Mucosal melanoma

disease
On this page

Summary

Mucosal melanoma (MONDO:0000544) is a cancer with 2 cohort genes (2 CIViC-evidence somatic drivers) and 61 clinical trials. Molecularly, KIT Amplification is associated with resistance to Imatinib in Mucosal Melanoma (CIViC Level B); 2 further subtype–drug associations are mapped below. Top therapeutic interventions include toripalimab, sorafenib, and axitinib.

At a glance

  • Classification: Cancer
  • Cohort genes: 2
  • Clinical trials: 61
  • Precision-medicine evidence (CIViC): 3 subtype–drug associations

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namemucosal melanoma
Mondo IDMONDO:0000544
DOIDDOID:0050929
NCITC114828
UMLSC3898222
MedGen857816
Is cancer (heuristic)yes

Also known as: mucosal melanoma

Data availability: 10 cell lines.

Disease family

An umbrella term covering 2 Mondo subtypes.

Classification path: disease › human disease › disease by etiologic mechanism › cancer or benign tumorneoplastic disease or syndromeneoplasmmelanocytic neoplasmmelanomanon-cutaneous melanomamucosal melanoma

Related subtypes (3): vulvar melanoma, primary melanoma of the central nervous system, digestive system melanoma

Subtypes (2): cervix melanoma, vaginal melanoma

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

No tiered GWAS variants or ClinVar records for this disease.

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 26 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Somatic driver evidence (intOGen + CIViC, cohort fanout)

GeneintOGen roleCancer typesCIViC
ALKActBRCA,HCC,NBL,NSCLC,PROSTATE,SCLCCIViC #1
KITActAML,GIST,MEL,MGCTCIViC #29

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
ALKOrphanet:146Differentiated thyroid carcinoma
ALKOrphanet:178342Inflammatory myofibroblastic tumor
ALKOrphanet:251877Ganglioneuroblastoma
ALKOrphanet:251992Ganglioneuroma
ALKOrphanet:300895ALK-positive anaplastic large cell lymphoma
ALKOrphanet:364043ALK-positive large B-cell lymphoma
ALKOrphanet:626Large/giant congenital melanocytic nevus
ALKOrphanet:635Neuroblastoma
KITOrphanet:102724Acute myeloid leukemia with t(8;21)(q22;q22) translocation
KITOrphanet:158766Typical urticaria pigmentosa
KITOrphanet:158769Plaque-form urticaria pigmentosa
KITOrphanet:158772Nodular urticaria pigmentosa
KITOrphanet:158775Smoldering systemic mastocytosis
KITOrphanet:158778Isolated bone marrow mastocytosis
KITOrphanet:280785Bullous diffuse cutaneous mastocytosis
KITOrphanet:280794Pseudoxanthomatous diffuse cutaneous mastocytosis
KITOrphanet:2884Piebaldism
KITOrphanet:44890Gastrointestinal stromal tumor
KITOrphanet:566393Acute mast cell leukemia
KITOrphanet:566396Chronic mast cell leukemia
KITOrphanet:79455Cutaneous mastocytoma
KITOrphanet:842Testicular seminomatous germ cell tumor
KITOrphanet:90389Telangiectasia macularis eruptiva perstans
KITOrphanet:98829Acute myeloid leukemia with abnormal bone marrow eosinophils inv(16)(p13q22) or t(16;16)(p13;q22)
KITOrphanet:98834Acute myeloblastic leukemia with maturation
KITOrphanet:98849Systemic mastocytosis with associated hematologic neoplasm

Cohort genes → proteins

2 cohort genes, 2 distinct canonical proteins.

Evidence partition

SubsetGenes
civic_only2

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
ALKHGNC:427ENSG00000171094Q9UM73ALK tyrosine kinase receptorcivic_evidence
KITHGNC:6342ENSG00000157404P10721Mast/stem cell growth factor receptor Kitcivic_evidence

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
ALKALK tyrosine kinase receptorNeuronal receptor tyrosine kinase that is essentially and transiently expressed in specific regions of the central and peripheral nervous systems and plays an important role in the genesis and differentiation of the nervous system.
KITMast/stem cell growth factor receptor KitTyrosine-protein kinase that acts as a cell-surface receptor for the cytokine KITLG/SCF and plays an essential role in the regulation of cell survival and proliferation, hematopoiesis, stem cell maintenance, gametogenesis, mast cell develo…

Protein-family classification

Druggable: 2 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0

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
Kinase227.7×0.001

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
ALKKinaseyes2.7.10.1Prot_kinase_dom, MAM_dom, Ser-Thr/Tyr_kinase_cat_dom
KITKinaseyes2.7.10.1Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom, Tyr_kinase_rcpt_3_CS

Expression context

Cohort genes with no expression data: 0.

