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Atlas / Disease / Nasopharyngeal neoplasm

Nasopharyngeal neoplasm

disease
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Also known as nasopharyngeal neoplasmsnasopharyngeal tumornasopharyngeal tumournasopharynx neoplasmnasopharynx neoplasm (disease)nasopharynx tumornasopharynx tumourneoplasm of nasopharynxneoplasm of the nasopharynxtumor of nasopharynxtumor of the nasopharynxtumour of nasopharynxtumour of the nasopharynx

Summary

Nasopharyngeal neoplasm (MONDO:0005375) is a cancer with 14 cohort genes (73 GWAS associations across 12 studies; 8 CIViC-evidence somatic drivers) and 55 clinical trials. The dominant Reactome pathway is Endosomal/Vacuolar pathway (4 cohort genes). Top therapeutic interventions include cisplatin, interferon beta-1a, and pembrolizumab.

At a glance

  • Classification: Cancer
  • Cohort genes: 14
  • GWAS associations: 73
  • Clinical trials: 55

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namenasopharyngeal neoplasm
Mondo IDMONDO:0005375
EFOEFO:0004252
MeSHD009303
NCITC3257
SNOMED CT126680004
UMLSC0027439
MedGen6526
Anatomy (UBERON)UBERON:0001728
Is cancer (heuristic)yes

Also known as: nasopharyngeal neoplasms · nasopharyngeal tumor · nasopharyngeal tumour · nasopharynx neoplasm · nasopharynx neoplasm (disease) · nasopharynx tumor · nasopharynx tumour · neoplasm of nasopharynx · neoplasm of the nasopharynx · tumor of nasopharynx · tumor of the nasopharynx · tumour of nasopharynx · tumour of the nasopharynx

Data availability: 73 GWAS associations (12 studies).

Disease family

An umbrella term covering 3 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › respiratory system disorder › upper respiratory tract disorder › nasopharyngeal disorder › nasopharyngeal neoplasm

Related subtypes (2): nasopharyngitis, nasopharyngeal diphtheria

Subtypes (3): nasopharyngeal teratoma, malignant tumor of nasopharynx, benign neoplasm of nasopharynx

Genetics & variants

GWAS landscape

73 GWAS associations across 12 studies. Top hits map to 8 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs28605805e-67POLR1HASP, POLR1HASP?1.72
rs28942073e-33LINC02571?1.64
rs25177134e-20POLR1HASP, POLR1HASPA1.88
A*11:012e-19?1.69
rs284216662e-18HLA-DRB1 - HLA-DQA1?1.49
rs292329e-17SUMO2P1 - MOGA1.67
rs4016813e-14CLPTM1L?1.22
rs314896e-13CLPTM1L?1.23
rs67744942e-12MECOM?1.19
rs31290557e-11ZFP57 - HLA-F-AS1G1.51
B*38:027e-11?1.67
rs22373531e-10CREB5 x MTCO1P40 - RPS2P48G
B*55:025e-10?3.85
rs95107875e-10TNFRSF19?1.16
rs64606649e-10GALNT17 x C5A
rs68216969e-10MIR1973 - TRMT112P1 x ADAM12A
rs109331551e-09IRS1 - RHBDD1 x ERGA
rs104877811e-09DGKB x PIGCP2 - DLDA
rs46601762e-09KCNQ4 x DPP6A
rs13321732e-09RN7SKP120 - TUSC1 x RBFOX1A
rs67262612e-09ADCY3 - DNAJC27 x SLC28A3 - NTRK2A
rs75896362e-09EIF2S2P7 - ACTG1P22 x RNA5SP94 - MIR4432HGA
rs45714723e-09FBXL7 x LINC02929G
rs65456483e-09EIF2S2P7 - ACTG1P22 x RNA5SP94 - MIR4432HGA
rs287469693e-09HLA-DQB1 - MTCO3P1?
rs64981144e-09CIITA?1.15
rs19043825e-09MRPL35P2 - RPL7AP50 x RPS3AP24 - RN7SKP106G
rs65395985e-09PPFIA2 - LINC02426 x WDR45BP1 - RHOT1G
rs371817e-09COMMD10 x NRG3A
rs25238498e-09HCG22 x RNU6-1133P - C6orf15G

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90093313He YQ20224,5065,384A polygenic risk score for nasopharyngeal carcinoma shows potential for risk stratification and personalized screening.
GCST005113Bei JX20162,1523,740A GWAS Meta-analysis and Replication Study Identifies a Novel Locus within CLPTM1L/TERT Associated with Nasopharyngeal Carcinoma in Individuals of Chinese Ancestry.
GCST010978Zuo XY20191,6151,025X-chromosome association study reveals genetic susceptibility loci of nasopharyngeal carcinoma.
GCST003578Cui Q20161,5832,979An extended genome-wide association study identifies novel susceptibility loci for nasopharyngeal carcinoma.
GCST000687Bei JX20101,5831,894A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci.
GCST001752Tang M20121,4052,650The principal genetic determinants for nasopharyngeal carcinoma in China involve the HLA class I antigen recognition groove.
GCST90651354Liu TY2025596231,112Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST006524Su WH20132770How genome-wide SNP-SNP interactions relate to nasopharyngeal carcinoma susceptibility.
GCST000460Tse KP20092770Genome-wide association study reveals multiple nasopharyngeal carcinoma-associated loci within the HLA region at chromosome 6p21.3.
GCST90481481Verma A2024215451,014Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding0
Tier 2: splice/UTR0
Tier 3: regulatory1
Tier 4: intronic/intergenic49

