Lymphoproliferative syndrome

disease
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Also known as lymphoproliferative disorder

Summary

Lymphoproliferative syndrome (MONDO:0016537) is a disease (an umbrella term covering 8 Mondo subtypes) caused by ITK (GenCC Definitive), with 3 cohort genes and 105 clinical trials. Top therapeutic interventions include epoetin alfa, amitriptyline, and tabelecleucel.

At a glance

  • Causal gene: ITK (GenCC Definitive)
  • Umbrella term: 8 Mondo subtypes
  • Cohort genes: 3
  • ClinVar variants: 1
  • Clinical trials: 105

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namelymphoproliferative syndrome
Mondo IDMONDO:0016537
MeSHD008232
OMIM308240
Orphanet238510
DOIDDOID:0060704
NCITC9308
SNOMED CT277466009
UMLSC0024314
MedGen6162
GARD0020633
Is cancer (heuristic)no

Also known as: lymphoproliferative disorder · lymphoproliferative syndrome

Data availability: 1 ClinVar variant · 2 GenCC gene-disease records.

Disease family

An umbrella term covering 8 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › immune system disorderinborn error of immunitylymphoproliferative syndrome

Related subtypes (40): B cell deficiency, complement deficiency, phagocyte bactericidal dysfunction, trichohepatoenteric syndrome, hepatic veno-occlusive disease-immunodeficiency syndrome, immunodeficiency with defective T-cell response to interleukin 1, Say-Barber-Miller syndrome, familial isolated congenital asplenia, X-linked immunoneurologic disorder, ectodermal dysplasia and immune deficiency, immunodeficiency 33, immunodeficiency 47, combined immunodeficiency due to moesin deficiency, immunodeficiency, X-linked, with deficiency of 115,000 Dalton surface glycoprotein, properdin deficiency, X-linked, combined immunodeficiency with faciooculoskeletal anomalies, recurrent infections associated with rare immunoglobulin isotypes deficiency, immunodeficiency 28, autosomal recessive primary immunodeficiency with defective spontaneous natural killer cell cytotoxicity, immunodeficiency 37, immunodeficiency 39, BENTA disease, primary immunodeficiency with post-measles-mumps-rubella vaccine viral infection, immunodeficiency 49, chronic mucocutaneous candidiasis, hereditary hemophagocytic lymphohistiocytosis, immunoglobulin heavy chain deficiency, immuno-osseous dysplasia, IL10-related early-onset inflammatory bowel disease, T-cell immunodeficiency with epidermodysplasia verruciformis, Aicardi-Goutieres syndrome, immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections-lymphopenia syndrome, inflammatory bowel disease-recurrent sinopulmonary infections syndrome, A20 haploinsufficiency, NK cell deficiency, T cell and NK cell immunodeficiency, dendritic cell deficiency, immunodysregulation with variable immunodeficiency and autoimmunity, immune dysregulation with immunodeficiency due to AIOLOS haploinsufficiency, STAT5 haploinsufficiency

Subtypes (8): X-linked lymphoproliferative syndrome, Dianzani autoimmune lymphoproliferative disease, lymphoproliferative syndrome 1, lymphoproliferative syndrome 2, Castleman disease, autoimmune lymphoproliferative syndrome, severe combined immunodeficiency due to CD70 deficiency, atypical lymphoproliferative disorder

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

1 retrieved; paginated sample, class counts are floors:

1 conflicting classifications of pathogenicity

ClinVarVariant (HGVS)GeneClassificationReview
871639NM_002351.5(SH2D1A):c.164G>A (p.Arg55Gln)SH2D1AConflicting classifications of pathogenicitycriteria provided, conflicting classifications

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 8 · Orphanet: 2 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
ITKDefinitiveAutosomal recessivelymphoproliferative syndrome 15
NFATC2ModerateAutosomal recessivelymphoproliferative syndrome3

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
ITKOrphanet:538963Combined immunodeficiency due to ITK deficiency
SH2D1AOrphanet:538931X-linked lymphoproliferative disease due to SAP deficiency

