Cervical intraepithelial neoplasia grade 2/3

disease
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Also known as CIN 2/3

Summary

Cervical intraepithelial neoplasia grade 2/3 (MONDO:0006137) is a disease with 6 cohort genes (8 GWAS associations across 2 studies) and 29 clinical trials. The dominant Reactome pathway is Interferon gamma signaling (3 cohort genes). Top therapeutic interventions include artesunate and celecoxib.

At a glance

  • Cohort genes: 6
  • GWAS associations: 8
  • Clinical trials: 29

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namecervical intraepithelial neoplasia grade 2/3
Mondo IDMONDO:0006137
EFOEFO:1000166
NCITC94676
UMLSC2986622
MedGen458848
GARD0024305
Is cancer (heuristic)no

Also known as: CIN 2/3

Data availability: 8 GWAS associations (2 studies).

Disease family

Classification path: disease › human disease › disease by body system or component › reproductive system disorderdysplasia of cervixcervical intraepithelial neoplasiacervical intraepithelial neoplasia grade 2/3

Related subtypes (1): cervical squamous intraepithelial neoplasia

Genetics & variants

GWAS landscape

8 GWAS associations across 2 studies. Top hits map to 5 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs92720503e-28HLA-DQA1?1.27
rs559860916e-22HLA-DQA1 - HLA-DQB1?0.66
rs69384532e-17MICA?0.79
rs92722455e-12HLA-DQA1?1.44
rs101754621e-09PAX8, PAX8-AS1?0.87
rs270693e-09CLPTM1L - LINC01511?0.88
rs1504061454e-08SILC1 - LINC01247?2.37
rs92661832e-06HLA-B?0.73

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST012476Bowden SJ20214,005145,545Genetic variation in cervical preinvasive and invasive disease: a genome-wide association study.
GCST012475Bowden SJ2021764145,545Genetic variation in cervical preinvasive and invasive disease: a genome-wide association study.

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)7
low_freq (0.01-0.05)0
rare (<0.01)0
unknown1

Functional consequences

ConsequenceCount
intergenic_variant4
intron_variant2
non_coding_transcript_exon_variant1
missense_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs9272050632631294G>A0.05intergenic_variantHLA-DQA13e-28Tier 4: intronic/intergenic
rs55986091632655936G>A0.05intergenic_variantHLA-DQA1 - HLA-DQB16e-22Tier 4: intronic/intergenic
rs6938453631410016T>A0.05intron_variantMICA2e-17Tier 4: intronic/intergenic
rs9272245632635095C>G,T0.05intergenic_variantHLA-DQA15e-12Tier 4: intronic/intergenic
rs101754622113230915G>A,T0.05intron_variantPAX8, PAX8-AS11e-09Tier 4: intronic/intergenic
rs2706951347013C>T0.05non_coding_transcript_exon_variantCLPTM1L - LINC015113e-09Tier 4: intronic/intergenic
rs15040614526231058G>Aintergenic_variantSILC1 - LINC012474e-08Tier 4: intronic/intergenic
rs9266183631356870T>A,C0.05missense_variantHLA-B2e-06Tier 1: coding

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 17 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
HLA-BOrphanet:117Behçet disease
HLA-BOrphanet:275798Pulmonary arterial hypertension associated with connective tissue disease
HLA-BOrphanet:29207Reactive arthritis
HLA-BOrphanet:3287Takayasu arteritis
HLA-BOrphanet:36426Stevens-Johnson syndrome
HLA-BOrphanet:397Giant cell arteritis
HLA-DQA1Orphanet:391490Adult-onset myasthenia gravis
HLA-DQA1Orphanet:930Idiopathic achalasia
HLA-DQB1Orphanet:2073Narcolepsy type 1
HLA-DQB1Orphanet:477738Pediatric multiple sclerosis
HLA-DQB1Orphanet:703Bullous pemphigoid
HLA-DQB1Orphanet:83465Narcolepsy type 2
HLA-DQB1Orphanet:930Idiopathic achalasia
PAX8Orphanet:146Differentiated thyroid carcinoma
PAX8Orphanet:95712Thyroid ectopia
PAX8Orphanet:95713Athyreosis
PAX8Orphanet:95720Thyroid hypoplasia