MAF distribution

BucketVariants
common (>=0.05)47
low_freq (0.01-0.05)0
rare (<0.01)0
unknown3

Functional consequences

ConsequenceCount
intron_variant x intron_variant15
intron_variant10
intergenic_variant x intron_variant7
intron_variant x intergenic_variant5
intergenic_variant4
unknown3
intergenic_variant x intergenic_variant3
intron_variant x regulatory_region_variant1
intergenic_variant x non_coding_transcript_exon_variant1
missense_variant x intron_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs2860580629938914A>C,G,T0.38intergenic_variantPOLR1HASP, POLR1HASP5e-67Tier 4: intronic/intergenic
rs2894207631295974T>C0.18intron_variantLINC025713e-33Tier 4: intronic/intergenic
rs2517713629950322G>A,C,T0.38intron_variantPOLR1HASP, POLR1HASP4e-20Tier 4: intronic/intergenic
A*11:012e-19Tier 4: intronic/intergenic
rs28421666632624960A>G0.12intergenic_variantHLA-DRB1 - HLA-DQA12e-18Tier 4: intronic/intergenic
rs29232629643654C>A,G,T0.46intron_variantSUMO2P1 - MOG9e-17Tier 4: intronic/intergenic
rs40168151321972C>T0.33intron_variantCLPTM1L3e-14Tier 4: intronic/intergenic
rs3148951342599C>A0.05intron_variantCLPTM1L6e-13Tier 4: intronic/intergenic
rs67744943169364845G>A,T0.05intron_variantMECOM2e-12Tier 4: intronic/intergenic
rs3129055629702484A>C,G,T0.31intron_variantZFP57 - HLA-F-AS17e-11Tier 4: intronic/intergenic
B*38:027e-11Tier 4: intronic/intergenic
rs22373537 x 1728758597C>A,G,T0.05intron_variant x intergenic_variantCREB5 x MTCO1P40 - RPS2P481e-10Tier 4: intronic/intergenic
B*55:025e-10Tier 4: intronic/intergenic
rs95107871323631056A>G,T0.05intron_variantTNFRSF195e-10Tier 4: intronic/intergenic
rs64606647 x 971535629T>A,G0.05intron_variant x intron_variantGALNT17 x C59e-10Tier 4: intronic/intergenic
rs68216964 x 10116305153A>C,G,T0.05intergenic_variant x intron_variantMIR1973 - TRMT112P1 x ADAM129e-10Tier 4: intronic/intergenic
rs109331552 x 21226822191C>T0.05intergenic_variant x intron_variantIRS1 - RHBDD1 x ERG1e-09Tier 4: intronic/intergenic
rs104877817 x 714829580A>G,T0.05intron_variant x regulatory_region_variantDGKB x PIGCP2 - DLD1e-09Tier 3: regulatory
rs46601761 x 740827977C>T0.05intron_variant x intron_variantKCNQ4 x DPP62e-09Tier 4: intronic/intergenic
rs13321739 x 1625500240A>C,G,T0.05intergenic_variant x intron_variantRN7SKP120 - TUSC1 x RBFOX12e-09Tier 4: intronic/intergenic
rs67262612 x 924931117T>C,G0.05intron_variant x intron_variantADCY3 - DNAJC27 x SLC28A3 - NTRK22e-09Tier 4: intronic/intergenic
rs75896362 x 257462898A>C,G0.05intron_variant x intron_variantEIF2S2P7 - ACTG1P22 x RNA5SP94 - MIR4432HG2e-09Tier 4: intronic/intergenic
rs45714725 x 1015721251A>G,T0.05intron_variant x intron_variantFBXL7 x LINC029293e-09Tier 4: intronic/intergenic
rs65456482 x 257430809A>G,T0.05intron_variant x intron_variantEIF2S2P7 - ACTG1P22 x RNA5SP94 - MIR4432HG3e-09Tier 4: intronic/intergenic
rs28746969632685471A>G0.05intergenic_variantHLA-DQB1 - MTCO3P13e-09Tier 4: intronic/intergenic
rs64981141610870261G>A,T0.46intron_variantCIITA4e-09Tier 4: intronic/intergenic
rs190438210 x 663790926A>G0.05intergenic_variant x intergenic_variantMRPL35P2 - RPL7AP50 x RPS3AP24 - RN7SKP1065e-09Tier 4: intronic/intergenic
rs653959812 x 1781896204C>G,T0.05intergenic_variant x non_coding_transcript_exon_variantPPFIA2 - LINC02426 x WDR45BP1 - RHOT15e-09Tier 4: intronic/intergenic
rs371815 x 10116294307T>A,C,G0.05intergenic_variant x intron_variantCOMMD10 x NRG37e-09Tier 4: intronic/intergenic
rs25238496 x 631057274T>A,C0.05intron_variant x intergenic_variantHCG22 x RNU6-1133P - C6orf158e-09Tier 4: intronic/intergenic

