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Atlas / Disease / Oropharynx cancer

Oropharynx cancer

disease
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Also known as cancer of oropharynxmalignant neoplasm of junctional region of oropharynxmalignant neoplasm of lateral wall of oropharynxmalignant neoplasm of oropharynxmalignant neoplasm of posterior wall of oropharynxmalignant neoplasm of the oropharynxmalignant oropharyngeal neoplasmmalignant oropharyngeal tumormalignant oropharyngeal tumourmalignant oropharynx neoplasmmalignant tumor of mesopharynxmalignant tumor of oropharynxmalignant tumor of posterior wall of oropharynxmalignant tumor of the oropharynxmalignant tumour of mesopharynxmalignant tumour of oropharynxmalignant tumour of posterior wall of oropharynxmalignant tumour of the oropharynxoropharyngeal canceroropharyngeal carcinoma

Summary

Oropharynx cancer (MONDO:0004608) is a cancer with 13 cohort genes (72 GWAS associations across 16 studies; 3 CIViC-evidence somatic drivers) and 203 clinical trials. Molecularly, CDKN2A p16 Expression is associated with resistance to Cetuximab in Oropharynx Cancer (CIViC Level B). Top therapeutic interventions include carboplatin, alpelisib, and cemiplimab.

At a glance

  • Classification: Cancer
  • Cohort genes: 13
  • GWAS associations: 72
  • Clinical trials: 203
  • Precision-medicine evidence (CIViC): 1 subtype–drug association

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameoropharynx cancer
Mondo IDMONDO:0004608
EFOEFO:1001931
MeSHD009959
DOIDDOID:8557
ICD-10-CMC10
ICD-111172876400
NCITC7398
UMLSC0153382
MedGen57783
GARD0009358
Anatomy (UBERON)UBERON:0001729
Is cancer (heuristic)yes

Also known as: cancer of oropharynx · malignant neoplasm of junctional region of oropharynx · malignant neoplasm of lateral wall of oropharynx · malignant neoplasm of oropharynx · malignant neoplasm of posterior wall of oropharynx · malignant neoplasm of the oropharynx · malignant oropharyngeal neoplasm · malignant oropharyngeal tumor · malignant oropharyngeal tumour · malignant oropharynx neoplasm · malignant tumor of mesopharynx · malignant tumor of oropharynx · malignant tumor of posterior wall of oropharynx · malignant tumor of the oropharynx · malignant tumour of mesopharynx · malignant tumour of oropharynx · malignant tumour of posterior wall of oropharynx · malignant tumour of the oropharynx · oropharyngeal cancer · oropharyngeal carcinoma (+2 more)

Data availability: 72 GWAS associations (16 studies).

Disease family

An umbrella term covering 4 Mondo subtypes.

Classification path: disease › human disease › disease by etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › cancer › respiratory system cancer › pharynx cancer › oropharynx cancer

Related subtypes (4): pharyngeal squamous cell carcinoma, hypopharynx cancer, pharyngeal adenoid cystic carcinoma, malignant tumor of nasopharynx

Subtypes (4): vallecula cancer, soft palate cancer, Waldeyer’s ring cancer, oropharyngeal carcinoma

Genetics & variants

GWAS landscape

72 GWAS associations across 16 studies. Top hits map to 33 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs345188603e-17HLA-DRB1 - HLA-DQA1G1.64
rs92749261e-15HLA-DQB1 - MTCO3P1T0.33
rs92663291e-12HLA-BA0.61
rs38288052e-12HLA-DQB1C1.37
rs1136581055e-12RBPMST1.9
rs5715743375e-12MIR99AHGT3.61
rs284184268e-12HLA-DQA1 - HLA-DQB1C1.56
rs12299841e-11ADH1B?
rs132119721e-10MUC21 - MUC22A1.55
rs351896401e-09ABTB3T2.75
rs43184313e-09CAPN13 - GALNT14T1.39
rs25236793e-09HCP5T0.51
rs1896021393e-08RNU6-474P - CTLA4A3.61
rs98362821e-07CBX1P5 - PPIAP74C0.75
rs15165351e-07TENM3C1.43
rs7293532e-07MAT2B - RNU6-168PA1.4
rs558647362e-07MYO16A1.45
rs1469523712e-07RBFOX1T2.53
rs30174912e-07SHANK2?
rs19616373e-07ACSL3 - KCNE4T1.21
rs617768193e-07MACO1 - LDLRAP1T2.05
rs176969323e-07CCDC192C3.33
rs756222793e-07CNTN4A2.03
rs1404710804e-07RERGLC3.78
rs1161689674e-07CBLB - Y_RNAA1.83
rs120793624e-07PADI2 - LINC02783A3.98
rs730182585e-07MTDHP3A1.73
rs1152109255e-07HLA-DQA1G1.46
rs743933976e-07STK31 - RNA5SP228C2.18
rs340171016e-07IL1A - IL1BT2.11