Cohort genes → proteins

6 cohort genes, 6 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only6

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
CLPTM1LHGNC:24308ENSG00000049656Q96KA5Lipid scramblase CLPTM1Lgwas
HLA-BHGNC:4932ENSG00000234745P01889HLA class I histocompatibility antigen, B alpha chaingwas
HLA-DQA1HGNC:4942ENSG00000196735P01909HLA class II histocompatibility antigen, DQ alpha 1 chaingwas
HLA-DQB1HGNC:4944ENSG00000179344P01920HLA class II histocompatibility antigen, DQ beta 1 chaingwas
MICAHGNC:7090ENSG00000204520Q29983MHC class I polypeptide-related sequence Agwas
PAX8HGNC:8622ENSG00000125618Q06710Paired box protein Pax-8gwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
CLPTM1LLipid scramblase CLPTM1LScramblase that mediates the translocation of glucosaminylphosphatidylinositol (alpha-D-GlcN-(1-6)-(1,2-diacyl-sn-glycero-3-phospho)-1D-myo-inositol, GlcN-PI) across the endoplasmic reticulum (ER) membrane, from the cytosolic leaflet to th…
HLA-BHLA class I histocompatibility antigen, B alpha chainAntigen-presenting major histocompatibility complex class I (MHCI) molecule.
HLA-DQA1HLA class II histocompatibility antigen, DQ alpha 1 chainBinds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC) and presents them on the cell surface for recognition by the CD4 T-cells.
HLA-DQB1HLA class II histocompatibility antigen, DQ beta 1 chainBinds peptides derived from antigens that access the endocytic route of antigen presenting cells (APC) and presents them on the cell surface for recognition by the CD4 T-cells.
MICAMHC class I polypeptide-related sequence AWidely expressed membrane-bound protein which acts as a ligand to stimulate an activating receptor KLRK1/NKG2D, expressed on the surface of essentially all human natural killer (NK), gammadelta T and CD8 alphabeta T-cells.
PAX8Paired box protein Pax-8Transcription factor for the thyroid-specific expression of the genes exclusively expressed in the thyroid cell type, maintaining the functional differentiation of such cells.

Protein-family classification

Druggable: 4 · Difficult: 1 · 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
Antibody/Immunoglobulin419.5×6e-05
Transcription factor11.4×0.809
Other/Unknown10.3×0.993

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
CLPTM1LOther/UnknownnoCLPTM1
HLA-BAntibody/ImmunoglobulinyesMHC_I_a_a1/a2, Ig/MHC_CS, Ig_C1-set
HLA-DQA1Antibody/ImmunoglobulinyesMHC_II_a_N, Ig/MHC_CS, Ig_C1-set
HLA-DQB1Antibody/ImmunoglobulinyesMHC_II_b_N, Ig/MHC_CS, Ig_C1-set
MICAAntibody/ImmunoglobulinyesIg_C1-set, Ig-like_dom, MHC_I-like_Ag-recog
PAX8Transcription factornoPaired_dom, Homeodomain-like_sf, Pax2_C

Expression context

Cohort genes with no expression data: 0.

