Childhood low-grade glioma

disease
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Summary

Childhood low-grade glioma (MONDO:0859591) is a cancer with 8 cohort genes (8 CIViC-evidence somatic drivers). Molecularly, BRAF V600 OR v::BRAF Fusion confers sensitivity to Tovorafenib in Childhood Low-grade Glioma (CIViC Level A); 6 further subtype–drug associations are mapped below.

At a glance

  • Classification: Cancer
  • Cohort genes: 8
  • Precision-medicine evidence (CIViC): 7 subtype–drug associations

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namechildhood low-grade glioma
Mondo IDMONDO:0859591
DOIDDOID:0080830
NCITC202299
UMLSC5908420
MedGen1861125
GARD0026753
Is cancer (heuristic)yes

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › cancer or benign tumorneoplastic disease or syndromeneoplasmnervous system neoplasmneuroepithelial neoplasmgliomalow grade gliomachildhood low-grade glioma

Related subtypes (5): schwannoma, angiocentric glioma, low grade astrocytic tumor, grade II glioma, diffuse low-grade glioma, MAPK pathway–altered

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: 61 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Somatic driver evidence (intOGen + CIViC, cohort fanout)

GeneintOGen roleCancer typesCIViC
BRAFActBLCA,BRCA,CHOL,CLLSLL,COAD,COADREAD,CSCC,DLBCLNOS,GBM,GIST,HGGNOS,LGGNOS,LUAD,MEL,MLYM,NSCLC,OVT,PAST,PCM,PRAD,PRCC,PROSTATE,READ,SACA,SKCM,STAD,UCEC,WDTCCIViC #5
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
FGFR1ActBLCA,GBM,OVT,PANCREAS,PAST,PGNG,WDTCCIViC #1885
H3-3AActHGGNOS,PASTCIViC #2537
MYBCIViC #3730
NF1LoFACC,ALL,AML,ANGS,BLCA,BRCA,CCRCC,CHOL,CLLSLL,COADREAD,GB,GBM,GIST,HCC,HNSC,LGGNOS,LMS,LUAD,LUNG,LUSC,MEL,NBL,NSCLC,OVT,PAST,PGNG,PLMESO,RMS,SKCM,SOFT_TISSUE,STAD,THYM,UCSCIViC #3867
ATRXLoFACC,CLLSLL,GB,GBM,HGGNOS,LGGNOS,LMS,NBL,OS,OVT,PANET,PAST,SARCNOS,SOFT_TISSUECIViC #525

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
BRAFOrphanet:1340Cardiofaciocutaneous syndrome
BRAFOrphanet:146Differentiated thyroid carcinoma
BRAFOrphanet:251615Pilomyxoid astrocytoma
BRAFOrphanet:389Langerhans cell histiocytosis
BRAFOrphanet:500Noonan syndrome with multiple lentigines
BRAFOrphanet:54595Craniopharyngioma
BRAFOrphanet:58017Classic hairy cell leukemia
BRAFOrphanet:626Large/giant congenital melanocytic nevus
BRAFOrphanet:648Noonan syndrome
BRAFOrphanet:840Syringocystadenoma papilliferum
BRAFOrphanet:96253Cushing 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
FGFR1Orphanet:168953Myeloid/lymphoid neoplasm associated with FGFR1 rearrangement
FGFR1Orphanet:2117Hartsfield syndrome
FGFR1Orphanet:220386Semilobar holoprosencephaly
FGFR1Orphanet:2396Encephalocraniocutaneous lipomatosis
FGFR1Orphanet:251576Gliosarcoma
FGFR1Orphanet:251579Giant cell glioblastoma
FGFR1Orphanet:251615Pilomyxoid astrocytoma
FGFR1Orphanet:2645Osteoglosphonic dysplasia
FGFR1Orphanet:280200Microform holoprosencephaly
FGFR1Orphanet:314950Primary hypereosinophilic syndrome
FGFR1Orphanet:3157Septo-optic dysplasia spectrum
FGFR1Orphanet:3366Non-syndromic metopic craniosynostosis
FGFR1Orphanet:432Normosmic congenital hypogonadotropic hypogonadism
FGFR1Orphanet:478Kallmann syndrome
FGFR1Orphanet:93258Pfeiffer syndrome type 1
FGFR1Orphanet:93924Lobar holoprosencephaly
FGFR1Orphanet:99798Oligodontia
MYBOrphanet:251671Angiocentric glioma
MYBOrphanet:86849Acute basophilic leukemia
MYBOrphanet:99861Precursor T-cell acute lymphoblastic leukemia
NF1Orphanet:13947417q11.2 microduplication syndrome
NF1Orphanet:29072Hereditary pheochromocytoma-paraganglioma

Cohort genes → proteins

8 cohort genes, 8 distinct canonical proteins.