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 31 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Somatic driver evidence (intOGen + CIViC, cohort fanout)

GeneintOGen roleCancer typesCIViC
TERTActPRCCCIViC #79
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
CDKN2BCIViC #916
MECOMActBRCA,MEL,PRAD,UCECCIViC #1771
HLA-ALoFACYC,AML,BL,BLCA,CEAD,CESC,COAD,DLBCLNOS,ESCA,HNSC,LUSC,MEL,MLYM,NPCCIViC #2606
HLA-BLoFCESC,DLBCLNOS,ESCA,HNSC,MLYMCIViC #2607
HLA-CLoFDLBCLNOSCIViC #2608
CIITAActDLBCLNOS,HNSCCIViC #3512

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
TERTOrphanet:146Differentiated thyroid carcinoma
TERTOrphanet:1501Adrenocortical carcinoma
TERTOrphanet:1775Dyskeratosis congenita
TERTOrphanet:2032Idiopathic pulmonary fibrosis
TERTOrphanet:2495Meningioma
TERTOrphanet:3322Hoyeraal-Hreidarsson syndrome
TERTOrphanet:457246Clear cell sarcoma of kidney
TERTOrphanet:618Familial melanoma
TERTOrphanet:88Idiopathic aplastic anemia
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
CDKN2BOrphanet:618Familial melanoma
CDKN2BOrphanet:652Multiple endocrine neoplasia type 1
MECOMOrphanet:402020Acute myeloid leukemia with inv(3)(q21q26.2) or t(3;3)(q21;q26.2)
MECOMOrphanet:71289Radio-ulnar synostosis-amegakaryocytic thrombocytopenia syndrome
GABBR1Orphanet:178469Autosomal dominant non-syndromic intellectual disability
HLA-AOrphanet:179Birdshot chorioretinopathy
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-COrphanet:585909B-lymphoblastic leukemia/lymphoma with t(9;22)(q34.1;q11.2)
CIITAOrphanet:572Immunodeficiency by defective expression of MHC class II

Cohort genes → proteins

14 cohort genes, 14 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only14

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
TERTHGNC:11730ENSG00000164362O14746Telomerase reverse transcriptasegwas
TNFRSF19HGNC:11915ENSG00000127863Q9NS68Tumor necrosis factor receptor superfamily member 19gwas
CDKN2AHGNC:1787ENSG00000147889P42771Cyclin-dependent kinase inhibitor 2Agwas
CDKN2BHGNC:1788ENSG00000147883P42772Cyclin-dependent kinase 4 inhibitor Bgwas
CDKN2A-AS1HGNC:23831ENSG00000224854Q9UH64Putative uncharacterized protein CDKN2A-AS1gwas
CLPTM1LHGNC:24308ENSG00000049656Q96KA5Lipid scramblase CLPTM1Lgwas
MECOMHGNC:3498ENSG00000085276Q03112Histone-lysine N-methyltransferase MECOMgwas
GABBR1HGNC:4070ENSG00000204681Q9UBS5Gamma-aminobutyric acid type B receptor subunit 1gwas
HLA-AHGNC:4931ENSG00000206503P04439HLA class I histocompatibility antigen, A alpha chaingwas
HLA-BHGNC:4932ENSG00000234745P01889HLA class I histocompatibility antigen, B alpha chaingwas
HLA-CHGNC:4933ENSG00000204525P10321HLA class I histocompatibility antigen, C alpha chaingwas
HLA-FHGNC:4963ENSG00000204642P30511HLA class I histocompatibility antigen, alpha chain Fgwas
ITGA9HGNC:6145ENSG00000144668Q13797Integrin alpha-9gwas
CIITAHGNC:7067ENSG00000179583P33076MHC class II transactivatorgwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
TERTTelomerase reverse transcriptaseTelomerase is a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes.
TNFRSF19Tumor necrosis factor receptor superfamily member 19Can mediate activation of JNK and NF-kappa-B.
CDKN2ACyclin-dependent kinase inhibitor 2AActs as a negative regulator of the proliferation of normal cells by interacting strongly with CDK4 and CDK6.
CDKN2BCyclin-dependent kinase 4 inhibitor BInteracts strongly with CDK4 and CDK6.
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…
MECOMHistone-lysine N-methyltransferase MECOMFunctions as a transcriptional regulator binding to DNA sequences in the promoter region of target genes and regulating positively or negatively their expression.
GABBR1Gamma-aminobutyric acid type B receptor subunit 1Component of a heterodimeric G-protein coupled receptor for GABA, formed by GABBR1 and GABBR2.
HLA-AHLA class I histocompatibility antigen, A alpha chainAntigen-presenting major histocompatibility complex class I (MHCI) molecule.
HLA-BHLA class I histocompatibility antigen, B alpha chainAntigen-presenting major histocompatibility complex class I (MHCI) molecule.
HLA-CHLA class I histocompatibility antigen, C alpha chainAntigen-presenting major histocompatibility complex class I (MHCI) molecule with an important role in reproduction and antiviral immunity.
HLA-FHLA class I histocompatibility antigen, alpha chain FNon-classical major histocompatibility class Ib molecule postulated to play a role in immune surveillance, immune tolerance and inflammation.
ITGA9Integrin alpha-9Integrin alpha-9/beta-1 (ITGA9:ITGB1) is a receptor for VCAM1, cytotactin and osteopontin.
CIITAMHC class II transactivatorEssential for transcriptional activity of the HLA class II promoter; activation is via the proximal promoter.