6 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)6
unknown0

Top tissues across cohort

TissueCohort genes
right lobe of thyroid gland2
spleen2
ileal mucosa1
kidney epithelium1
blood1
granulocyte1
gall bladder1
monocyte1
rectum1
right lung1
upper lobe of left lung1
descending thoracic aorta1
left ovary1
popliteal artery1
left lobe of thyroid gland1
thyroid gland1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
CLPTM1L255ubiquitousmarkerileal mucosa, kidney epithelium, right lobe of thyroid gland
HLA-B134ubiquitousmarkerblood, spleen, granulocyte
HLA-DQA1244broadmarkergall bladder, rectum, monocyte
HLA-DQB1268broadmarkerright lung, spleen, upper lobe of left lung
MICA134ubiquitousmarkerdescending thoracic aorta, left ovary, popliteal artery
PAX8242ubiquitousmarkerright lobe of thyroid gland, left lobe of thyroid gland, thyroid gland

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
HLA-B3,209
PAX81,994
CLPTM1L1,606
MICA214
HLA-DQA1196
HLA-DQB1128

Intra-cohort edges

ABSources
HLA-DQA1HLA-DQB1biogrid_interaction, intact

Structural data

PDB: 5 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
HLA-BP01889237
HLA-DQA1P0190928
HLA-DQB1P0192010
MICAQ2998310
PAX8Q067101

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
CLPTM1LQ96KA578.54

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 17. Enrichment computed across 6 evidence-associated genes (4 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 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Interferon gamma signaling394.1×3e-05HLA-B, HLA-DQA1, HLA-DQB1
Formation of intermediate mesoderm1356.9×0.018PAX8
Endosomal/Vacuolar pathway1259.6×0.018HLA-B
Translocation of ZAP-70 to Immunological synapse1158.6×0.018HLA-DQA1
Formation of the nephric duct1158.6×0.018PAX8
Phosphorylation of CD3 and TCR zeta chains1135.9×0.018HLA-DQA1
Co-inhibition by PD-11129.8×0.018HLA-DQA1
DAP12 interactions1119.0×0.018HLA-B
Antigen Presentation: Folding, assembly and peptide loading of class I MHC198.5×0.019HLA-B
Generation of second messenger molecules186.5×0.020HLA-DQA1
Interferon alpha/beta signaling138.1×0.040HLA-B
ER-Phagosome pathway132.4×0.040HLA-B
Downstream TCR signaling132.1×0.040HLA-DQA1
MHC class II antigen presentation122.3×0.048HLA-DQA1
SARS-CoV-2 activates/modulates innate and adaptive immune responses122.3×0.048HLA-B
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell121.8×0.048HLA-B
Neutrophil degranulation15.8×0.162HLA-B

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
immune response431.4×2e-04HLA-B, HLA-DQA1, HLA-DQB1, MICA
peptide antigen assembly with MHC class II protein complex2351.1×4e-04HLA-DQA1, HLA-DQB1
adaptive immune response342.1×7e-04HLA-B, HLA-DQA1, HLA-DQB1
antigen processing and presentation of exogenous peptide antigen via MHC class II2181.2×8e-04HLA-DQA1, HLA-DQB1
positive regulation of immune response2160.5×8e-04HLA-DQA1, HLA-DQB1
positive regulation of T cell activation2147.8×8e-04HLA-DQA1, HLA-DQB1
regulation of thyroid-stimulating hormone secretion12808.7×0.003PAX8
pronephric field specification11404.3×0.004PAX8
metanephric comma-shaped body morphogenesis11404.3×0.004PAX8
obsolete negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis11404.3×0.004PAX8
obsolete negative regulation of apoptotic process involved in metanephric collecting duct development11404.3×0.004PAX8
obsolete negative regulation of apoptotic process involved in metanephric nephron tubule development11404.3×0.004PAX8
positive regulation of metanephric DCT cell differentiation11404.3×0.004PAX8
immune response to tumor cell1936.2×0.005MICA
negative regulation of mesenchymal cell apoptotic process involved in metanephros development1936.2×0.005PAX8
regulation of dendritic cell differentiation1936.2×0.005HLA-B
regulation of T cell anergy1702.2×0.005HLA-B
regulation of interleukin-12 production1702.2×0.005HLA-B
metanephric distal convoluted tubule development1702.2×0.005PAX8
metanephric S-shaped body morphogenesis1702.2×0.005PAX8
positive regulation of thyroid hormone generation1702.2×0.005PAX8
metanephric epithelium development1561.7×0.005PAX8
metanephric nephron tubule formation1561.7×0.005PAX8
regulation of metanephric nephron tubule epithelial cell differentiation1561.7×0.005PAX8
protection from natural killer cell mediated cytotoxicity1468.1×0.005HLA-B
cellular response to gonadotropin stimulus1468.1×0.005PAX8
otic vesicle development1468.1×0.005PAX8
positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis1468.1×0.005PAX8
pronephros development1401.2×0.006PAX8
mesenchymal to epithelial transition involved in metanephros morphogenesis1351.1×0.006PAX8

