type 1, idiopathic chronic pancreatitis

Genetics & variants

GWAS landscape

9 GWAS associations across 10 studies. Top hits map to 5 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs1489117342e-17SPINK1 - SCGB3A2C0.78
rs28559725e-17PRSS1 - PRSS2C0.18
rs4970782e-15CTRCC0.24
rs1816494722e-12EIF3KP3 - TTC39CP1G2.98
rs5746936765e-12ATF7, ATF7-NPFFG1.9
rs37828869e-12BRAP?
rs1139939602e-11CFTR?3.14
chr5:1472152814e-11C0.69

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90476108Verma A20242,972446,161Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90476107Verma A20241,475119,625Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90480358Verma A20241,475119,625Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90651233Liu TY2025557234,326Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90080311Backman JD2021535387,394Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90084297Backman JD2021535387,394Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90436396Zhou W2018514406,271Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90482192Verma A202436759,289Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90044205Jiang L2021322456,026A generalized linear mixed model association tool for biobank-scale data.
GCST90837487Koyama S202500Genetics and context for precision health in Greater Boston.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding1
Tier 2: splice/UTR0
Tier 3: regulatory0
Tier 4: intronic/intergenic7

MAF distribution

BucketVariants
common (>=0.05)4
low_freq (0.01-0.05)1
rare (<0.01)3
unknown0

Functional consequences

ConsequenceCount
intergenic_variant2
synonymous_variant2
intron_variant2
inframe_insertion1
unknown1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs1489117345147838808C>A,T0.008intergenic_variantSPINK1 - SCGB3A22e-17Tier 4: intronic/intergenic
rs28559727142756070C>A,G,T0.459intergenic_variantPRSS1 - PRSS25e-17Tier 4: intronic/intergenic
rs497078115440540C>A,T0.112synonymous_variantCTRC2e-15Tier 4: intronic/intergenic
rs1816494724116090374G>A,T0intron_variantEIF3KP3 - TTC39CP12e-12Tier 4: intronic/intergenic
rs5746936761253611660G>A0intron_variantATF7, ATF7-NPFF5e-12Tier 4: intronic/intergenic
rs378288612111672685T>A,C,G0.05synonymous_variantBRAP9e-12Tier 4: intronic/intergenic
rs1139939607117559591ATCT>A,ATCTTCT0.05inframe_insertionCFTR2e-11Tier 1: coding
chr5:1472152810.014e-11Tier 4: intronic/intergenic

ClinVar germline variants

4 retrieved; paginated sample, class counts are floors:

2 conflicting classifications of pathogenicity, 1 pathogenic/likely pathogenic, 1 likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
132142NM_001379610.1(SPINK1):c.194+2T>CSPINK1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
523496NM_007272.3(CTRC):c.699_703del (p.Ile234fs)CTRCLikely pathogeniccriteria provided, single submitter
219537NM_000492.4(CFTR):c.2900T>C (p.Leu967Ser)CFTRConflicting classifications of pathogenicitycriteria provided, conflicting classifications
53983NM_000492.4(CFTR):c.509G>A (p.Arg170His)CFTRConflicting classifications of pathogenicitycriteria provided, conflicting classifications

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 10 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SPINK1Orphanet:103918Tropical pancreatitis
SPINK1Orphanet:700124Autosomal recessive hereditary chronic pancreatitis
CFTROrphanet:399805Male infertility with azoospermia or oligozoospermia due to single gene mutation
CFTROrphanet:48Congenital bilateral absence of vas deferens
CFTROrphanet:498359Aquagenic palmoplantar keratoderma
CFTROrphanet:586Cystic fibrosis
CFTROrphanet:60033Idiopathic bronchiectasis
CFTROrphanet:700124Autosomal recessive hereditary chronic pancreatitis
CTRCOrphanet:103918Tropical pancreatitis
CTRCOrphanet:676Autosomal dominant hereditary chronic pancreatitis

Cohort genes → proteins

3 cohort genes, 3 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence3

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SPINK1HGNC:11244ENSG00000164266P00995Serine protease inhibitor Kazal-type 1clinvar
CFTRHGNC:1884ENSG00000001626P13569Cystic fibrosis transmembrane conductance regulatorclinvar
CTRCHGNC:2523ENSG00000162438Q99895Chymotrypsin-Cclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SPINK1Serine protease inhibitor Kazal-type 1Serine protease inhibitor which exhibits anti-trypsin activity.
CFTRCystic fibrosis transmembrane conductance regulatorEpithelial ion channel that plays an important role in the regulation of epithelial ion and water transport and fluid homeostasis.
CTRCChymotrypsin-CRegulates activation and degradation of trypsinogens and procarboxypeptidases by targeting specific cleavage sites within their zymogen precursors.