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST003859Lesseur C20162,5065,984Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer.
GCST90477171Verma A20242,259448,448Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90651238Liu TY20251,677231,112Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90011806Rashkin SR20201,223410,350Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts.
GCST010286Shete S20201,1444,493A genome-wide association study identifies two novel susceptible regions for squamous cell carcinoma of the head and neck.
GCST012242Lesseur C20161,1192,329Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer.
GCST012241Lesseur C20161,0902,928Genome-wide association analyses identify new susceptibility loci for oral cavity and pharyngeal cancer.
GCST90085699Ferreiro-Iglesias A20211,0785,256Germline determinants of humoral immune response to HPV-16 protect against oropharyngeal cancer.
GCST90085700Ferreiro-Iglesias A20215655,256Germline determinants of humoral immune response to HPV-16 protect against oropharyngeal cancer.
GCST90651976Liu TY2025410231,112Diversity 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)

TierVariants
Tier 1: coding1
Tier 2: splice/UTR1
Tier 3: regulatory1
Tier 4: intronic/intergenic47

MAF distribution

BucketVariants
common (>=0.05)39
low_freq (0.01-0.05)6
rare (<0.01)2
unknown3

Functional consequences

ConsequenceCount
intron_variant25
intergenic_variant20
non_coding_transcript_exon_variant2
regulatory_region_variant1
missense_variant1
3_prime_UTR_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs34518860632626326G>A,T0.11intergenic_variantHLA-DRB1 - HLA-DQA13e-17Tier 4: intronic/intergenic
rs9274926632673639T>C0.436intergenic_variantHLA-DQB1 - MTCO3P11e-15Tier 4: intronic/intergenic
rs9266329631363011G>A0.05non_coding_transcript_exon_variantHLA-B1e-12Tier 4: intronic/intergenic
rs3828805632668343T>A,C,G0.28regulatory_region_variantHLA-DQB12e-12Tier 3: regulatory
rs113658105830554434T>C0.002intron_variantRBPMS5e-12Tier 4: intronic/intergenic
rs5715743372116232677T>A,C0intron_variantMIR99AHG5e-12Tier 4: intronic/intergenic
rs28418426632651877T>C0.05intergenic_variantHLA-DQA1 - HLA-DQB18e-12Tier 4: intronic/intergenic
rs1229984499318162T>A,C,G0.05missense_variantADH1B1e-11Tier 1: coding
rs13211972630991224G>A0.05intergenic_variantMUC21 - MUC221e-10Tier 4: intronic/intergenic
rs3518964012107582831C>T0.05intron_variantABTB31e-09Tier 4: intronic/intergenic
rs4318431230875199C>T0.08intergenic_variantCAPN13 - GALNT143e-09Tier 4: intronic/intergenic
rs2523679631466557C>G,T0.05intron_variantHCP53e-09Tier 4: intronic/intergenic
rs1896021392203794513G>A,Tintergenic_variantRNU6-474P - CTLA43e-08Tier 4: intronic/intergenic
rs98362823167024803T>C0.05intergenic_variantCBX1P5 - PPIAP741e-07Tier 4: intronic/intergenic
rs15165354182334536G>C0.05intron_variantTENM31e-07Tier 4: intronic/intergenic
rs7293535163522414T>A,C,G0.05intergenic_variantMAT2B - RNU6-168P2e-07Tier 4: intronic/intergenic
rs5586473613109162764G>A0.05intron_variantMYO162e-07Tier 4: intronic/intergenic
rs146952371167451808C>A,T0.05intron_variantRBFOX12e-07Tier 4: intronic/intergenic
rs30174911170814146C>A0.05intron_variantSHANK22e-07Tier 4: intronic/intergenic
rs19616372223040390G>C,T0.399intergenic_variantACSL3 - KCNE43e-07Tier 4: intronic/intergenic
rs61776819125540804T>A,C,G0.013intergenic_variantMACO1 - LDLRAP13e-07Tier 4: intronic/intergenic
rs176969325127807962T>C0.05intron_variantCCDC1923e-07Tier 4: intronic/intergenic
rs7562227932863372G>A0.05intron_variantCNTN43e-07Tier 4: intronic/intergenic
rs1404710801218182994T>Cintergenic_variantRERGL4e-07Tier 4: intronic/intergenic
rs1161689673106482561G>A0.018intron_variantCBLB - Y_RNA4e-07Tier 4: intronic/intergenic
rs12079362117150268G>A0.05intergenic_variantPADI2 - LINC027834e-07Tier 4: intronic/intergenic
rs730182581921678153C>A,G,T0.027non_coding_transcript_exon_variantMTDHP35e-07Tier 4: intronic/intergenic
rs115210925632646317C>G0.05intergenic_variantHLA-DQA15e-07Tier 4: intronic/intergenic
rs74393397723842997G>A,C0.01intergenic_variantSTK31 - RNA5SP2286e-07Tier 4: intronic/intergenic
rs340171012112804195C>T0.013intron_variantIL1A - IL1B6e-07Tier 4: intronic/intergenic