Protein-family classification

Druggable: 6 · Difficult: 3 · Unknown: 5 · Druggable fraction: 0.43

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/Immunoglobulin510.4×4e-04
Scaffold/PPI22.5×0.481
GPCR11.7×0.750
Other/Unknown50.6×0.963
Transcription factor10.6×0.963

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
TERTOther/UnknownnoRT_dom, Telomerase_RT, Telomerase_RBD
TNFRSF19Other/UnknownnoTNFR/NGFR_Cys_rich_reg, TNFR_19, TNFRSF19_N
CDKN2AScaffold/PPInoAnkyrin_rpt-contain_sf, Ank_Repeat/CDKN_Inhibitor, Tumor_suppres_ARF
CDKN2BScaffold/PPInoAnkyrin_rpt, Ankyrin_rpt-contain_sf, Ank_Repeat/CDKN_Inhibitor
CDKN2A-AS1Other/Unknownno
CLPTM1LOther/UnknownnoCLPTM1
MECOMTranscription factornoSET_dom, Znf_C2H2_type, Znf_C2H2_sf
GABBR1GPCRyesSushi_SCR_CCP_dom, ANF_lig-bd_rcpt, GPCR3_GABA-B
HLA-AAntibody/ImmunoglobulinyesMHC_I_a_a1/a2, Ig/MHC_CS, Ig_C1-set
HLA-BAntibody/ImmunoglobulinyesMHC_I_a_a1/a2, Ig/MHC_CS, Ig_C1-set
HLA-CAntibody/ImmunoglobulinyesMHC_I_a_a1/a2, Ig_C1-set, Ig-like_dom
HLA-FAntibody/ImmunoglobulinyesMHC_I_a_a1/a2, Ig/MHC_CS, Ig_C1-set
ITGA9Antibody/ImmunoglobulinyesIntegrin_alpha, FG-GAP, Int_alpha_beta-p
CIITAOther/UnknownnoLeu-rich_rpt, NACHT_NTPase, MHC_II_transact

Expression context

Cohort genes with no expression data: 0.

11 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)14
unknown0

Top tissues across cohort

TissueCohort genes
blood4
granulocyte4
spleen3
stromal cell of endometrium2
parotid gland2
olfactory bulb1
type B pancreatic cell1
bronchial epithelial cell1
upper arm skin1
upper leg skin1
cervix squamous epithelium1
pituitary gland1
colonic mucosa1
jejunal mucosa1
lower esophagus mucosa1
gingival epithelium1
primordial germ cell in gonad1
ileal mucosa1
kidney epithelium1
right lobe of thyroid gland1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
TERT105broadyesstromal cell of endometrium, type B pancreatic cell, olfactory bulb
TNFRSF19224ubiquitousmarkerupper arm skin, upper leg skin, bronchial epithelial cell
CDKN2A220ubiquitousmarkerparotid gland, cervix squamous epithelium, pituitary gland
CDKN2B219ubiquitousmarkerjejunal mucosa, colonic mucosa, lower esophagus mucosa
CDKN2A-AS154yesprimordial germ cell in gonad, gingival epithelium, parotid gland
CLPTM1L255ubiquitousmarkerileal mucosa, kidney epithelium, right lobe of thyroid gland
MECOM276ubiquitousmarkercardia of stomach, renal medulla, pylorus
GABBR1194ubiquitousyesright hemisphere of cerebellum, cerebellar hemisphere, right frontal lobe
HLA-A134ubiquitousmarkerblood, granulocyte, stromal cell of endometrium
HLA-B134ubiquitousmarkerblood, spleen, granulocyte
HLA-C134ubiquitousmarkerblood, right lung, spleen
HLA-F139ubiquitousmarkergranulocyte, spleen, blood
ITGA9248broadmarkerurethra, saphenous vein, visceral pleura
CIITA200broadmarkermonocyte, granulocyte, mononuclear cell

Protein interactions among cohort

Intra-cohort edges: 8.