Protein-family classification

Druggable: 2 · Difficult: 0 · Unknown: 1 · 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
Transporter125.9×0.114
Protease112.2×0.120
Other/Unknown10.6×0.914

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SPINK1Other/UnknownnoProt_inh_Kazal-m, Kazal_dom, Kazal_dom_sf
CFTRTransporteryes2.7.4.3ABC_transporter-like_ATP-bd, AAA+_ATPase, CFTR/ABCC7
CTRCProteaseyes3.4.21.2Trypsin_dom, Peptidase_S1A, Peptidase_S1_PA

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
body of pancreas3
islet of Langerhans2
pancreas2
epithelial cell of pancreas1
gall bladder1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SPINK1192broadmarkerbody of pancreas, islet of Langerhans, epithelial cell of pancreas
CFTR193broadmarkerbody of pancreas, gall bladder, pancreas
CTRC162tissue_specificmarkerbody of pancreas, pancreas, islet of Langerhans

Protein interactions among cohort

Intra-cohort edges: 3.

Hub genes (top 10 by interactor count)

SymbolInteractor count
CFTR7,664
SPINK1888
CTRC714

Intra-cohort edges

ABSources
CFTRCTRCstring_interaction
CFTRSPINK1string_interaction
CTRCSPINK1string_interaction

Structural data

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

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
CFTRP1356958
SPINK1P009955
CTRCQ998951

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
Developmental Lineage of Pancreatic Acinar Cells2200.3×5e-04SPINK1, CTRC
RHO GTPases regulate CFTR trafficking11268.9×0.006CFTR
Chaperone Mediated Autophagy1165.5×0.024CFTR
Late endosomal microautophagy1108.8×0.024CFTR
Aggrephagy182.8×0.024CFTR
Developmental Lineage of Pancreatic Ductal Cells176.1×0.024CFTR
Developmental Cell Lineages174.6×0.024SPINK1
Defective CFTR causes cystic fibrosis173.2×0.024CFTR
RHOQ GTPase cycle160.4×0.026CFTR
ABC-family protein mediated transport140.5×0.034CFTR
Cargo recognition for clathrin-mediated endocytosis134.9×0.036CFTR
Clathrin-mediated endocytosis128.4×0.041CFTR
Ub-specific processing proteases117.7×0.060CFTR
Developmental Biology14.8×0.194SPINK1

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
sperm capacitation2449.4×2e-04SPINK1, CFTR
obsolete negative regulation of nitric oxide mediated signal transduction12808.7×0.004SPINK1
intracellular pH elevation11872.4×0.004CFTR
transepithelial water transport11123.5×0.004CFTR
regulation of acrosome reaction11123.5×0.004SPINK1
positive regulation of enamel mineralization11123.5×0.004CFTR
negative regulation of calcium ion import1802.5×0.004SPINK1
membrane hyperpolarization1624.1×0.005CFTR
multicellular organismal-level water homeostasis1561.7×0.005CFTR
amelogenesis1468.1×0.005CFTR
obsolete nitric oxide mediated signal transduction1432.1×0.005SPINK1
cellular response to forskolin1374.5×0.005CFTR
regulation of store-operated calcium entry1351.1×0.005SPINK1
water transport1330.4×0.005CFTR
bicarbonate transport1267.5×0.006CFTR
cholesterol transport1244.2×0.006CFTR
cholesterol biosynthetic process1140.4×0.010CFTR
cellular response to cAMP196.8×0.014CFTR
chloride transmembrane transport179.1×0.016CFTR
transmembrane transport156.2×0.020CFTR
response to endoplasmic reticulum stress155.6×0.020CFTR
establishment of localization in cell153.5×0.020CFTR
intracellular calcium ion homeostasis148.4×0.021CTRC
proteolysis111.4×0.085CTRC

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.

DrugDevelopment status
BupivacainePhase 3 (in late-stage trials)
PancrelipasePhase 3 (in late-stage trials)
TriamcinolonePhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Lipase (Pancrelipase), Pregabalin, Reparixin, Sodium Chloride, Tanezumab, Thalidomide.