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 18 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Somatic driver evidence (intOGen + CIViC, cohort fanout)

GeneintOGen roleCancer typesCIViC
CDKN2ALoFACYC,BLCA,BRCA,CHOL,COAD,COADREAD,CSCC,EGC,ESCA,ESCC,GBM,HCC,HNSC,LGGNOS,LUAD,LUSC,MEL,MLYM,NPC,NSCLC,OS,PAAD,PANCREAS,RCC,SKCM,SKIN,STAD,STOMACH,WDTCCIViC #14
GALNT14CIViC #14923
HLA-DQA1ActPLMESO

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
CDKN2AOrphanet:1333Familial pancreatic carcinoma
CDKN2AOrphanet:1501Adrenocortical carcinoma
CDKN2AOrphanet:252206Melanoma and neural system tumor syndrome
CDKN2AOrphanet:404560Familial atypical multiple mole melanoma syndrome
CDKN2AOrphanet:524Li-Fraumeni syndrome
CDKN2AOrphanet:585909B-lymphoblastic leukemia/lymphoma with t(9;22)(q34.1;q11.2)
CDKN2AOrphanet:618Familial melanoma
CDKN2AOrphanet:99861Precursor T-cell acute lymphoblastic leukemia
WDFY3Orphanet:528084Non-specific syndromic intellectual disability
CSGALNACT1Orphanet:1425Desbuquois syndrome
TENM3Orphanet:98938Colobomatous microphthalmia
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

Cohort genes → proteins

13 cohort genes, 12 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only12
civic_only1

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
CDKN2AHGNC:1787ENSG00000147889P42771Cyclin-dependent kinase inhibitor 2Acivic_evidence
WDFY3HGNC:20751ENSG00000163625Q8IZQ1WD repeat and FYVE domain-containing protein 3gwas
MUC21HGNC:21661ENSG00000204544Q5SSG8Mucin-21gwas
GALNT14HGNC:22946ENSG00000158089Q96FL9Polypeptide N-acetylgalactosaminyltransferase 14gwas
ADCY2HGNC:233ENSG00000078295Q08462Adenylate cyclase type 2gwas
ABTB3HGNC:23844ENSG00000151136A6QL63Ankyrin repeat- and BTB/POZ domain-containing protein 3gwas
CSGALNACT1HGNC:24290ENSG00000147408Q8TDX6Chondroitin sulfate N-acetylgalactosaminyltransferase 1gwas
ADH1BHGNC:250ENSG00000196616P00325All-trans-retinol dehydrogenase [NAD(+)] ADH1Bgwas
TENM3HGNC:29944ENSG00000218336Q9P273Teneurin-3gwas
HLA-DQA1HGNC:4942ENSG00000196735P01909HLA class II histocompatibility antigen, DQ alpha 1 chaingwas
HLA-DQB1HGNC:4944ENSG00000179344P01920HLA class II histocompatibility antigen, DQ beta 1 chaingwas
LINC01229HGNC:49682ENSG00000260876long intergenic non-protein coding RNA 1229gwas
KCNC4HGNC:6236ENSG00000116396Q03721Voltage-gated potassium channel KCNC4gwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
CDKN2ACyclin-dependent kinase inhibitor 2AActs as a negative regulator of the proliferation of normal cells by interacting strongly with CDK4 and CDK6.
WDFY3WD repeat and FYVE domain-containing protein 3Required for selective macroautophagy (aggrephagy).
GALNT14Polypeptide N-acetylgalactosaminyltransferase 14Catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor.
ADCY2Adenylate cyclase type 2Catalyzes the formation of the signaling molecule cAMP in response to G-protein signaling.
ABTB3Ankyrin repeat- and BTB/POZ domain-containing protein 3Cortical and hippocampal inhibitory interneuron-specific protein localized at glutamatergic (excitatory) synapses, where it supports cell type-specific synaptic function.
CSGALNACT1Chondroitin sulfate N-acetylgalactosaminyltransferase 1Transfers 1,4-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of glucuronic acid (GlcUA).
ADH1BAll-trans-retinol dehydrogenase [NAD(+)] ADH1BCatalyzes the NAD-dependent oxidation of all-trans-retinol and its derivatives such as all-trans-4-hydroxyretinol and may participate in retinoid metabolism.
TENM3Teneurin-3Involved in neural development by regulating the establishment of proper connectivity within the nervous system.
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.
KCNC4Voltage-gated potassium channel KCNC4Voltage-gated potassium channel that opens in response to the voltage difference across the membrane, forming a potassium-selective channel through which potassium ions pass in accordance with their electrochemical gradient.