Cohort genes → proteins

3 cohort genes, 3 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence3

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
ITKHGNC:6171ENSG00000113263Q08881Tyrosine-protein kinase ITK/TSKgencc
NFATC2HGNC:7776ENSG00000101096Q13469Nuclear factor of activated T-cells, cytoplasmic 2gencc
SH2D1AHGNC:10820ENSG00000183918O60880SH2 domain-containing protein 1Aclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
ITKTyrosine-protein kinase ITK/TSKTyrosine kinase that plays an essential role in regulation of the adaptive immune response.
NFATC2Nuclear factor of activated T-cells, cytoplasmic 2Plays a role in the inducible expression of cytokine genes in T-cells, especially in the induction of the IL-2, IL-3, IL-4, TNF or GM-CSF.
SH2D1ASH2 domain-containing protein 1ACytoplasmic adapter regulating receptors of the signaling lymphocytic activation molecule (SLAM) family such as SLAMF1, CD244, LY9, CD84, SLAMF6 and SLAMF7.

Protein-family classification

Druggable: 1 · Difficult: 2 · Unknown: 0 · Druggable fraction: 0.33

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
Kinase19.2×0.246
Scaffold/PPI15.8×0.246
Transcription factor12.8×0.321

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
ITKKinaseyes2.7.10.2Prot_kinase_dom, SH2, Ser-Thr/Tyr_kinase_cat_dom
NFATC2Transcription factornoIPT_dom, NFAT, p53-like_TF_DNA-bd_sf
SH2D1AScaffold/PPInoSH2, SH2_prot_1A, SH2D1A_SH2

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
granulocyte2
thymus2
blood1
layer of synovial tissue1
synovial joint1
vena cava1
lymph node1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
ITK198broadmarkergranulocyte, thymus, blood
NFATC2230ubiquitousmarkervena cava, synovial joint, layer of synovial tissue
SH2D1A170broadmarkerthymus, lymph node, granulocyte

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
ITK2,670
NFATC22,524
SH2D1A1,548

Structural data

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

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
ITKQ0888137
NFATC2Q1346912
SH2D1AO608806

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 12. 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
FCERI mediated Ca+2 mobilization2237.9×3e-04ITK, NFATC2
Calcineurin activates NFAT1423.0×0.008NFATC2
RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs)1380.7×0.008NFATC2
CLEC7A (Dectin-1) induces NFAT activation1346.1×0.008NFATC2
Adaptive Immune System219.9×0.008SH2D1A, ITK
TCR signaling1165.5×0.012ITK
Generation of second messenger molecules1115.3×0.015ITK
Fc epsilon receptor (FCERI) signaling190.6×0.016ITK
Immune System28.6×0.023SH2D1A, ITK
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)148.8×0.024NFATC2
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell129.1×0.037SH2D1A
Innate Immune System18.5×0.113ITK

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
B cell receptor signaling pathway2267.5×5e-04ITK, NFATC2
cellular defense response2212.0×5e-04SH2D1A, ITK
NK T cell differentiation11404.3×0.004ITK
lncRNA transcription11404.3×0.004NFATC2
myotube cell development11123.5×0.004NFATC2
negative regulation of vascular associated smooth muscle cell differentiation11123.5×0.004NFATC2
adaptive immune response256.2×0.004SH2D1A, ITK
gamma-delta T cell activation1702.2×0.006ITK
positive regulation of myoblast fusion1351.1×0.011NFATC2
calcineurin-NFAT signaling cascade1280.9×0.012NFATC2
natural killer cell activation1193.7×0.015SH2D1A
positive regulation of natural killer cell mediated cytotoxicity1187.2×0.015SH2D1A
regulation of immune response1165.2×0.016SH2D1A
natural killer cell mediated cytotoxicity1144.0×0.017SH2D1A
negative regulation of T cell receptor signaling pathway1122.1×0.018SH2D1A
positive regulation of B cell proliferation1114.6×0.018NFATC2
humoral immune response193.6×0.020SH2D1A
positive regulation of cytokine production190.6×0.020ITK
T cell activation186.4×0.020ITK
cartilage development183.8×0.020NFATC2
cellular response to calcium ion166.9×0.024NFATC2
T cell receptor signaling pathway150.6×0.030ITK
transcription by RNA polymerase II123.5×0.058NFATC2
cell-cell signaling123.2×0.058SH2D1A
response to xenobiotic stimulus123.0×0.058NFATC2
cell migration120.5×0.063NFATC2
DNA damage response117.8×0.069NFATC2
positive regulation of gene expression112.9×0.090NFATC2
intracellular signal transduction112.7×0.090ITK
regulation of DNA-templated transcription110.5×0.104NFATC2