2 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)2
unknown0

Top tissues across cohort

TissueCohort genes
male germ cell1
male germ line stem cell (sensu Vertebrata) in testis1
sperm1
lateral nuclear group of thalamus1
oocyte1
secondary oocyte1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
ALK181broadmarkersperm, male germ cell, male germ line stem cell (sensu Vertebrata) in testis
KIT263broadmarkerlateral nuclear group of thalamus, secondary oocyte, oocyte

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
KIT6,087
ALK4,792

Structural data

PDB: 2 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
ALKQ9UM7379
KITP1072152

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 52. Enrichment computed across 2 evidence-associated genes (2 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 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Dasatinib-resistant KIT mutants15710.0×5e-04KIT
Imatinib-resistant KIT mutants15710.0×5e-04KIT
KIT mutants bind TKIs15710.0×5e-04KIT
Masitinib-resistant KIT mutants15710.0×5e-04KIT
Nilotinib-resistant KIT mutants15710.0×5e-04KIT
Regorafenib-resistant KIT mutants15710.0×5e-04KIT
Signaling by kinase domain mutants of KIT15710.0×5e-04KIT
Sunitinib-resistant KIT mutants15710.0×5e-04KIT
Signaling by juxtamembrane domain KIT mutants15710.0×5e-04KIT
Sorafenib-resistant KIT mutants15710.0×5e-04KIT
Drug resistance of KIT mutants15710.0×5e-04KIT
Signaling by extracellular domain mutants of KIT15710.0×5e-04KIT
Drug resistance of ALK mutants15710.0×5e-04ALK
ASP-3026-resistant ALK mutants15710.0×5e-04ALK
NVP-TAE684-resistant ALK mutants15710.0×5e-04ALK
alectinib-resistant ALK mutants15710.0×5e-04ALK
brigatinib-resistant ALK mutants15710.0×5e-04ALK
ceritinib-resistant ALK mutants15710.0×5e-04ALK
crizotinib-resistant ALK mutants15710.0×5e-04ALK
lorlatinib-resistant ALK mutants15710.0×5e-04ALK
Diseases of signal transduction by growth factor receptors and second messengers256.8×8e-04ALK, KIT
Signaling by Receptor Tyrosine Kinases251.7×9e-04ALK, KIT
MDK and PTN in ALK signaling11427.5×0.002ALK
Signaling by KIT in disease1571.0×0.004KIT
ALK mutants bind TKIs1475.8×0.004ALK
TFAP2 (AP-2) family regulates transcription of growth factors and their receptors1380.7×0.005KIT
Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors1317.2×0.006KIT
Developmental Lineage of Mammary Gland Alveolar Cells1317.2×0.006KIT
Regulation of KIT signaling1300.5×0.006KIT
Signaling by ALK1285.5×0.006ALK