Protein-family classification

Druggable: 6 · Difficult: 4 · Unknown: 3 · Druggable fraction: 0.46

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
Ion channel18.6×0.166
Antibody/Immunoglobulin24.5×0.166
Scaffold/PPI34.0×0.166
Enzyme (other)32.8×0.166
Transcription factor10.6×0.976
Other/Unknown30.4×0.997

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
CDKN2AScaffold/PPInoAnkyrin_rpt-contain_sf, Ank_Repeat/CDKN_Inhibitor, Tumor_suppres_ARF
WDFY3Transcription factornoZnf_FYVE, BEACH_dom, WD40_rpt
MUC21Other/UnknownnoTandem-repeating_mucin, Mucin_dom
GALNT14Enzyme (other)yes2.4.1.41Ricin_B_lectin, Glyco_trans_2-like, Nucleotide-diphossugar_trans
ADCY2Enzyme (other)yes4.6.1.1A/G_cyclase, Adcy_conserved_dom, A/G_cyclase_CS
ABTB3Scaffold/PPInoBTB/POZ_dom, Ankyrin_rpt, Histone-fold
CSGALNACT1Enzyme (other)yes2.4.1.174Chond_GalNAc, Nucleotide-diphossugar_trans, CS_glycosyltransferase
ADH1BOther/UnknownnoADH_Zn_CS, GroES-like_sf, ADH-like_C
TENM3Scaffold/PPInoEGF, YD, CarboxyPept-like_regulatory
HLA-DQA1Antibody/ImmunoglobulinyesMHC_II_a_N, Ig/MHC_CS, Ig_C1-set
HLA-DQB1Antibody/ImmunoglobulinyesMHC_II_b_N, Ig/MHC_CS, Ig_C1-set
LINC01229Other/Unknownno
KCNC4Ion channelyesBTB/POZ_dom, T1-type_BTB, K_chnl_volt-dep_Kv

Expression context

Cohort genes with no expression data: 0.

13 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)13
unknown0

Top tissues across cohort

TissueCohort genes
lower esophagus mucosa3
sural nerve2
cervix squamous epithelium1
parotid gland1
pituitary gland1
calcaneal tendon1
corpus callosum1
esophagus mucosa1
vagina1
adult mammalian kidney1
nephron tubule1
Brodmann (1909) area 231
dorsal motor nucleus of vagus nerve1
middle temporal gyrus1
esophagus squamous epithelium1
upper arm skin1
cardiac muscle of right atrium1
cartilage tissue1
synovial joint1
lower lobe of lung1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
CDKN2A220ubiquitousmarkerparotid gland, cervix squamous epithelium, pituitary gland
WDFY3293ubiquitousmarkersural nerve, calcaneal tendon, corpus callosum
MUC21103tissue_specificmarkerlower esophagus mucosa, esophagus mucosa, vagina
GALNT14194broadmarkerlower esophagus mucosa, adult mammalian kidney, nephron tubule
ADCY2254broadmarkermiddle temporal gyrus, Brodmann (1909) area 23, dorsal motor nucleus of vagus nerve
ABTB3205ubiquitousmarkerlower esophagus mucosa, esophagus squamous epithelium, upper arm skin
CSGALNACT1280broadmarkercartilage tissue, cardiac muscle of right atrium, synovial joint
ADH1B244broadmarkerright lobe of liver, right coronary artery, lower lobe of lung
TENM3189ubiquitousmarkersural nerve, adrenal tissue, stromal cell of endometrium
HLA-DQA1244broadmarkergall bladder, rectum, monocyte
HLA-DQB1268broadmarkerright lung, spleen, upper lobe of left lung
LINC01229127tissue_specificmarkermale germ line stem cell (sensu Vertebrata) in testis, primordial germ cell in gonad, testis
KCNC4197ubiquitousmarkerright frontal lobe, cingulate cortex, prefrontal cortex