Evidence partition

SubsetGenes
civic_only8

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
BRAFHGNC:1097ENSG00000157764P15056Serine/threonine-protein kinase B-rafcivic_evidence
TERTHGNC:11730ENSG00000164362O14746Telomerase reverse transcriptasecivic_evidence
CDKN2AHGNC:1787ENSG00000147889P42771Cyclin-dependent kinase inhibitor 2Acivic_evidence
FGFR1HGNC:3688ENSG00000077782P11362Fibroblast growth factor receptor 1civic_evidence
H3-3AHGNC:4764ENSG00000163041P84243Histone H3.3civic_evidence
MYBHGNC:7545ENSG00000118513P10242Transcriptional activator Mybcivic_evidence
NF1HGNC:7765ENSG00000196712P21359Neurofibromincivic_evidence
ATRXHGNC:886ENSG00000085224P46100Transcriptional regulator ATRXcivic_evidence

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
BRAFSerine/threonine-protein kinase B-rafProtein kinase involved in the transduction of mitogenic signals from the cell membrane to the nucleus.
TERTTelomerase reverse transcriptaseTelomerase is a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes.
CDKN2ACyclin-dependent kinase inhibitor 2AActs as a negative regulator of the proliferation of normal cells by interacting strongly with CDK4 and CDK6.
FGFR1Fibroblast growth factor receptor 1Tyrosine-protein kinase that acts as a cell-surface receptor for fibroblast growth factors and plays an essential role in the regulation of embryonic development, cell proliferation, differentiation and migration.
H3-3AHistone H3.3Variant histone H3 which replaces conventional H3 in a wide range of nucleosomes in active genes.
MYBTranscriptional activator MybTranscriptional activator; DNA-binding protein that specifically recognize the sequence 5’-YAAC[GT]G-3'.
NF1NeurofibrominStimulates the GTPase activity of Ras.
ATRXTranscriptional regulator ATRXInvolved in transcriptional regulation and chromatin remodeling.

Protein-family classification

Druggable: 2 · Difficult: 3 · Unknown: 3 · Druggable fraction: 0.25

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
Kinase26.9×0.126
Transcription factor22.1×0.503
Scaffold/PPI12.2×0.506
Other/Unknown30.7×0.919

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
BRAFKinaseyes2.7.10.2Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom, PKC_DAG/PE
TERTOther/UnknownnoRT_dom, Telomerase_RT, Telomerase_RBD
CDKN2AScaffold/PPInoAnkyrin_rpt-contain_sf, Ank_Repeat/CDKN_Inhibitor, Tumor_suppres_ARF
FGFR1Kinaseyes2.7.10.1Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom, Ig_sub2
H3-3AOther/UnknownnoHistone_H3/CENP-A, H2A/H2B/H3, Histone-fold
MYBTranscription factornoSANT/Myb, Homeodomain-like_sf, Tscrpt_reg_Wos2-domain
NF1Other/UnknownnoCRAL-TRIO_dom, RasGAP_dom, Rho_GTPase_activation_prot
ATRXTranscription factornoSNF2_N, Helicase_C-like, Znf_FYVE_PHD

Expression context

Cohort genes with no expression data: 0.

7 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)8
unknown0

Top tissues across cohort

TissueCohort genes
calcaneal tendon4
colonic epithelium3
buccal mucosa cell2
stromal cell of endometrium2
olfactory bulb1
type B pancreatic cell1
cervix squamous epithelium1
parotid gland1
pituitary gland1
ganglionic eminence1
monocyte1
ventricular zone1
bronchial epithelial cell1
epithelium of bronchus1
mucosa of sigmoid colon1
adrenal tissue1
endothelial cell1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
BRAF265ubiquitousmarkerbuccal mucosa cell, colonic epithelium, calcaneal tendon
TERT105broadyesstromal cell of endometrium, type B pancreatic cell, olfactory bulb
CDKN2A220ubiquitousmarkerparotid gland, cervix squamous epithelium, pituitary gland
FGFR1292ubiquitousmarkerbuccal mucosa cell, stromal cell of endometrium, calcaneal tendon
H3-3A134ubiquitousmarkerganglionic eminence, monocyte, ventricular zone
MYB183broadmarkermucosa of sigmoid colon, bronchial epithelial cell, epithelium of bronchus
NF1283ubiquitousmarkercolonic epithelium, calcaneal tendon, adrenal tissue
ATRX294ubiquitousmarkerendothelial cell, calcaneal tendon, colonic epithelium

Protein interactions among cohort

Intra-cohort edges: 3.