Hub genes (top 10 by interactor count)

SymbolInteractor count
CDKN2A9,311
TERT5,717
CDKN2B3,431
HLA-B3,209
MECOM2,442
CIITA2,388
GABBR11,688
CLPTM1L1,606
HLA-F1,296
ITGA91,225

Intra-cohort edges

ABSources
CDKN2ACDKN2Bbiogrid_interaction
CLPTM1LTERTstring_interaction
HLA-AHLA-Bbiogrid_interaction, intact
HLA-AHLA-Cbiogrid_interaction, intact
HLA-AHLA-Fintact
HLA-BHLA-Cbiogrid_interaction, intact
HLA-CHLA-Fbiogrid_interaction
MECOMTNFRSF19string_interaction

Structural data

PDB: 8 · AlphaFold-only: 6 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
HLA-AP04439403
HLA-BP01889237
GABBR1Q9UBS524
TERTO1474623
HLA-CP1032113
CDKN2AP427715
HLA-FP305112
MECOMQ031121

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
CDKN2BP4277290.12
ITGA9Q1379784.98
CLPTM1LQ96KA578.54
CIITAP3307669.10
TNFRSF19Q9NS6860.50
CDKN2A-AS1Q9UH6449.21

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 106. Enrichment computed across 14 evidence-associated genes (11 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 11 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Endosomal/Vacuolar pathway4377.5×2e-08HLA-A, HLA-B, HLA-C, HLA-F
Antigen Presentation: Folding, assembly and peptide loading of class I MHC4143.2×5e-07HLA-A, HLA-B, HLA-C, HLA-F
Interferon gamma signaling557.0×5e-07HLA-A, HLA-B, HLA-C, HLA-F, CIITA
Interferon alpha/beta signaling455.4×1e-05HLA-A, HLA-B, HLA-C, HLA-F
ER-Phagosome pathway447.2×2e-05HLA-A, HLA-B, HLA-C, HLA-F
SARS-CoV-2 activates/modulates innate and adaptive immune responses432.4×8e-05HLA-A, HLA-B, HLA-C, HLA-F
Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell431.7×8e-05HLA-A, HLA-B, HLA-C, HLA-F
DAP12 interactions286.5×0.003HLA-B, HLA-C
G1 Phase271.6×0.004CDKN2A, CDKN2B
Oncogene Induced Senescence261.1×0.005CDKN2A, CDKN2B
Evasion of Oncogene Induced Senescence Due to p14ARF Defects11038.2×0.008CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to p14ARF Defects11038.2×0.008CDKN2A
Cyclin D associated events in G1242.4×0.008CDKN2A, CDKN2B
Mitotic G1 phase and G1/S transition233.5×0.011CDKN2A, CDKN2B
MITF-M-dependent gene expression233.0×0.011TERT, CDKN2A
Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK41519.1×0.011CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK41519.1×0.011CDKN2A
Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function1519.1×0.011CDKN2A
Diseases of Cellular Senescence1346.1×0.012CDKN2A
Evasion of Oncogene Induced Senescence Due to p16INK4A Defects1346.1×0.012CDKN2A
Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK61346.1×0.012CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to p16INK4A Defects1346.1×0.012CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK61346.1×0.012CDKN2A
Diseases of cellular response to stress1346.1×0.012CDKN2A
Cellular Senescence225.0×0.012CDKN2A, CDKN2B
Cell Cycle39.8×0.012TERT, CDKN2A, CDKN2B
MITF-M-regulated melanocyte development220.8×0.016TERT, CDKN2A
Senescence-Associated Secretory Phenotype (SASP)218.1×0.019CDKN2A, CDKN2B
Developmental Biology45.3×0.019TERT, CDKN2A, MECOM, ITGA9
Oxidative Stress Induced Senescence216.5×0.022CDKN2A, CDKN2B