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

SymbolInteractor count
CDKN2A9,311
ADH1B2,091
WDFY31,780
KCNC41,708
TENM31,704
ADCY21,629
CSGALNACT1932
GALNT14809
MUC21588
ABTB3583

Intra-cohort edges

ABSources
HLA-DQA1HLA-DQB1biogrid_interaction, intact

Structural data

PDB: 6 · AlphaFold-only: 6 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
HLA-DQA1P0190928
HLA-DQB1P0192010
ADH1BP003259
CDKN2AP427715
KCNC4Q037213
WDFY3Q8IZQ12

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
GALNT14Q96FL989.23
CSGALNACT1Q8TDX687.71
ADCY2Q0846278.91
TENM3Q9P27377.76
MUC21Q5SSG874.30
ABTB3A6QL6373.18

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 128. Enrichment computed across 13 evidence-associated genes (9 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 9 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Evasion of Oncogene Induced Senescence Due to p14ARF Defects11268.9×0.023CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to p14ARF Defects11268.9×0.023CDKN2A
Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK41634.4×0.023CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK41634.4×0.023CDKN2A
Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function1634.4×0.023CDKN2A
Diseases of Cellular Senescence1423.0×0.023CDKN2A
Evasion of Oncogene Induced Senescence Due to p16INK4A Defects1423.0×0.023CDKN2A
Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK61423.0×0.023CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to p16INK4A Defects1423.0×0.023CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK61423.0×0.023CDKN2A
Diseases of cellular response to stress1423.0×0.023CDKN2A
O-linked glycosylation of mucins240.9×0.023MUC21, GALNT14
Interferon gamma signaling227.9×0.023HLA-DQA1, HLA-DQB1
Adenylate cyclase activating pathway1126.9×0.055ADCY2
RUNX3 regulates p14-ARF1126.9×0.055CDKN2A
Ethanol oxidation1105.7×0.055ADH1B
Apoptotic factor-mediated response197.6×0.055CDKN2A
Adenylate cyclase inhibitory pathway184.6×0.055ADCY2
Stabilization of p53184.6×0.055CDKN2A
Defective Intrinsic Pathway for Apoptosis184.6×0.055CDKN2A
Defective GALNT3 causes HFTC179.3×0.055MUC21
Defective GALNT12 causes CRCS1179.3×0.055MUC21
p53-Dependent G1 DNA Damage Response179.3×0.055CDKN2A
p53-Dependent G1/S DNA damage checkpoint179.3×0.055CDKN2A
PKA activation in glucagon signalling174.6×0.055ADCY2
Defective C1GALT1C1 causes TNPS174.6×0.055MUC21
G1/S DNA Damage Checkpoints174.6×0.055CDKN2A
PKA activation170.5×0.055ADCY2
Translocation of ZAP-70 to Immunological synapse170.5×0.055HLA-DQA1
Diseases of programmed cell death170.5×0.055CDKN2A