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
melanocyte adhesion18426.0×0.002KIT
positive regulation of pyloric antrum smooth muscle contraction18426.0×0.002KIT
positive regulation of colon smooth muscle contraction18426.0×0.002KIT
protein autophosphorylation2145.3×0.002ALK, KIT
regulation of cell population proliferation2115.4×0.002ALK, KIT
response to environmental enrichment14213.0×0.002ALK
positive regulation of vascular associated smooth muscle cell differentiation14213.0×0.002KIT
Fc receptor signaling pathway12808.7×0.002KIT
Kit signaling pathway12808.7×0.002KIT
melanocyte migration12808.7×0.002KIT
obsolete regulation of bile acid metabolic process12808.7×0.002KIT
positive regulation of small intestine smooth muscle contraction12808.7×0.002KIT
mast cell chemotaxis12106.5×0.002KIT
hematopoietic stem cell migration12106.5×0.002KIT
regulation of dopamine receptor signaling pathway12106.5×0.002ALK
mast cell differentiation12106.5×0.002KIT
positive regulation of dendritic cell cytokine production11685.2×0.002KIT
positive regulation of mast cell cytokine production11685.2×0.002KIT
swimming behavior11685.2×0.002ALK
mast cell proliferation11685.2×0.002KIT
positive regulation of mast cell proliferation11685.2×0.002KIT
lymphoid progenitor cell differentiation11404.3×0.003KIT
erythropoietin-mediated signaling pathway11404.3×0.003KIT
myeloid progenitor cell differentiation11203.7×0.003KIT
immature B cell differentiation11203.7×0.003KIT
glycosphingolipid metabolic process11203.7×0.003KIT
response to stress11203.7×0.003ALK
tongue development11053.2×0.003KIT
primordial germ cell migration1936.2×0.003KIT
peptidyl-tyrosine autophosphorylation1936.2×0.003ALK

Therapeutics

Drug target analysis

Approved (phase 4): 2 · Phase ≥3: 2 · Phased (≥1): 2 · Undrugged: 0

Druggability breadth: 2 of 2 evidence-associated genes (100%) 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
ALKCERITINIB
KITPONATINIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
KIT994
ALK614

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
CERITINIB4ALK, KIT
BOSUTINIB4ALK, KIT
CRIZOTINIB4ALK, KIT
ALECTINIB4ALK
ENTRECTINIB4ALK, KIT
LORLATINIB4ALK
GILTERITINIB4ALK
OSIMERTINIB4ALK
BRIGATINIB4ALK, KIT
REPOTRECTINIB4ALK
FEDRATINIB4ALK, KIT
RUXOLITINIB4ALK, KIT
INFIGRATINIB PHOSPHATE4ALK, KIT
INFIGRATINIB4ALK, KIT
PALBOCICLIB4ALK
VANDETANIB4ALK, KIT
UPADACITINIB4ALK
PAZOPANIB4ALK, KIT
NINTEDANIB4ALK, KIT
SUNITINIB4ALK, KIT
ERLOTINIB4ALK, KIT
MIDOSTAURIN4ALK, KIT
PONATINIB4KIT
TIVOZANIB4KIT
LENVATINIB4KIT
AXITINIB4KIT
SORAFENIB4KIT
DASATINIB ANHYDROUS4KIT
NICLOSAMIDE4KIT
IMATINIB MESYLATE4KIT

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

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

SymbolAssaysType breakdown
KIT2,305Binding:2242, ADMET:32, Functional:22, Toxicity:9
ALK1,815Binding:1801, Functional:13, ADMET:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
ALK2.7.10.1receptor protein-tyrosine kinase
KIT2.7.10.1receptor protein-tyrosine kinase

Cohort genes with high screening signal

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

SymbolChEMBL assays
ALK1,815
KIT2,305

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; with CPIC/DPWG dosing guidelines: 0.

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

Drug repurposing candidates

28 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)
CERITINIB4ALK, KIT
BOSUTINIB4ALK, KIT
CRIZOTINIB4ALK, KIT
ALECTINIB4ALK
ENTRECTINIB4ALK, KIT
LORLATINIB4ALK
GILTERITINIB4ALK
OSIMERTINIB4ALK
BRIGATINIB4ALK, KIT
REPOTRECTINIB4ALK
FEDRATINIB4ALK, KIT
RUXOLITINIB4ALK, KIT
INFIGRATINIB PHOSPHATE4ALK, KIT
INFIGRATINIB4ALK, KIT
PALBOCICLIB4ALK
VANDETANIB4ALK, KIT
UPADACITINIB4ALK
PAZOPANIB4ALK, KIT
NINTEDANIB4ALK, KIT
SUNITINIB4ALK, KIT
ERLOTINIB4ALK, KIT
MIDOSTAURIN4ALK, KIT
PONATINIB4KIT
TIVOZANIB4KIT
LENVATINIB4KIT
DASATINIB ANHYDROUS4KIT
NICLOSAMIDE4KIT
IMATINIB MESYLATE4KIT

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)2ALK, KIT
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug0

Undrugged target profiles

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

Clinical trials & evidence

Clinical trials

Clinical trials: 61.