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 13 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
antigen processing and presentation of endogenous peptide antigen via MHC class Ib4398.9×1e-08HLA-A, HLA-B, HLA-C, HLA-F
antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent4398.9×1e-08HLA-A, HLA-B, HLA-C, HLA-F
positive regulation of T cell mediated cytotoxicity4157.1×5e-07HLA-A, HLA-B, HLA-C, HLA-F
immune response518.1×2e-04HLA-A, HLA-B, HLA-C, HLA-F, CIITA
protection from natural killer cell mediated cytotoxicity2432.1×3e-04HLA-A, HLA-B
detection of bacterium2216.1×1e-03HLA-A, HLA-B
replicative senescence2152.5×0.002TERT, CDKN2A
RNA-templated transcription11296.3×0.010TERT
DNA strand elongation11296.3×0.010TERT
negative regulation of natural killer cell degranulation11296.3×0.010HLA-F
siRNA transcription11296.3×0.010TERT
positive regulation of transdifferentiation11296.3×0.010TERT
regulation of G1/S transition of mitotic cell cycle247.1×0.010CDKN2A, CDKN2B
cellular senescence245.5×0.010CDKN2A, CDKN2B
antigen processing and presentation of exogenous peptide antigen via MHC class Ib1648.1×0.011HLA-F
antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent1648.1×0.011HLA-A
negative regulation of natural killer cell cytokine production1648.1×0.011HLA-F
RNA-templated DNA biosynthetic process1648.1×0.011TERT
negative regulation of gamma-aminobutyric acid secretion1648.1×0.011GABBR1
nuclear body organization1648.1×0.011CDKN2A
positive regulation of hair cycle1648.1×0.011TERT
positive regulation of memory T cell activation1648.1×0.011HLA-A
positive regulation of CD8-positive, alpha-beta T cell activation1648.1×0.011HLA-A
T cell mediated cytotoxicity directed against tumor cell target1432.1×0.014HLA-A
apoptotic process involved in mammary gland involution1432.1×0.014CDKN2A
positive regulation of macrophage apoptotic process1432.1×0.014CDKN2A
positive regulation of CD8-positive, alpha-beta T cell proliferation1432.1×0.014HLA-A
regulation of dendritic cell differentiation1432.1×0.014HLA-B
regulation of T cell anergy1324.1×0.015HLA-B
regulation of interleukin-12 production1324.1×0.015HLA-B

Therapeutics

Drugs indicated for this disease

1 approved, 10 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

DrugDevelopment status
SotagliflozinApproved (phase 4)
CamrelizumabPhase 3 (in late-stage trials)
CapecitabinePhase 3 (in late-stage trials)
CisplatinPhase 3 (in late-stage trials)
FluorouracilPhase 3 (in late-stage trials)
GemcitabinePhase 3 (in late-stage trials)
NimotuzumabPhase 3 (in late-stage trials)
PaclitaxelPhase 3 (in late-stage trials)
PembrolizumabPhase 3 (in late-stage trials)
SintilimabPhase 3 (in late-stage trials)
ToripalimabPhase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Avelumab, Axitinib, Azacitidine, Becotatug Vedotin, Bevacizumab, Bortezomib, Cadonilimab, Carboplatin, Catequentinib, Cyanocobalamin, Doxorubicin, Endostatin, Endostatin, N-Terminal-Mggshhhhh, Envafolimab, Erlotinib, Famitinib, Ifosfamide, Lobaplatin, Nivolumab, Oxaliplatin, Pemetrexed, Penpulimab, Regramostim, Rivoceranib, Serplulimab, Sorafenib, Tislelizumab.

Drug target analysis

Approved (phase 4): 3 · Phase ≥3: 3 · Phased (≥1): 3 · Undrugged: 11

Druggability breadth: 9 of 14 evidence-associated genes (64%) 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
TERTBERBERINE
GABBR1BACLOFEN
HLA-ARALOXIFENE HYDROCHLORIDE

Top cohort targets by molecule count

SymbolMoleculesMax phase
TERT104
HLA-A84
GABBR144
TNFRSF1900
CDKN2A00
CDKN2B00
CDKN2A-AS100
CLPTM1L00
MECOM00
HLA-B00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
BERBERINE4TERT
DOXORUBICIN4TERT
BACLOFEN4GABBR1
RALOXIFENE HYDROCHLORIDE4HLA-A
DOXAZOSIN MESYLATE4HLA-A
TRAZODONE HYDROCHLORIDE4HLA-A
ASTEMIZOLE4HLA-A
RESVERATROL3TERT
EPIGALOCATECHIN GALLATE3TERT
PERIFOSINE3TERT
ARBACLOFEN3GABBR1
VATALANIB3HLA-A
ISOMETAMIDIUM2TERT
HOMIDIUM BROMIDE2TERT
ALLICIN2TERT
OLEIC ACID2TERT
ETHACRIDINE2TERT
SGS-7422GABBR1
DISOMOTIDE2HLA-A
OVEMOTIDE2HLA-A
SPIPERONE2HLA-A
GAMMA-AMINOBUTYRIC ACID1GABBR1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

SymbolAssaysType breakdown
TERT391Binding:389, Functional:2
GABBR194Binding:71, Functional:22, ADMET:1
HLA-A4Binding:4
ITGA93Binding:3
CDKN2A2Binding:2
CLPTM1L1Binding:1
MECOM1Binding:1
HLA-B1Binding:1
HLA-C1Binding:1

Cohort genes with high screening signal

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

SymbolChEMBL assays
TERT391

Pharmacogenomics

Cohort genes with a PharmGKB record: 13; with CPIC/DPWG dosing guidelines: 2.

Cohort genes with a CPIC/DPWG dosing guideline

SymbolCPIC guidelines
HLA-A1
HLA-B1

Drug repurposing candidates

22 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.