Therapeutics

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 1 · Phased (≥1): 1 · Undrugged: 5

Druggability breadth: 4 of 6 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
PAX8SORAFENIB TOSYLATE

Top cohort targets by molecule count

SymbolMoleculesMax phase
PAX8144
CLPTM1L00
HLA-B00
HLA-DQA100
HLA-DQB100
MICA00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
SORAFENIB TOSYLATE4PAX8
MITOXANTRONE HYDROCHLORIDE4PAX8
TEGASEROD MALEATE4PAX8
DAUNORUBICIN HYDROCHLORIDE4PAX8
DIGOXIN4PAX8
DOXORUBICIN HYDROCHLORIDE4PAX8
HEXACHLOROPHENE4PAX8
THIOGUANINE4PAX8
CHLORHEXIDINE4PAX8
VORINOSTAT4PAX8
ENPIROLINE2PAX8
PINAFIDE2PAX8
LANATOSIDE C2PAX8
IODOQUINOL2PAX8

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

SymbolAssaysType breakdown
PAX83Functional:3
HLA-DQA12Binding:2
CLPTM1L1Binding:1
HLA-B1Binding:1
MICA1Binding:1

Pharmacogenomics

Cohort genes with a PharmGKB record: 6; with CPIC/DPWG dosing guidelines: 1.

Cohort genes with a CPIC/DPWG dosing guideline

SymbolCPIC guidelines
HLA-B1

Chemical tractability of cohort targets

14 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)
SORAFENIB TOSYLATE4PAX8
MITOXANTRONE HYDROCHLORIDE4PAX8
TEGASEROD MALEATE4PAX8
DAUNORUBICIN HYDROCHLORIDE4PAX8
DIGOXIN4PAX8
DOXORUBICIN HYDROCHLORIDE4PAX8
HEXACHLOROPHENE4PAX8
THIOGUANINE4PAX8
CHLORHEXIDINE4PAX8
VORINOSTAT4PAX8
ENPIROLINE2PAX8
PINAFIDE2PAX8
LANATOSIDE C2PAX8
IODOQUINOL2PAX8

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1PAX8
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug4HLA-B, HLA-DQA1, HLA-DQB1, MICA
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug1CLPTM1L

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
CLPTM1L1
HLA-B1
HLA-DQA12
HLA-DQB10
MICA1