Phase distribution (across all retrieved trials)

PhaseTrials
PHASE240
PHASE110
Not specified4
PHASE33
PHASE1/PHASE23
EARLY_PHASE11

Top trials by phase / activity

NCTPhaseStatusTitle
NCT02506153PHASE3ACTIVE_NOT_RECRUITINGPhysician/Patient Choice of Either High-Dose Recombinant Interferon Alfa-2B or Ipilimumab, Versus Pembrolizumab in Treating Patients With Stage III-IV High Risk Melanoma That Has Been Removed by Surgery
NCT00110019PHASE3COMPLETEDCarboplatin and Paclitaxel With or Without Sorafenib Tosylate in Treating Patients With Stage III or Stage IV Melanoma That Cannot Be Removed by Surgery
NCT01989572PHASE3COMPLETEDSargramostim, Vaccine Therapy, or Sargramostim and Vaccine Therapy in Preventing Disease Recurrence in Patients With Melanoma That Has Been Removed By Surgery
NCT00937937PHASE2ACTIVE_NOT_RECRUITINGDinaciclib in Treating Patients With Stage IV Melanoma
NCT03241186PHASE2ACTIVE_NOT_RECRUITINGIpilimumab and Nivolumab as Adjuvant Treatment of Mucosal Melanoma
NCT03611868PHASE1/PHASE2ACTIVE_NOT_RECRUITINGA Study of APG-115 in as a Monotherapy or Combination With Pembrolizumab in Patients With Metastatic Melanomas or Advanced Solid Tumors
NCT03698019PHASE2ACTIVE_NOT_RECRUITINGA Study to Compare the Administration of Pembrolizumab After Surgery Versus Administration Both Before and After Surgery for High-Risk Melanoma
NCT04511013PHASE2RECRUITINGA Study to Compare the Administration of Encorafenib + Binimetinib + Nivolumab Versus Ipilimumab + Nivolumab in BRAF-V600 Mutant Melanoma With Brain Metastases
NCT04645680PHASE2ACTIVE_NOT_RECRUITINGDiet and Immune Effects Trial: DIET- A Randomized Double Blinded Dietary Intervention Study in Patients With Metastatic Melanoma Receiving Immunotherapy
NCT05086692PHASE1/PHASE2RECRUITINGA Beta-only IL-2 ImmunoTherapY Study
NCT05111574PHASE2RECRUITINGUsing Nivolumab Alone or With Cabozantinib to Prevent Mucosal Melanoma Return After Surgery
NCT05384496PHASE2RECRUITINGAxitinib and Nivolumab for the Treatment of Mucosal Melanoma
NCT06319196PHASE2RECRUITINGClear Me: Interception Trial to Detect and Clear Molecular Residual Disease in Patients With High-risk Melanoma
NCT06999980PHASE2RECRUITINGNeo IRENIE (NEOadjuvant Ipilimumab, RElatlimab, NIvolumab Evaluation)
NCT07155317PHASE2RECRUITINGTime-of-Day Specified Immunotherapy for Advanced Melanoma, The TIME Trial
NCT07230613PHASE2RECRUITINGNeo-adjuvant Immunotherapy in Patients With Localized Melanoma
NCT07236528PHASE2NOT_YET_RECRUITINGCombination of Carilizumab, Apatinib, and Radiotherapy for Advanced Mucosal Melanoma
NCT07347444PHASE2NOT_YET_RECRUITINGIparomlimab and Tuvoraleimab Injection in Combination With Bevacizumab, Albumin-bound Paclitaxel, and Carboplatin as First- or Second-line Treatment for Patients With Advanced Acral and Mucosal Melanoma
NCT07400302PHASE2RECRUITINGSintilimab Combined With Chemotherapy for Adjuvant Treatment of Mucosal Melanoma After Surgery
NCT07576725PHASE2NOT_YET_RECRUITINGLow Dose, Reduced Frequency Nivolumab for the Treatment of Unresectable or Metastatic Cancer, AFFORD IO Trial
NCT00085189PHASE2COMPLETEDVaccine Therapy in Treating Patients With Stage IIC-IV Melanoma