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 12 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
peptide antigen assembly with MHC class II protein complex2175.5×0.005HLA-DQA1, HLA-DQB1
antigen processing and presentation of exogenous peptide antigen via MHC class II290.6×0.008HLA-DQA1, HLA-DQB1
positive regulation of immune response280.2×0.008HLA-DQA1, HLA-DQB1
positive regulation of T cell activation273.9×0.008HLA-DQA1, HLA-DQB1
UDP-glucuronate metabolic process11404.3×0.014CSGALNACT1
nuclear body organization1702.2×0.020CDKN2A
regulation of homophilic cell adhesion1702.2×0.020TENM3
apoptotic process involved in mammary gland involution1468.1×0.023CDKN2A
positive regulation of macrophage apoptotic process1468.1×0.023CDKN2A
UDP-N-acetylgalactosamine metabolic process1351.1×0.023CSGALNACT1
positive regulation of apoptotic process involved in mammary gland involution1351.1×0.023CDKN2A
obsolete negative regulation of proteolysis involved in protein catabolic process1351.1×0.023CDKN2A
negative regulation of mammary gland epithelial cell proliferation1280.9×0.027CDKN2A
negative regulation of immature T cell proliferation in thymus1234.1×0.029CDKN2A
positive regulation of smooth muscle cell apoptotic process1200.6×0.029CDKN2A
mitochondrial depolarization1200.6×0.029CDKN2A
oncogene-induced cell senescence1200.6×0.029CDKN2A
negative regulation of cyclin-dependent protein serine/threonine kinase activity1175.5×0.029CDKN2A
obsolete regulation of protein targeting to mitochondrion1175.5×0.029CDKN2A
regulation of nucleocytoplasmic transport1156.0×0.029CDKN2A
heparin proteoglycan biosynthetic process1140.4×0.029CSGALNACT1
aggrephagy1140.4×0.029WDFY3
dermatan sulfate proteoglycan biosynthetic process1140.4×0.029CSGALNACT1
mammary gland epithelial cell proliferation1127.7×0.029CDKN2A
regulation of protein export from nucleus1127.7×0.029CDKN2A
somatic stem cell division1127.7×0.029CDKN2A
protein localization to nucleolus1127.7×0.029CDKN2A
cAMP biosynthetic process1117.0×0.029ADCY2
adaptive immune response214.0×0.029HLA-DQA1, HLA-DQB1
positive regulation of protein sumoylation1108.0×0.030CDKN2A

Therapeutics

Drugs indicated for this disease

0 approved, 5 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
CarboplatinPhase 3 (in late-stage trials)
CisplatinPhase 3 (in late-stage trials)
DurvalumabPhase 3 (in late-stage trials)
GabapentinPhase 3 (in late-stage trials)
Sodium BicarbonatePhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Atezolizumab, Balstilimab, Capecitabine, Cemiplimab, Cetuximab, Etoposide, Ixabepilone, Minocycline, Nimotuzumab, Nivolumab, Paclitaxel, Pembrolizumab, Transplatin.

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 13

Druggability breadth: 7 of 13 evidence-associated genes (54%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
CDKN2A00
WDFY300
MUC2100
GALNT1400
ADCY200
ABTB300
CSGALNACT100
ADH1B00
TENM300
HLA-DQA100

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 3.

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

SymbolAssaysType breakdown
ADCY231Binding:29, Functional:2
KCNC421Binding:20, Toxicity:1
ADH1B13Binding:13
CSGALNACT19Binding:9
CDKN2A2Binding:2
HLA-DQA12Binding:2
GALNT141Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
GALNT142.4.1.41polypeptide N-acetylgalactosaminyltransferase
ADCY24.6.1.1adenylate cyclase
CSGALNACT12.4.1.174, 2.4.1.175glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase, glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase

Pharmacogenomics

Cohort genes with a PharmGKB record: 12; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Drug repurposing candidates

0 approved/phased drugs hit cohort targets but don’t yet appear in disease-level clinical trials. Target-inhibition rationale is strongest for cancer driver genes; a bioactivity hit is a screening signal, not a treatment claim.

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug3HLA-DQA1, HLA-DQB1, KCNC4
DDruggable family + AlphaFold only, no drug3GALNT14, ADCY2, CSGALNACT1
EDifficult family or no structure, no drug7CDKN2A, WDFY3, MUC21, ABTB3, ADH1B, TENM3, LINC01229

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
CDKN2A2—
WDFY30—
MUC210—
GALNT141—
ADCY231—
ABTB30—
CSGALNACT19—
ADH1B13—
TENM30—
HLA-DQA12—
HLA-DQB10—
LINC012290—
KCNC421—

Clinical trials & evidence

Clinical trials

Clinical trials: 203.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified102
PHASE256
PHASE316
PHASE114
PHASE1/PHASE212
PHASE2/PHASE32
PHASE41