Therapeutics

Drugs indicated for this disease

2 approved, 1 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
Idecabtagene VicleucelApproved (phase 4)
TabelecleucelApproved (phase 4)
MAS-825Phase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Bortezomib, Leflunomide, Methylprednisolone, Prednisone, Rituximab.

Drug target analysis

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

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
ITKFEDRATINIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
ITK394
NFATC200
SH2D1A00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
FEDRATINIB4ITK
AXITINIB4ITK
IBRUTINIB4ITK
BOSUTINIB4ITK
ACALABRUTINIB4ITK
ZANUBRUTINIB4ITK
RITLECITINIB4ITK
NINTEDANIB4ITK
SUNITINIB4ITK
DASATINIB4ITK
QUIZARTINIB4ITK
CRIZOTINIB4ITK
CANERTINIB3ITK
EVOBRUTINIB3ITK
REMIBRUTINIB3ITK
DOVITINIB3ITK
LESTAURTINIB3ITK
FORETINIB2ITK
TANDUTINIB2ITK
SU-0148132ITK
REBASTINIB2ITK
CENISERTIB2ITK
ILORASERTIB2ITK
OSI-6322ITK
SPEBRUTINIB2ITK
BMS-9861422ITK
BMS-9193732ITK
ATUZABRUTINIB2ITK
CERDULATINIB2ITK
BRANEBRUTINIB2ITK

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
ITK563Binding:547, Functional:10, ADMET:6
SH2D1A5Binding:5

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
ITK2.7.10.2non-specific protein-tyrosine kinase

Cohort genes with high screening signal

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

SymbolChEMBL assays
ITK563

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

28 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)
FEDRATINIB4ITK
AXITINIB4ITK
BOSUTINIB4ITK
ZANUBRUTINIB4ITK
RITLECITINIB4ITK
NINTEDANIB4ITK
SUNITINIB4ITK
DASATINIB4ITK
QUIZARTINIB4ITK
CRIZOTINIB4ITK
CANERTINIB3ITK
EVOBRUTINIB3ITK
REMIBRUTINIB3ITK
DOVITINIB3ITK
LESTAURTINIB3ITK
FORETINIB2ITK
TANDUTINIB2ITK
SU-0148132ITK
REBASTINIB2ITK
CENISERTIB2ITK
ILORASERTIB2ITK
OSI-6322ITK
SPEBRUTINIB2ITK
BMS-9861422ITK
BMS-9193732ITK
ATUZABRUTINIB2ITK
CERDULATINIB2ITK
BRANEBRUTINIB2ITK

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1ITK
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug2NFATC2, SH2D1A