Hub genes (top 10 by interactor count)

SymbolInteractor count
CDKN2A9,311
BRAF7,394
ATRX5,796
TERT5,717
FGFR15,693
NF15,540
MYB3,155
H3-3A1,595

Intra-cohort edges

ABSources
ATRXH3-3Aintact
BRAFCDKN2Astring_interaction
BRAFNF1string_interaction

Structural data

PDB: 7 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
BRAFP15056131
H3-3AP84243103
FGFR1P1136283
NF1P2135926
TERTO1474623
ATRXP4610012
CDKN2AP427715

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
MYBP1024259.16

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 174. Enrichment computed across 8 evidence-associated genes (8 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 8 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Alternative Lengthening of Telomeres (ALT)11427.5×0.012ATRX
Evasion of Oncogene Induced Senescence Due to p14ARF Defects11427.5×0.012CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to p14ARF Defects11427.5×0.012CDKN2A
Defective Inhibition of DNA Recombination at Telomere11427.5×0.012ATRX
Diseases of Telomere Maintenance11427.5×0.012ATRX
Signaling by FGFR1 amplification mutants1713.8×0.012FGFR1
Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK41713.8×0.012CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK41713.8×0.012CDKN2A
Defective Intrinsic Pathway for Apoptosis Due to p14ARF Loss of Function1713.8×0.012CDKN2A
Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations1713.8×0.012ATRX
Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations1713.8×0.012ATRX
Diseases of Cellular Senescence1475.8×0.012CDKN2A
Evasion of Oncogene Induced Senescence Due to p16INK4A Defects1475.8×0.012CDKN2A
Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK61475.8×0.012CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to p16INK4A Defects1475.8×0.012CDKN2A
Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK61475.8×0.012CDKN2A
Diseases of cellular response to stress1475.8×0.012CDKN2A
Telomere Maintenance292.1×0.012TERT, ATRX
Negative regulation of FGFR1 signaling292.1×0.012BRAF, FGFR1
Oncogenic MAPK signaling262.1×0.012BRAF, NF1
Chromosome Maintenance252.9×0.012TERT, ATRX
MITF-M-dependent gene expression245.3×0.012TERT, CDKN2A
Inhibition of DNA recombination at telomere242.0×0.012H3-3A, ATRX
MAPK1/MAPK3 signaling232.8×0.012BRAF, NF1
Transcriptional regulation of granulopoiesis231.4×0.012H3-3A, MYB
Formation of the beta-catenin:TCF transactivating complex230.1×0.012TERT, H3-3A
MITF-M-regulated melanocyte development228.6×0.012TERT, CDKN2A
RAF/MAP kinase cascade322.9×0.012BRAF, FGFR1, NF1
Cell Cycle313.5×0.012TERT, CDKN2A, ATRX
Disease46.5×0.012BRAF, CDKN2A, NF1, ATRX

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 8 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
subtelomeric heterochromatin formation2383.0×0.002H3-3A, ATRX
MAPK cascade357.5×0.002BRAF, FGFR1, NF1
replicative senescence2247.8×0.003TERT, CDKN2A
negative regulation of cell-matrix adhesion2221.7×0.003CDKN2A, NF1
positive regulation of stem cell proliferation2131.7×0.006TERT, FGFR1
negative regulation of endothelial cell apoptotic process2123.9×0.006BRAF, TERT
positive regulation of vascular associated smooth muscle cell proliferation2108.0×0.007TERT, NF1
RNA-templated transcription12106.5×0.007TERT
DNA strand elongation12106.5×0.007TERT
positive regulation of mast cell apoptotic process12106.5×0.007NF1
regulation of glial cell differentiation12106.5×0.007NF1
observational learning12106.5×0.007NF1
siRNA transcription12106.5×0.007TERT
positive regulation of transdifferentiation12106.5×0.007TERT
thymus development284.3×0.007BRAF, MYB
stem cell proliferation278.0×0.007FGFR1, NF1
visual learning276.6×0.007BRAF, NF1
positive regulation of miRNA transcription272.6×0.007TERT, MYB
long-term synaptic potentiation270.2×0.007BRAF, NF1
positive regulation of neuron apoptotic process268.0×0.007MYB, NF1
somatic stem cell population maintenance262.0×0.007BRAF, CDKN2A
cellular response to hydrogen peroxide258.5×0.007CDKN2A, MYB
Ras protein signal transduction251.4×0.009CDKN2A, NF1
RNA-templated DNA biosynthetic process11053.2×0.009TERT
nuclear body organization11053.2×0.009CDKN2A
post-embryonic forelimb morphogenesis11053.2×0.009ATRX
positive regulation of hair cycle11053.2×0.009TERT
gamma-aminobutyric acid secretion, neurotransmission11053.2×0.009NF1
vitamin D3 metabolic process11053.2×0.009FGFR1
positive regulation of mitotic cell cycle DNA replication11053.2×0.009FGFR1