Top trials by phase / activity

NCTPhaseStatusTitle
NCT03691441PHASE4UNKNOWNComparative Effectiveness Trial of Transoral Head and Neck Surgery Followed by Adjuvant Radio(Chemo)Therapy Versus Primary Radiochemotherapy for Oropharyngeal Cancer
NCT04019548PHASE3RECRUITINGAssessment of Swallowing Function and Quality of Life in Oropharyngeal Cancer Patients Treated by Chemo-radiotherapy
NCT04116047PHASE3ACTIVE_NOT_RECRUITINGCompARE: Escalating Treatment of Intermediate and High-risk Oropharyngeal Cancer (OPC)
NCT04178174PHASE3RECRUITINGStereotactic Boost and Short-course Radiation Therapy for Oropharynx Cancer
NCT05451004PHASE3RECRUITINGSPECT-CT Guided ELEctive Contralateral Neck Treatment for Patients With Lateralized Oropharyngeal Cancer
NCT06706401PHASE3RECRUITINGLymphocyte-Sparing And Radio-Immunotherapy in Head and Neck Carcinoma
NCT07402538PHASE3NOT_YET_RECRUITINGSurgery With or Without Neoadjuvant Treatment of SBRT Plus Chemoimmunotherapy in Resectable Locally Advanced Oral and HPV-unrelated Oropharyngeal Squamous Cell Carcinoma
NCT00158652PHASE3COMPLETEDAccelerated Radiotherapy and Concomitant Chemo-radiotherapy in HNSCC
NCT00158678PHASE3COMPLETEDIMRT Plus Cisplatin Versus Conventional Radiotherapy Plus Cisplatin in Stage III-IV HNSCC
NCT00162708PHASE2/PHASE3COMPLETEDVery Intense Radiotherapy-Chemotherapy Regimen in Advanced HNSCC
NCT00537199PHASE3TERMINATEDOraTest in Combination With Visual Examination and Visual Examination Alone
NCT00964977PHASE3COMPLETEDEffectiveness of Adjuvant Radiotherapy in Small Oropharyngeal Squamous Cell Cancer and Single Lymph Node Metastasis.
NCT01066741PHASE3TERMINATEDPrevention of Radiation-induced Severe Oral Mucositis in Oral Cavity, Oropharynx, Hypopharynx, and Cavum Cancer
NCT01434394PHASE2/PHASE3COMPLETEDNeoadjuvant Erbitux Based Chemotherapy for Locally Advanced Oral/Oropharyngeal Cancer
NCT01874587PHASE3COMPLETEDAdaptative Radiotherapy to Decrease Xerostomia in Oropharynx Carcinoma
NCT02908477PHASE3COMPLETEDEvaluation of De-escalated Adjuvant Radiation Therapy for Human Papillomavirus (HPV)-Associated Oropharynx Cancer
NCT03269344PHASE3COMPLETEDGabapentin for the Reduction of Radiation Therapy Induced Pain During the Treatment of Oropharyngeal Cancer
NCT04189107PHASE3COMPLETEDPostoperative Pain, Why Still in Hospital and DAOH Following TORS for SCCUP & OSAS
NCT05369234PHASE3COMPLETEDEffects of Oral Aloe Vera Juice on Chemotherapy and Radiation-induced Oral Mucositis and Esophagitis
NCT03174275PHASE2ACTIVE_NOT_RECRUITINGCarboplatin, Nab-Paclitaxel, Durvalumab Before Surgery and Adjuvant Therapy in Head and Neck Squamous Cell Carcinoma
NCT03215719PHASE2RECRUITINGAdaptive Treatment De-escalation in Favorable Risk HPV-Positive Oropharyngeal Carcinoma
NCT03224000PHASE2ACTIVE_NOT_RECRUITINGTrial of Magnetic Resonance Imaging Guided Radiotherapy Dose Adaptation in Human Papilloma Virus Positive Oropharyngeal Cancer
NCT03383094PHASE2ACTIVE_NOT_RECRUITINGChemoradiation vs Immunotherapy and Radiation for Head and Neck Cancer
NCT03822897PHASE2ACTIVE_NOT_RECRUITINGDe-Escalation Radiotherapy in Patients With Low-Risk HPV-Related Oropharyngeal Squamous Cell Carcinoma
NCT04151082PHASE1/PHASE2ACTIVE_NOT_RECRUITINGHigh Dose Steroid Therapy (Prednisone or Methylprednisolone) for the Improvement of Symptoms of Late Radiation-Associated Lower Cranial Neuropathy in Oropharyngeal Cancer Survivors
NCT04277858PHASE2RECRUITINGNeoadjuvant Chemotherapy and Transoral Robotic Surgery for Oropharyngeal Cancer.
NCT04287868PHASE1/PHASE2ACTIVE_NOT_RECRUITINGCombination Immunotherapy in Subjects With Advanced HPV Associated Malignancies
NCT04432597PHASE1/PHASE2ACTIVE_NOT_RECRUITINGHPV Vaccine PRGN-2009 Alone or in Combination With Anti-PDL1/TGF-Beta Trap (M7824) in Subjects With HPV Associated Cancers
NCT04444869PHASE2RECRUITINGTesting Less Intensive Radiation With Chemotherapy to Treat Low-risk Patients With HPV-positive Oropharyngeal Cancer
NCT04609280PHASE2ACTIVE_NOT_RECRUITINGSelective Avoidance of Nodal VolumEs at Minimal Risk (GCC 20110)
NCT04708470PHASE1/PHASE2ACTIVE_NOT_RECRUITINGA Phase I/II Study of Combination Immunotherapy for Advanced Cancers Including HPV-Associated Malignancies, Small Bowel, and Colon Cancers
NCT04901234PHASE2RECRUITINGAdaptive RadioTherapy for OroPharynx Cancer
NCT05075980PHASE2ACTIVE_NOT_RECRUITINGIntensity Modulated Proton or X-Ray Therapy After Surgery for Treatment of Head and Neck Cancer, the HEADLIGHT Study
NCT05232851PHASE1/PHASE2ACTIVE_NOT_RECRUITINGA Vaccine (PDS0101) Alone or in Combination With Pembrolizumab for the Treatment of Locally Advanced Human Papillomavirus-Associated Oropharynx Cancer
NCT05307939PHASE2RECRUITINGA Study on Using Cell-Free Tumor DNA (ctDNA) Testing to Decide When to StartRoutine Treatment in People With Human Papilloma Virus (HPV)- Associated Oropharynx Cancer (OPC)
NCT05388773PHASE2RECRUITINGTransoral Surgical Resection Followed by De-escalated Adjuvant IMRT in Resectable p16+ Locally Advanced Oropharynx Cancer
NCT05491512PHASE2RECRUITINGA Study of Reduced Radiation Therapy and Standard-of-Care Chemotherapy in People With HPV-Positive Throat Cancer
NCT05639972PHASE1/PHASE2RECRUITINGE7 T-cell Receptor (TCR) -T Cell Induction Therapy for Locoregionally Advanced HPV-associated Cancers
NCT05686226PHASE2RECRUITINGE7 TCR-T Cell Immunotherapy for Human Papillomavirus (HPV) Associated Cancers
NCT05787639PHASE2ACTIVE_NOT_RECRUITINGNeoadjuvant Immunoradiotherapy With Evorpacept and Pembrolizumab in HPVOPC (Human Papilloma Virus Oropharynx Cancer)