Clinical trials & evidence

Clinical trials

Clinical trials: 29.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified15
PHASE26
PHASE13
PHASE32
PHASE41
PHASE1/PHASE21
EARLY_PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT04910802PHASE4RECRUITINGConcomitant HPV Vaccination and HPV Screening HPV Infection and Cervical Cancer in Sweden
NCT03366493PHASE3UNKNOWNThe Study of Folate Receptor-Mediated Staining Solution (FRD™) In Cervical Lesion Detection
NCT04484415PHASE3UNKNOWNEfficacy and Safety of Cevira® in Patients With Cervical Histologic High-grade Squamous Intraepithelial Lesions (HSIL)
NCT04098744PHASE2RECRUITINGArtesunate Vaginal Inserts for the Treatment of Cervical Intraepithelial Neoplasia (CIN2/3)
NCT06273553PHASE1/PHASE2NOT_YET_RECRUITINGA Study in Subjects With Human Papillomavirus 16 or 18 Associated Cervical Intraepithelial Neoplasia Grade 2 or 3
NCT07095478PHASE2NOT_YET_RECRUITINGSafety and Efficacy of Oral Artesunate for Pre-cervical Cancer
NCT07454915PHASE2RECRUITINGPVX4 for the Treatment of Human Papilloma Virus (HPV)16+ Cervical Dysplasia
NCT07545746PHASE2NOT_YET_RECRUITINGAdjuvant 5-Fluorouracil Following Thermal Ablation to Improve HPV Treatment Outcomes in Women With HIV in Kenya
NCT00081263PHASE2COMPLETEDCelecoxib in Treating Patients With Cervical Intraepithelial Neoplasia
NCT03274206PHASE2UNKNOWNA Trial to Evaluate the Efficacy and Safety of BLS-ILB-E710c in Patients With Cervical Intraepithelial Neoplasia 2/3 (CIN2/3)
NCT02354534PHASE1COMPLETEDIntravaginal Artesunate for the Treatment of HPV+ High Grade Cervical Intraepithelial Neoplasia (CIN2/3)
NCT03141463PHASE1COMPLETEDVvax001 Cancer Vaccine in (Pre) Malignant Cervical Lesions
NCT05362955PHASE1COMPLETED5-fluorouracil Following Cervical Intraepithelial Neoplasia Treatment Among HIV-positive Women in East Africa
NCT03196180EARLY_PHASE1COMPLETEDTopical Fluorouracil and Imiquimod in Treating Patients With High-Grade Cervical Intraepithelial Neoplasia
NCT02149030Not specifiedACTIVE_NOT_RECRUITINGEffectiveness of Cervical Screening in HPV Vaccinated Women
NCT03064087Not specifiedACTIVE_NOT_RECRUITINGValidation of Human Papillomavirus Assays and Collection Devices for Self-samples and Urine Samples
NCT04755517Not specifiedENROLLING_BY_INVITATIONEffectiveness of Cervical Screening in Unvaccinated, Herd Effect Protected Women (HPV400)
NCT05405270Not specifiedRECRUITINGPredicting Response In Cervical Intraepithelial Neoplasia to Topical Imiquimod Treatment
NCT06326294Not specifiedRECRUITINGAssessment of the Effectiveness of TA Versus LEEP for Cervical Cancer Risk Reduction in WLHIV in Mozambique
NCT07606677Not specifiedNOT_YET_RECRUITINGPeripheral Blood CyTOF Immune Model for Cervical Lesion Detection in HPV16/18+ Women
NCT01550783Not specifiedCOMPLETEDHome-Based or Clinic-Based Human Papillomavirus (HPV) Screening
NCT02067468Not specifiedCOMPLETEDOptimal Strategy for the Management of ASCUS Cytology in Health Care Services of Medellin, Colombia
NCT02811367Not specifiedCOMPLETEDThe HPV Self-test as a Test of Cure in Madagascar
NCT04191967Not specifiedCOMPLETEDThermocoagulation for Treatment of Precancerous Cervical Lesions
NCT04312737Not specifiedCOMPLETEDEvaluation of in Vitro Devices on Self-collected Vaginal Swab and Urine Sample for Testing of Human Papilloma Virus
NCT04423679Not specifiedCOMPLETEDThe Selfie Study- Assessing Novel Markers for Cervical Cancer Screening From Self-collected Samples
NCT04788849Not specifiedCOMPLETEDExtended VALidation of HUman Papillomavirus Assays and Collection DEvices for HPV Testing on Self-samples
NCT05851079Not specifiedUNKNOWNAccurate Screening and Prevention of Cervical Lesions– Development of Accurate Screening Methods for Cervical Lesions
NCT06258564Not specifiedCOMPLETEDThe Adjuvant Effect of HPV Vaccination on Recurrence of Cervical Precancer or Carcinoma in Women Undergoing Conization

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
ARTESUNATE42
CELECOXIB41