Supratentorial primitive neuroectodermal tumor

Summary

Supratentorial primitive neuroectodermal tumor (MONDO:0003145) is a cancer with 1 cohort gene (1 CIViC-evidence somatic driver; 1 ClinVar predisposition record) and 2 clinical trials. Top therapeutic interventions include carboplatin, temozolomide, and thiotepa.

At a glance

• Classification: Cancer
• Cohort genes: 1
• ClinVar variants: 1
• Clinical trials: 2

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	supratentorial primitive neuroectodermal tumor
Mondo ID	MONDO:0003145
DOID	DOID:4791
NCIT	C6968
SNOMED CT	699318007
UMLS	C1336538
MedGen	234914
GARD	0027632
Is cancer (heuristic)	yes

Also known as: CNS/supratentorial PNET · supratent. primitive neuro. tumor · supratent. primitive neuro. tumour · supratentorial PNET · supratentorial primitive neuroectodermal tumor

Data availability: 1 ClinVar variant.

Disease family

An umbrella term covering 1 Mondo subtype.

Classification path: human disease › disease by etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › cancer › nervous system cancer › central nervous system cancer › brain cancer › supratentorial cancer › supratentorial primitive neuroectodermal tumor

Related subtypes (3): childhood choroid plexus carcinoma, cerebral hemisphere cancer, diencephalic cancer

Subtypes (1): cerebral primitive neuroectodermal tumor

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

ClinVar germline variants

1 retrieved; paginated sample, class counts are floors:

1 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
661301	NM_177438.3(DICER1):c.5425G>A (p.Gly1809Arg)	DICER1	Pathogenic	reviewed by expert panel

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 7 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Somatic driver evidence (intOGen + CIViC, cohort fanout)

Gene	intOGen role	Cancer types	CIViC
DICER1	LoF	COADREAD,CSCC,MEL,UCEC	CIViC #9533

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
DICER1	Orphanet:276399	Familial multinodular goiter
DICER1	Orphanet:284343	DICER1 tumor-predisposition syndrome
DICER1	Orphanet:404476	Global developmental delay-lung cysts-overgrowth-Wilms tumor syndrome
DICER1	Orphanet:99757	Embryonal rhabdomyosarcoma
DICER1	Orphanet:99914	Gynandroblastoma
DICER1	Orphanet:99915	Malignant granulosa cell tumor of the ovary
DICER1	Orphanet:99916	Malignant Sertoli-Leydig cell tumor of the ovary

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
DICER1	HGNC:17098	ENSG00000100697	Q9UPY3	Endoribonuclease Dicer	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
DICER1	Endoribonuclease Dicer	Double-stranded RNA (dsRNA) endoribonuclease playing a central role in short dsRNA-mediated post-transcriptional gene silencing.

Protein-family classification

Druggable: 1 · 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.

Family	Genes	Fold	FDR
Enzyme (other)	1	12.0×	0.083

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
DICER1	Enzyme (other)	yes	3.1.26.3	RNase_III_dom, Helicase_C-like, PAZ_dom

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
caput epididymis	1
cauda epididymis	1
tongue squamous epithelium	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
DICER1	295	ubiquitous	marker	cauda epididymis, caput epididymis, tongue squamous epithelium

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
DICER1	8,268

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
DICER1	Q9UPY3	21

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 5. Enrichment computed across 1 evidence-associated genes (1 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 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis	1	3806.7×	0.001	DICER1
Small interfering RNA (siRNA) biogenesis	1	1142.0×	0.002	DICER1
Regulation of MITF-M-dependent genes involved in apoptosis	1	634.4×	0.003	DICER1
MicroRNA (miRNA) biogenesis	1	456.8×	0.003	DICER1
M-decay: degradation of maternal mRNAs by maternally stored factors	1	326.3×	0.003	DICER1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
positive regulation of Schwann cell differentiation	1	8426.0×	0.001	DICER1
peripheral nervous system myelin formation	1	5617.3×	0.001	DICER1
global gene silencing by mRNA cleavage	1	5617.3×	0.001	DICER1
tRNA decay	1	3370.4×	0.001	DICER1
negative regulation of Schwann cell proliferation	1	2407.4×	0.001	DICER1
siRNA processing	1	1872.4×	0.002	DICER1
RISC complex assembly	1	1532.0×	0.002	DICER1
miRNA metabolic process	1	1404.3×	0.002	DICER1
apoptotic DNA fragmentation	1	1203.7×	0.002	DICER1
pre-miRNA processing	1	1123.5×	0.002	DICER1
miRNA processing	1	1053.2×	0.002	DICER1
nerve development	1	936.2×	0.002	DICER1
positive regulation of myelination	1	766.0×	0.002	DICER1
negative regulation of tumor necrosis factor-mediated signaling pathway	1	455.5×	0.003	DICER1
neuron projection morphogenesis	1	276.3×	0.004	DICER1
negative regulation of tumor necrosis factor production	1	251.5×	0.004	DICER1
negative regulation of gene expression	1	69.1×	0.015	DICER1
negative regulation of transcription by RNA polymerase II	1	17.7×	0.056	DICER1

Therapeutics

Drug target analysis

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

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
DICER1	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

Symbol	Assays	Type breakdown
DICER1	8	Binding:8

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
DICER1	3.1.26.3	ribonuclease III

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; 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):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	1	DICER1
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	0

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
DICER1	8	—

Clinical trials & evidence

Clinical trials

Clinical trials: 2.

Phase distribution (across all retrieved trials)

Phase	Trials
PHASE2/PHASE3	1
Not specified	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT00749723	PHASE2/PHASE3	COMPLETED	Therapy Optimization Trial for the Treatment of Relapsed or Refractory Brain Tumors in Children
NCT05934630	Not specified	TERMINATED	Testing Cerebrospinal Fluid for Cell-free Tumor DNA in Children, Adolescents, and Young Adults With Brain Tumors

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
CARBOPLATIN	4	1
TEMOZOLOMIDE	4	1
THIOTEPA	4	1
TROFOSFAMIDE	3	1
CHEMBL4228794	0	1
CHEMBL4248195	0	1