Polymorphous low grade neuroepithelial tumor of the young

Summary

Polymorphous low grade neuroepithelial tumor of the young (MONDO:0858959) is a cancer with 1 cohort gene (1 CIViC-evidence somatic driver; 1 ClinVar predisposition record).

At a glance

• Classification: Cancer
• Cohort genes: 1
• ClinVar variants: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	polymorphous low grade neuroepithelial tumor of the young
Mondo ID	MONDO:0858959
DOID	DOID:0081305
NCIT	C180378
UMLS	C5556330
MedGen	1792771
Is cancer (heuristic)	yes

Data availability: 1 ClinVar variant.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › benign neoplasm › nervous system benign neoplasm › central nervous system organ benign neoplasm › polymorphous low grade neuroepithelial tumor of the young

Related subtypes (12): central nervous system chondroma, central nervous system hemangioma, central nervous system leiomyoma, central nervous system lipoma, craniopharyngioma, benign neoplasm of brain, benign neoplasm of spinal cord, benign neoplasm of meninges, benign neoplasm of peripheral nervous system, myxoid glioneuronal tumor, diffuse leptomeningeal glioneuronal tumor, multinodular and vacuolating neuronal 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 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
225054	NM_003579.4(RAD54L):c.1624C>T (p.Arg542Cys)	RAD54L	Likely pathogenic	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 1 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Somatic driver evidence (intOGen + CIViC, cohort fanout)

Gene	intOGen role	Cancer types	CIViC
RAD54L			CIViC #6676

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
RAD54L	Orphanet:227535	Hereditary breast cancer

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
RAD54L	HGNC:9826	ENSG00000085999	Q92698	DNA repair and recombination protein RAD54-like	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
RAD54L	DNA repair and recombination protein RAD54-like	Multifunctional ATPase that plays a role in homologous recombination (HR) which is a major pathway for repairing DNA double-strand breaks (DSBs), single-stranded DNA (ssDNA) gaps, and stalled or collapsed replication forks.

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)
RAD54L	Enzyme (other)	yes	3.6.4.B9	SNF2_N, Helicase_C-like, Helicase_ATP-bd

Expression context

Cohort genes with no expression data: 0.

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
left testis	1
right testis	1
ventricular zone	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
RAD54L	173	ubiquitous	yes	left testis, right testis, ventricular zone

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
RAD54L	2,927

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
RAD54L	Q92698	1

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 1 evidence-associated genes (0 with Reactome annotation).

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
double-strand break repair via synthesis-dependent strand annealing	1	4213.0×	0.002	RAD54L
chromosome organization	1	581.1×	0.005	RAD54L
reciprocal meiotic recombination	1	561.7×	0.005	RAD54L
determination of adult lifespan	1	432.1×	0.005	RAD54L
response to ionizing radiation	1	411.0×	0.005	RAD54L
DNA recombination	1	337.0×	0.005	RAD54L
meiotic cell cycle	1	244.2×	0.006	RAD54L
double-strand break repair via homologous recombination	1	156.0×	0.008	RAD54L
response to xenobiotic stimulus	1	69.1×	0.016	RAD54L
DNA repair	1	63.8×	0.016	RAD54L

Therapeutics

Drug target analysis

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

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
RAD54L	1	2

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
STREPTONIGRIN	2	RAD54L

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

Symbol	Assays	Type breakdown
RAD54L	3	Functional:2, Binding:1

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
RAD54L	3.6.4.B9

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

1 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.

Compound	Max phase	Cohort target (bioactivity)
STREPTONIGRIN	2	RAD54L

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	1	RAD54L
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	0

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: 0.