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
NFATC20
SH2D1A5

Clinical trials & evidence

Clinical trials

Clinical trials: 105.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified31
PHASE126
PHASE225
PHASE311
PHASE1/PHASE27
PHASE2/PHASE34
EARLY_PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT03394365PHASE3RECRUITINGA Phase 3 Study of Tabelecleucel for Participants With Epstein-Barr Virus-Associated Post-Transplant Lymphoproliferative Disease After Failure With Rituximab or Rituximab and Chemotherapy
NCT05770037PHASE2/PHASE3RECRUITINGDETERMINE Trial Treatment Arm 01: Alectinib in Adult, Paediatric and Teenage/Young Adult Patients With ALK Positive Cancers
NCT05770102PHASE2/PHASE3RECRUITINGDETERMINE Trial Treatment Arm 02: Atezolizumab in Adult, Paediatric and Teenage/Young Adult Patients With Cancers With High Tumour Mutational Burden (TMB) or Microsatellite Instability-high (MSI-high) or Proven Constitutional Mismatch Repair Deficiency (CMMRD) Disposition
NCT05770544PHASE2/PHASE3RECRUITINGDETERMINE Trial Treatment Arm 03: Entrectinib in Adult, Paediatric and Teenage/Young Adult Patients With ROS1 Gene Fusion-Positive Cancers.
NCT07440290PHASE2/PHASE3NOT_YET_RECRUITINGDETERMINE Trial Treatment Arm 07: Dabrafenib in Combination With Trametinib in Adult, Paediatric and Teenage/Young Adult Patients With BRAF V600 Mutation-Positive Cancers.
NCT00033475PHASE3COMPLETEDReduced Immunosuppressive Therapy With or Without Donor White Blood Cells in Treating Patients With Lymphoproliferative Disease After Organ Transplantation
NCT00053053PHASE3COMPLETEDComparison of Nutritional Supplements in Preventing Weight Loss in Patients With Cancer
NCT00058331PHASE3COMPLETEDEpoetin Alfa in Treating Anemia in Patients With Solid Tumors
NCT00070382PHASE3COMPLETEDDarbepoetin Alfa Compared With Epoetin Alfa in Treating Anemia in Patients Receiving Chemotherapy for Cancer
NCT00516503PHASE3COMPLETEDBaclofen-Amitriptyline Hydrochloride-Ketamine Gel in Treating Peripheral Neuropathy Caused by Chemotherapy in Patients With Cancer
NCT00661999PHASE3COMPLETEDDarbepoetin Alfa With or Without Iron in Treating Anemia Caused By Chemotherapy in Patients With Cancer
NCT00666211PHASE3COMPLETEDOpioid Titration Order Sheet or Standard Care in Treating Patients With Cancer Pain
NCT00719563PHASE3COMPLETEDAmerican Ginseng in Treating Patients With Fatigue Caused by Cancer
NCT00750009PHASE3COMPLETEDPersonalized Information or Basic Information in Helping Patients Make Decisions About Participating in a Clinical Trial
NCT05431179PHASE3WITHDRAWNA Study of Zilovertamab and Ibrutinib in Patients With Relapsed or Refractory Mantle Cell Lymphoma
NCT00092222PHASE2ACTIVE_NOT_RECRUITINGVirotherapy and Natural History Study of KHSV-Associated Multricentric Castleman s Disease With Correlates of Disease Activity
NCT02579967PHASE2RECRUITINGPilot Trial of Allogeneic Blood or Marrow Transplantation for Primary Immunodeficiencies
NCT02690545PHASE1/PHASE2ACTIVE_NOT_RECRUITINGStudy of CD30 CAR for Relapsed/Refractory CD30+ HL and CD30+ NHL
NCT02861417PHASE2ACTIVE_NOT_RECRUITINGBusulfan, Fludarabine Phosphate, and Post-Transplant Cyclophosphamide in Treating Patients With Blood Cancer Undergoing Donor Stem Cell Transplant
NCT03258567PHASE2RECRUITINGNivolumab in Epstein-Barr Virus (EBV)-Positive Lymphoproliferative Disorders and EBV-Positive Non-HodgkinLymphomas