NCT00424515PHASE2COMPLETEDImatinib in Patients With Mucosal or Acral/Lentiginous Melanoma
NCT01166126PHASE2TERMINATEDTemsirolimus/AZD 6244 for Treatment-naive With BRAF Mutant Unresectable Stage IV
NCT01961115PHASE2COMPLETEDEpacadostat and Vaccine Therapy in Treating Patients With Stage III-IV Melanoma
NCT02126579PHASE1/PHASE2COMPLETEDPhase I/II Trial of a Long Peptide Vaccine (LPV7) Plus TLR Agonists
NCT02129075PHASE2COMPLETEDA Vaccine (CDX-1401) With or Without a Biologic Drug (CDX-301) for the Treatment of Patients With Stage IIB-IV Melanoma
NCT02158520PHASE2COMPLETEDNab-Paclitaxel and Bevacizumab or Ipilimumab as First-Line Therapy in Treating Patients With Stage IV Melanoma That Cannot Be Removed by Surgery
NCT02519322PHASE2COMPLETEDNeoadjuvant and Adjuvant Checkpoint Blockade
NCT02978443PHASE2TERMINATEDA Biomarker Study in Advanced Mucosal or Acral Lentiginous Melanoma Receiving Nivolumab in Combination With Ipilimumab
NCT03033576PHASE2COMPLETEDTesting Treatment With Ipilimumab and Nivolumab Compared to Treatment With Ipilimumab Alone in Advanced Melanoma
NCT03138642PHASE2UNKNOWNMucosal Melanoma of Head and Neck in Intensity-modulated Radiotherapy Era
NCT03178123PHASE2UNKNOWNThe Study of JS001 Compared to High-Dose Interferon In Patients With Mucosal Melanoma That Has Been Removed by Surgery
NCT03220009PHASE2WITHDRAWNNivolumab or Expectant Observation Following Ipilimumab, Nivolumab, and Surgery in Treating Patients With High Risk Localized, Locoregionally Advanced, or Recurrent Mucosal Melanoma
NCT03602547PHASE2UNKNOWNStudy of the Combination of CM082 With JS001 in Patients With Advanced Mucosal Melanoma.
NCT03941795PHASE2UNKNOWNPhase II Study in the Treatment of Patients With Advanced Mucinous Melanoma
NCT03986515PHASE2UNKNOWNApatinib Plus SHR1210 in Advanced Mucosal Melanoma
NCT04180995PHASE2UNKNOWNToripalimab in Combination With Axitinib in Patients With Localized Mucosal Melanoma
NCT04462965PHASE2UNKNOWNPostoperative Adjuvant Treatment of Completely Resected Mucosal Melanoma Phase II Study
NCT04472806PHASE2UNKNOWNMaintenance Treatment of Toripalimab(JS001) in Patients With Unresectable Locally Advanced or Metastatic Mucosal Melanoma
NCT04622566PHASE2UNKNOWNLenvatinib and Pembrolizumab in Resectable Mucosal Melanoma

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
TORIPALIMAB44
SORAFENIB43
AXITINIB41
BINIMETINIB41
CABOZANTINIB41
CISPLATIN41
ENCORAFENIB41
IPILIMUMAB41
PEMBROLIZUMAB41
RELATLIMAB41
SARGRAMOSTIM41
SELUMETINIB41
TEMSIROLIMUS41
TYROSINASE32
AGATOLIMOD SODIUM31
DINACICLIB31
EPACADOSTAT31
GP-100 ANTIGEN31
INCOMPLETE FREUND’S ADJUVANT31
HILTONOL22
NEMVALEUKIN ALFA21
RESIQUIMOD21
VACTOSERTIB21
YH-00321
CHEMBL236971702
CHEMBL393930702
CHEMBL200667401
CHEMBL517165701
CHEMBL540837401
CHEMBL446320901

Precision-medicine subtype map (CIViC)

Drug × molecular subtype: 3 predictive associations from 3 curated evidence items.

Molecular subtypeTherapyEffectLevelCIViC
KIT AmplificationImatinibResistanceCIViC BEID1466
ALK Alternative Transcript (ATI)EntrectinibSensitivity/ResponseCIViC CEID7421
KIT K642EImatinibSensitivity/ResponseCIViC CEID2889