Drug target analysis

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

Druggability breadth: 2 of 3 evidence-associated genes (67%) 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
CFTRIVACAFTOR

Top cohort targets by molecule count

SymbolMoleculesMax phase
CFTR144
CTRC33
SPINK100

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
IVACAFTOR4CFTR
LUMACAFTOR4CFTR
TEZACAFTOR4CFTR
ELEXACAFTOR4CFTR
GLYBURIDE4CFTR
RUTIN3CFTR
BAMOCAFTOR3CFTR
QUERCETIN3CFTR, CTRC
MILVEXIAN3CTRC
GALICAFTOR2CFTR
GENISTEIN2CFTR
ICENTICAFTOR2CFTR
NAVOCAFTOR2CFTR
RISELCAFTOR2CFTR
GLPG-27372CFTR
IODOPHTHALEIN2CTRC

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

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

SymbolAssaysType breakdown
CFTR520Binding:497, Functional:17, ADMET:5, Toxicity:1
CTRC125Binding:98, ADMET:24, Functional:2, Toxicity:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
CFTR2.7.4.3, 5.6.1.6adenylate kinase, channel-conductance-controlling ATPase
CTRC3.4.21.2chymotrypsin C

Cohort genes with high screening signal

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

SymbolChEMBL assays
CFTR520
CTRC125

Pharmacogenomics

Cohort genes with a PharmGKB record: 3; with CPIC/DPWG dosing guidelines: 1.

Cohort genes with a CPIC/DPWG dosing guideline

SymbolCPIC guidelines
CFTR1

Chemical tractability of cohort targets

16 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)
IVACAFTOR4CFTR
LUMACAFTOR4CFTR
TEZACAFTOR4CFTR
ELEXACAFTOR4CFTR
GLYBURIDE4CFTR
RUTIN3CFTR
BAMOCAFTOR3CFTR
QUERCETIN3CFTR, CTRC
MILVEXIAN3CTRC
GALICAFTOR2CFTR
GENISTEIN2CFTR
ICENTICAFTOR2CFTR
NAVOCAFTOR2CFTR
RISELCAFTOR2CFTR
GLPG-27372CFTR
IODOPHTHALEIN2CTRC

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1CFTR
BPhased (≥1) drug, not yet approved1CTRC
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug1SPINK1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
SPINK10CTRC

Clinical trials & evidence

Clinical trials

Clinical trials: 223.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified168
PHASE214
PHASE410
PHASE110
PHASE1/PHASE28
PHASE37
EARLY_PHASE15
PHASE2/PHASE31