NCT03663933PHASE2ACTIVE_NOT_RECRUITINGAllogeneic Hematopoietic Cell Transplantation for Disorders of T-cell Proliferation and/or Dysregulation
NCT03922724PHASE2RECRUITINGAllogeneic Hematopoietic Cell Transplantation for Peripheral T Cell Lymphoma
NCT04339777PHASE2RECRUITINGAllogeneic Hematopoietic Stem Cell Transplant for Patients With Inborn Errors of Immunity
NCT04554914PHASE2ACTIVE_NOT_RECRUITINGA Study to Evaluate Tabelecleucel in Participants With Epstein Barr Virus (EBV) Associated Diseases
NCT04858256PHASE2RECRUITINGPacritinib in Relapsed/Refractory T-cell Lymphoproliferative Neoplasms
NCT04883437PHASE2RECRUITINGAcalabrutinib and Obinutuzumab for the Treatment of Previously Untreated Follicular Lymphoma or Other Indolent Non-Hodgkin Lymphomas
NCT00001379PHASE2COMPLETEDTreatment and Natural History Study of Lymphomatoid Granulomatosis
NCT00001438PHASE2COMPLETEDA Pilot Study of the Combination of Retinoic Acid and Interferon-Alpha2a for the Treatment of Lymphoproliferative Disorders in Children With Immunodeficiency Syndromes
NCT00048412PHASE1/PHASE2COMPLETEDStem Cell Transplant for Patients With Blood Malignancy Using Donors and Less Toxic Chemotherapy With CAMPATH 1H
NCT00066469PHASE2COMPLETEDCyclophosphamide, Rituximab, and Either Prednisone or Methylprednisolone in Treating Patients With Lymphoproliferative Disease After Solid Organ Transplantation
NCT00255749PHASE2COMPLETEDEpoetin Alfa in Treating Patients With Anemia Who Are Undergoing Chemotherapy for Cancer
NCT00387530PHASE2WITHDRAWNPhenylbutyrate and Valganciclovir in Treating Patients With Relapsed or Refractory Epstein-Barr Virus-Positive Cancer
NCT00416624PHASE2COMPLETEDEpoetin Alfa or Darbepoetin Alfa in Treating Patients With Anemia Caused by Chemotherapy
NCT00436618PHASE2COMPLETEDEverolimus in Treating Patients With Lymphoma That Has Relapsed or Not Responded to Previous Treatment
NCT00579111PHASE1/PHASE2TERMINATEDReduced Intensity Preparative Regimen Followed by Stem Cell Transplant (FAB)
NCT00621036PHASE2WITHDRAWNVaccine Therapy and GM-CSF in Treating Patients With CNS Lymphoma
NCT00823524PHASE1/PHASE2COMPLETEDDonor Natural Killer Cells After Donor Stem Cell Transplant in Treating Patients With Advanced Cancer
NCT00869323PHASE2TERMINATEDBortezomib and Rituximab in Treating Patients With Post-Transplant Lymphoproliferative Disorders
NCT00992732PHASE2TERMINATEDStudy of HQK-1004 and Valganciclovir to Treat Epstein-Barr Virus (EBV) - Positive Lymphoid Malignancies or Lymphoproliferative Disorders
NCT01101412PHASE1/PHASE2WITHDRAWNAntimicrobial Solution or Saline Solution in Maintaining Catheter Patency and Preventing Catheter-Related Blood Infections in Patients With Malignancies

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
EPOETIN ALFA44
AMITRIPTYLINE43
TABELECLEUCEL43
VALGANCICLOVIR43
DARBEPOETIN ALFA42
PACRITINIB42
PHENYLBUTANOIC ACID42
ACALABRUTINIB41
ALCOHOL41
ALECTINIB41
BACLOFEN41
DABRAFENIB41
DAPSONE41
EDETATE CALCIUM DISODIUM MONOHYDRATE41
ENTRECTINIB41
EPOETIN BETA41
FENTANYL CITRATE41
FERROUS SULFATE41
FLUDEOXYGLUCOSE F 1841
GANCICLOVIR41
IBRUTINIB41
IMETELSTAT SODIUM41
LEFLUNOMIDE41
METHADONE HYDROCHLORIDE41
MORPHINE SULFATE41
ONDANSETRON HYDROCHLORIDE41
OXYCODONE HYDROCHLORIDE41
PENTOSTATIN41
PLERIXAFOR41
PYRIMETHAMINE41