CompoundMax phaseCohort target (bioactivity)
BERBERINE4TERT
DOXORUBICIN4TERT
BACLOFEN4GABBR1
RALOXIFENE HYDROCHLORIDE4HLA-A
DOXAZOSIN MESYLATE4HLA-A
TRAZODONE HYDROCHLORIDE4HLA-A
ASTEMIZOLE4HLA-A
RESVERATROL3TERT
EPIGALOCATECHIN GALLATE3TERT
PERIFOSINE3TERT
ARBACLOFEN3GABBR1
VATALANIB3HLA-A
ISOMETAMIDIUM2TERT
HOMIDIUM BROMIDE2TERT
ALLICIN2TERT
OLEIC ACID2TERT
ETHACRIDINE2TERT
SGS-7422GABBR1
DISOMOTIDE2HLA-A
OVEMOTIDE2HLA-A
SPIPERONE2HLA-A
GAMMA-AMINOBUTYRIC ACID1GABBR1

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3TERT, GABBR1, HLA-A
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug3HLA-B, HLA-C, HLA-F
DDruggable family + AlphaFold only, no drug1ITGA9
EDifficult family or no structure, no drug7TNFRSF19, CDKN2A, CDKN2B, CDKN2A-AS1, CLPTM1L, MECOM, CIITA

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
CLPTM1L1TERT
HLA-C1HLA-A
TNFRSF190—
CDKN2A2—
CDKN2B0—
CDKN2A-AS10—
MECOM1—
HLA-B1—
HLA-F0—
ITGA93—
CIITA0—

Clinical trials & evidence

Clinical trials

Clinical trials: 55.

Phase distribution (across all retrieved trials)