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
CARBOPLATIN47
ALPELISIB41
CEMIPLIMAB41
DEXLANSOPRAZOLE41
DIPHENHYDRAMINE41
DURVALUMAB41
ERLOTINIB HYDROCHLORIDE41
HYDROXYUREA41
MINOCYCLINE41
SACITUZUMAB GOVITECAN41
SUCRALFATE41
TRETINOIN41
VALPROIC ACID41
BINTRAFUSP ALFA34
VELIPARIB32
BALSTILIMAB31
ENTINOSTAT31
FICLATUZUMAB31
NIMOTUZUMAB31
UTOMILUMAB31
ZIMBERELIMAB31
CONTUSUGENE LADENOVEC21
ETRUMADENANT21
EVORPACEPT21
IMMUNOCYTOKINE NHS-IL1221
PEGENZILEUKIN21
PEXIPEPIMUT-S21
LONTUCIREV (REPLICATING ADENOVIRUS)11
PELTOPEPIMUT-S11

Precision-medicine subtype map (CIViC)

Drug × molecular subtype: 1 predictive associations from 1 curated evidence items; also 1 prognostic.

Molecular subtypeTherapyEffectLevelCIViC
CDKN2A p16 ExpressionCetuximabResistanceCIViC BEID759

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticscellosauruschembl_activitychembl_assaychembl_documentchembl_moleculechembl_targetciviccivic_evidenceclingen_dosageclinical_trialsclinvarctd_gene_interactiondbsnpdepmapdiamond_similaritydoidefoensemblentrezesm2_similarityfantom5_genefantom5_promotergardgenccgenerifgogtopdbgtopdb_interactiongwasgwas_studyhgncicd10cmicd11intactinterprointogenmedgenmeshmimmondomondochildmondoparentncitorphanetpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assayreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorstring_interactiontranscriptuberonufeatureumlsuniprot