Top trials by phase / activity

NCTPhaseStatusTitle
NCT06937294PHASE4RECRUITINGMetformin in Post Chronic Pancreatitis Diabetes Mellitus
NCT07285863PHASE4RECRUITINGA Study Of Effect Of Secretin For In Injection (Chirostim) On Pancreatic Fluid Composition In Healthy Subjects
NCT07418593PHASE4RECRUITINGMalabsorption Blood Test (MBT) to Determine Exocrine Pancreatic Function and Related Quality of Life in Chronic Pancreatitis
NCT00583479PHASE4COMPLETEDProspective Study of Celiac Block Injection: 1 vs. 2
NCT00744250PHASE4TERMINATEDIntraduodenal Aspiration Study to Assess the Bioavailability of Oral Pancrecarb® Compared to Placebo Control
NCT00956839PHASE4COMPLETEDProspective Study of Efficacy of Intra-muscular Vitamin D3 in Tropical Calcific Pancreatitis
NCT00957151PHASE4COMPLETEDEvaluation of the Digestive and Metabolic Utilisation of Dietary Protein in Patients With Chronic Pancreatitis
NCT01430234PHASE4COMPLETEDEnzyme Suppletion in Exocrine Pancreatic Dysfunction
NCT01642875PHASE4UNKNOWNEarly Oral Versus Enteral Nutrition After Pancreatoduodenectomy
NCT05069597PHASE4COMPLETEDStudy to Evaluate Symptoms of Exocrine Pancreatic Insufficiency in Adult Participants With Cystic Fibrosis or Chronic Pancreatitis Treated With Creon
NCT00319358PHASE3COMPLETEDRole of Antioxidants Supplementation in Chronic Pancreatitis
NCT00414908PHASE3COMPLETEDA Study to Investigate the Effect of Delayed Release Pancrelipase on Maldigestion in Patients With Exocrine Pancreatic Insufficiency Due to Chronic Pancreatitis and Pancreatectomy
NCT00559364PHASE3COMPLETEDSafety and Efficacy Study of Viokase® 16 for the Correction of Steatorrhea
NCT00658736PHASE3COMPLETEDEfficacy of EUS-guided Celiac Plexus Blockade in Chronic Pancreatitis
NCT00755573PHASE2/PHASE3COMPLETEDPain and Chronic Pancreatitis - Clinical End Experimental Studies
NCT00788593PHASE3COMPLETEDA Randomized, Double-Blind, Dose Response-Control, Crossover Study to Evaluate the Safety and Efficacy of Two Doses of EUR-1008 (APT-1008) in Chronic Pancreatitis (CP) Participants With Exocrine Pancreatic Insufficiency (EPI)
NCT01318590PHASE3TERMINATEDProspective Study on Endoscopic Ultrasound (EUS) Celiac Bloc Efficacy in Chronic Pancreatitis
NCT01731821PHASE3COMPLETEDNonstented Stump-closed vs Duct-to-Mucosa Pancreaticojejunostomy After Pancreaticoduodenectomy
NCT05453851PHASE1/PHASE2NOT_YET_RECRUITINGA Surgical Procedure (Total Pancreatectomy) With a Transplant Procedure (Islet Cell Autotransplantation) for the Treatment of Chronic Pancreatitis and Benign Pancreatic Tumors
NCT06426160PHASE2RECRUITINGTocilizumab for Painful Chronic Pancreatitis
NCT06729996PHASE2RECRUITINGPioglitazone Versus Empagliflozin for Chronic Pancreatitis/Recurrent Acute Pancreatitis Associated Diabetes Mellitus
NCT07171112PHASE2RECRUITINGSmoking Cessation Trial in Recurrent Acute Pancreatitis and Chronic Pancreatitis
NCT07447687PHASE1/PHASE2RECRUITINGSoy Tomato Juice to Improve Outcomes in Pancreatitis
NCT00469703PHASE2TERMINATEDSafety and Efficacy Study of Thalomid in Patients With Chronic Pancreatitis
NCT00782795PHASE2COMPLETEDChronic Pancreatitis. Effect of Pioglitazone on Endocrine Function, Exocrine Function & Structure, Pain & Life Quality
NCT01146561PHASE2TERMINATEDSafety And Efficacy Of Tanezumab In Patients With Chronic Pancreatitis
NCT01259544PHASE2COMPLETEDBreathID® Test: A Non-invasive Modality to Detect Pancreatic Exocrine Insufficiency
NCT01265875PHASE1/PHASE2COMPLETEDSecretin Infusion for Pain Due to Chronic Pancreatitis
NCT01318369PHASE2COMPLETEDEfficacy Study of Δ9-THC to Treat Chronic Abdominal Pain
NCT01551511PHASE2COMPLETEDΔ9-THC (Namisol®) in Chronic Pancreatitis Patients Suffering From Persistent Abdominal Pain
NCT02458118PHASE1/PHASE2UNKNOWNPancreatic Perfusion Using Secretin and MRI
NCT02567240PHASE1/PHASE2COMPLETEDCarbon Monoxide-Saturated Medium for Islet Isolation
NCT02693093PHASE1/PHASE2COMPLETEDA Dose Ranging Study Evaluating Efficacy and Safety of NI-03
NCT02849704PHASE2COMPLETEDFat Malabsorption in Chronic Pancreatitis
NCT02947087PHASE1/PHASE2COMPLETEDAlpha-1 Antitrypsin (AAT) Enhances Islet Autograft Survival in Patients With Chronic Pancreatitis
NCT03283566PHASE2COMPLETEDHydroxychloroquine and Metabolic Outcomes in Patients Undergoing TPAIT
NCT03481803PHASE2COMPLETEDA Phase IIa Study With Escalating Dose of MS1819-SD
NCT04207060PHASE1/PHASE2COMPLETEDTrial of Indomethacin in Chronic Pancreatitis
NCT05906615PHASE2COMPLETEDIntravenous Lidocaine for Pain Associated With Pancreatic Cancer and Chronic Pancreatitis
NCT06230120PHASE2COMPLETEDSpinal Cord Stimulation for the Treatment of Pain in Chronic Pancreatitis

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
PINAVERIUM43
SECRETIN42
TRIAMCINOLONE42
.ALPHA.1-PROTEINASE INHIBITOR HUMAN41
DIAZEPAM41
DRONABINOL41
ESOMEPRAZOLE41
INDOMETHACIN41
LACOSAMIDE41
METFORMIN41
OMEPRAZOLE41
PANCRELIPASE41
PARICALCITOL41
SECRETIN SYNTHETIC HUMAN41
PANCREATIN33
BLOOD, WHOLE31
TANEZUMAB31
MS-181921
CHEMBL430338301