PhaseTrials
PHASE227
Not specified16
PHASE36
PHASE1/PHASE24
PHASE12

Top trials by phase / activity

NCTPhaseStatusTitle
NCT03840421PHASE3ACTIVE_NOT_RECRUITINGGP Vs PF As Induction Chemotherapy Combined with CCRT for Locoregionally Advanced Nasopharyngeal Carcinoma
NCT01528618PHASE3COMPLETEDEffect and Safety Study of GP/FP Regimens in Advanced Nasopharyngeal Carcinoma
NCT02611960PHASE3COMPLETEDStudy of Pembrolizumab (MK-3475) in Platinum Pre-treated Recurrent/Metastatic Nasopharyngeal Cancer (MK-3475-122/KEYNOTE-122)
NCT03427827PHASE3UNKNOWNPD-1 Antibody Versus Best Supportive Care After Chemoradiation in Locoregionally Advanced Nasopharyngeal Carcinoma
NCT03700476PHASE3UNKNOWNSintilimab (PD-1 Antibody) and Chemoradiotherapy in Locoregionally-advanced Nasopharyngeal Carcinoma
NCT03837808PHASE3UNKNOWNRadiotherapy Plus Concurrent Nimotuzumab or Cisplatin in Stage II-III Nasopharyngeal Carcinoma
NCT05807880PHASE2ACTIVE_NOT_RECRUITINGAnlotinib, Penpulimab and Capecitabine in Recurrent/Metastatic Nasopharyngeal Carcinoma
NCT06019130PHASE2RECRUITINGNivolumab in Children and Adults With Nasopharyngeal Carcinoma
NCT06688175PHASE2ENROLLING_BY_INVITATIONIMRT Combined With Lobaplatin-based CCRT in Nasopharyngeal Carcinoma
NCT06811844PHASE2RECRUITINGTwo-cycle and Three-cycle Induction Therapy With Modified TPF Regimen Combined and Camrelizumab for LANPC
NCT07277764PHASE2RECRUITINGInduction High-Low Dose Radiotherapy Plus Anti-PD-1 Followed by Definitive Radiotherapy in Recurrent Nasopharyngeal Carcinoma (Single-Arm Phase II)
NCT00123864PHASE1/PHASE2COMPLETEDStudy Using Intensity-modulated Radiation Therapy in Patients With Nasopharynx Cancer to Permit Sparing of Contralateral Parotid Gland Function
NCT00188877PHASE2COMPLETEDIntensity Modulated Radiation Therapy for Head and Neck Cancer
NCT00363831PHASE2UNKNOWNCombination of Capecitabine and Oxaliplatin in Metastatic Nasopharyngeal Carcinoma
NCT00436293PHASE2COMPLETEDTaxotere + Cisplatin in Nasopharyngeal Carcinoma
NCT00436800PHASE2COMPLETEDGemcitabine and Oxaliplatin (GEMOX) in First Line Metastatic or Recurrent Nasopharyngeal Carcinoma
NCT00565448PHASE2COMPLETEDDocetaxel in Combination With Cisplatin-5-fluorouracil for the Induction Treatment of Nasopharyngeal Carcinoma in Children and Adolescents
NCT00630149PHASE2COMPLETEDStudy of Alimta in Patients With Recurrent or Metastatic Nasopharyngeal Carcinoma (NPC) Who Have Had Prior Platinum Based Chemotherapy
NCT00747799PHASE2COMPLETEDStudy of Combination of Sorafenib With Cisplatin and 5-fluorouracil as First-line Treatment of Recurrence After Radiotherapy Patients Who Failed With Radiotherapy in Recurrent or Metastatic Nasopharyngeal Carcinoma (NPC)
NCT01735409PHASE1/PHASE2UNKNOWNDose-finding Study of Abraxane in Combination With Cisplatin to Treat Advanced Nasopharyngeal Carcinoma
NCT01762514PHASE2UNKNOWNA Phase II Clinical Trial on Comparison of Effectiveness and Safeness of Different Amifostine Regimens
NCT01797900PHASE2COMPLETEDThe Role of Induction Chemotherapy for High-risk Locally Advanced Nasopharyngeal Carcinoma in the Era of IMRT
NCT02250599PHASE2UNKNOWNEfficacy and Safety of TC+AVASTIN Versus TC in Patients With Metastatic Nasopharyngeal Carcinoma
NCT02269943PHASE2COMPLETEDSafety and Efficacy of CC-486 in Previously Treated Patients With Locally Advanced or Metastatic Nasopharyngeal Carcinoma
NCT02360501PHASE2COMPLETEDCombination of Docetaxel, Cisplatin, and Capecitabine (DCX) in the Treatment of Nasopharyngeal Carcinoma
NCT02444949PHASE2COMPLETEDA Trial of Endostar in Combination With Chemotherapy of DF and Sequential Intensity Modulated Radiation Therapy for Patients With Advanced Nasopharyngeal Carcinoma
NCT02729324PHASE2UNKNOWNComparison of Efficacy and Safety Between Medical Radiation Protectants (FORRAD®) and Trolamine (Biafine) for the Management of Radiation Dermatitis in Patients With Nasopharyngeal Carcinoma Receiving IMRT
NCT02735317PHASE2UNKNOWNEfficacy and Safety of FORRAD® for the Management of Radiation-induced Mucositis in Patients With Nasopharyngeal Carcinoma Receiving IMRT
NCT02874651PHASE2TERMINATEDADjuVant Apatinib in Nasopharyngeal Carcinoma Patients With Residual Epstein-Barr Virus (EBV) DNA Following Radiotherapy
NCT02902432PHASE2UNKNOWNA Trial of Endostar in Patients With Carcinoma of the Head and Neck
NCT02980315PHASE1/PHASE2UNKNOWNA New EBV Related Technologies of T Cells in Treating Malignant Tumors and Clinical Application
NCT03180476PHASE2COMPLETEDMaintenance Therapy of Apatinib After Chemoradiotherapy in Metastatic Nasopharyngeal Carcinoma
NCT03619824PHASE2UNKNOWNPD-1 Blockade Combined With Definitive Chemoradiation in Locoregionally-advanced Nasopharyngeal Carcinoma
NCT03769467PHASE1/PHASE2TERMINATEDTabelecleucel in Combination With Pembrolizumab in Subjects With Epstein-Barr Virus-associated Nasopharyngeal Carcinoma (EBV+ NPC)
NCT03854838PHASE2UNKNOWNIMRT Combined With Toripalimab in Unresectable Locally Recurrent Nasopharyngeal Carcinoma.
NCT04446663PHASE2UNKNOWNToripalimab Combined With Chemoradiotherapy in Patients With Locoregionally-advanced Nasopharyngeal Carcinoma
NCT04870905PHASE2UNKNOWNTisleilizumab (PD-1 Antibody) and Chemoradiotherapy in Locoregionally-advanced Nasopharyngeal Carcinoma
NCT00078494PHASE1COMPLETEDPeptide Vaccine to Prevent Recurrence of Nasopharyngeal Cancer
NCT01256853PHASE1COMPLETEDModified Vaccinia Ankara (MVA) Vaccine Study
NCT07326358Not specifiedRECRUITINGAI System for Anatomic Recognition & Lesion Detection in Nasopharyngolaryngoscopy: A Prospective Study

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
CISPLATIN416
INTERFERON BETA-1A41
PEMBROLIZUMAB41
PROCAINE41
TABELECLEUCEL41
TORIPALIMAB41
ENDOSTATIN, N-TERMINAL-MGGSHHHHH32
RIVOCERANIB32
SINTILIMAB32
CAMRELIZUMAB31
NIMOTUZUMAB31
TROLAMINE21
CHEMBL485467001

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 72

This page pulls from 72 datasets indexed by BioBTree:

alphafoldantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticscellosauruschembl_activitychembl_assaychembl_documentchembl_moleculechembl_targetciviccivic_evidenceclingen_dosageclinical_trialsclinvarctd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityfantom5_genefantom5_promotergenccgenerifgogtopdbgtopdb_interactiongwasgwas_studyhgncintactinterprointogenmedgenmeshmimmondomondochildmondoparentncitorphanetpatent_compoundpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assayreactomerefseqrhearnacentralsctidscxa_expressionscxa_gene_experimentsignorstring_interactiontranscriptuberonufeatureumlsuniprot