Therapeutics

Drug target analysis

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

Druggability breadth: 6 of 8 evidence-associated genes (75%) 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
BRAFVEMURAFENIB
TERTBERBERINE
FGFR1PONATINIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
FGFR1934
BRAF484
TERT104
CDKN2A00
H3-3A00
MYB00
NF100
ATRX00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
VEMURAFENIB4BRAF
PONATINIB4BRAF, FGFR1
FEDRATINIB4BRAF, FGFR1
SORAFENIB4BRAF, FGFR1
DASATINIB ANHYDROUS4BRAF
RUXOLITINIB4BRAF
INFIGRATINIB PHOSPHATE4BRAF, FGFR1
INFIGRATINIB4BRAF, FGFR1
REGORAFENIB4BRAF, FGFR1
DABRAFENIB4BRAF
COBIMETINIB4BRAF
NILOTINIB4BRAF
ABEMACICLIB4BRAF
ENCORAFENIB4BRAF
TOVORAFENIB4BRAF
PAZOPANIB4BRAF, FGFR1
DASATINIB4BRAF, FGFR1
ERLOTINIB4BRAF
GEFITINIB4BRAF
IMATINIB4BRAF
BERBERINE4TERT
DOXORUBICIN4TERT
PEMIGATINIB4FGFR1
NINTEDANIB4FGFR1
TIVOZANIB4FGFR1
LENVATINIB4FGFR1
AXITINIB4FGFR1
NICLOSAMIDE4FGFR1
ENTRECTINIB4FGFR1
CABOZANTINIB4FGFR1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 2.

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

SymbolAssaysType breakdown
FGFR11,465Binding:1428, Functional:24, ADMET:13
BRAF1,442Binding:1400, Functional:37, ADMET:5
TERT391Binding:389, Functional:2
MYB7Binding:7
H3-3A6Binding:6
CDKN2A2Binding:2

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
BRAF2.7.10.2, 2.7.11.1non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase
FGFR12.7.10.1receptor protein-tyrosine kinase

Cohort genes with high screening signal

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

SymbolChEMBL assays
BRAF1,442
TERT391
FGFR11,465

Pharmacogenomics

Cohort genes with a PharmGKB record: 8; with CPIC/DPWG dosing guidelines: 0.

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

Drug repurposing candidates

30 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)
VEMURAFENIB4BRAF
PONATINIB4BRAF, FGFR1
FEDRATINIB4BRAF, FGFR1
SORAFENIB4BRAF, FGFR1
DASATINIB ANHYDROUS4BRAF
RUXOLITINIB4BRAF
INFIGRATINIB PHOSPHATE4BRAF, FGFR1
INFIGRATINIB4BRAF, FGFR1
REGORAFENIB4BRAF, FGFR1
DABRAFENIB4BRAF
COBIMETINIB4BRAF
NILOTINIB4BRAF
ABEMACICLIB4BRAF
ENCORAFENIB4BRAF
TOVORAFENIB4BRAF
PAZOPANIB4BRAF, FGFR1
DASATINIB4BRAF, FGFR1
ERLOTINIB4BRAF
GEFITINIB4BRAF
IMATINIB4BRAF
BERBERINE4TERT
DOXORUBICIN4TERT
PEMIGATINIB4FGFR1
NINTEDANIB4FGFR1
TIVOZANIB4FGFR1
LENVATINIB4FGFR1
AXITINIB4FGFR1
NICLOSAMIDE4FGFR1
ENTRECTINIB4FGFR1
CABOZANTINIB4FGFR1

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3BRAF, TERT, FGFR1
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug5CDKN2A, H3-3A, MYB, NF1, ATRX

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
NF10BRAF
CDKN2A2
H3-3A6
MYB7
ATRX0

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Precision-medicine subtype map (CIViC)

Drug × molecular subtype: 7 predictive associations from 7 curated evidence items; also 8 prognostic, 1 diagnostic.

Molecular subtypeTherapyEffectLevelCIViC
BRAF V600 OR v::BRAF FusionTovorafenibSensitivity/ResponseCIViC AEID12028
BRAF V600E OR KIAA1549::BRAF FusionTovorafenibSensitivity/ResponseCIViC AEID12016
BRAF V600DabrafenibSensitivity/ResponseCIViC BEID8034
NF1 MutationSelumetinibSensitivity/ResponseCIViC BEID7487
FAM131B::BRAF FusionEverolimus + TrametinibSensitivity/ResponseCIViC DEID7198
KIAA1549::BRAF FusionEverolimus + TrametinibSensitivity/ResponseCIViC DEID7199
KIAA1549::BRAF FusionVemurafenib + PLX4720Adverse ResponseCIViC DEID7204