Anaplastic/large cell medulloblastoma

Summary

Anaplastic/large cell medulloblastoma (MONDO:0016709) is a disease with 3 cohort genes.

At a glance

• Cohort genes: 3
• ClinVar variants: 3

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	anaplastic/large cell medulloblastoma
Mondo ID	MONDO:0016709
Orphanet	251855
NCIT	C129436
UMLS	C4330531
MedGen	1389864
GARD	0020717
Is cancer (heuristic)	no

Also known as: large cell/anaplastic medulloblastoma

Data availability: 3 ClinVar variants.

Disease family

Classification path: disease › human disease › disease by body system or component › nervous system disorder › central nervous system disorder › brain disorder › cerebellar disorder › cerebellar neoplasm › medulloblastoma › anaplastic/large cell medulloblastoma

Related subtypes (13): brain stem medulloblastoma, large cell medulloblastoma, cerebellar vermis medulloblastoma, adult medulloblastoma, melanotic medulloblastoma, childhood medulloblastoma, medullomyoblastoma with myogenic differentiation, medulloblastoma with extensive nodularity, desmoplastic/nodular medulloblastoma, classic medulloblastoma, medulloblastoma WNT activated, medulloblastoma SHH activated, medulloblastoma non-WNT/non-SHH

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

3 retrieved; paginated sample, class counts are floors:

2 conflicting classifications of pathogenicity, 1 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
12356	NM_000546.6(TP53):c.743G>A (p.Arg248Gln)	TP53	Pathogenic	reviewed by expert panel
41752	NM_001048174.2(MUTYH):c.1174C>A (p.Leu392Met)	MUTYH	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
127891	NM_002878.4(RAD51D):c.493C>T (p.Arg165Trp)	RAD51D	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 24 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
TP53	Orphanet:1333	Familial pancreatic carcinoma
TP53	Orphanet:145	Hereditary breast and/or ovarian cancer syndrome
TP53	Orphanet:1501	Adrenocortical carcinoma
TP53	Orphanet:210159	Adult hepatocellular carcinoma
TP53	Orphanet:251576	Gliosarcoma
TP53	Orphanet:251579	Giant cell glioblastoma
TP53	Orphanet:251899	Choroid plexus carcinoma
TP53	Orphanet:2807	Papilloma of choroid plexus
TP53	Orphanet:293199	Pleomorphic rhabdomyosarcoma
TP53	Orphanet:3318	Essential thrombocythemia
TP53	Orphanet:524	Li-Fraumeni syndrome
TP53	Orphanet:52688	Myelodysplastic syndrome
TP53	Orphanet:585909	B-lymphoblastic leukemia/lymphoma with t(9;22)(q34.1;q11.2)
TP53	Orphanet:667662	Breast implant-associated anaplastic large cell lymphoma
TP53	Orphanet:668	Osteosarcoma
TP53	Orphanet:67038	B-cell chronic lymphocytic leukemia
TP53	Orphanet:70573	Small cell lung cancer
TP53	Orphanet:96253	Cushing disease
TP53	Orphanet:99756	Alveolar rhabdomyosarcoma
TP53	Orphanet:99757	Embryonal rhabdomyosarcoma
MUTYH	Orphanet:247798	MUTYH-related polyposis
MUTYH	Orphanet:440437	Familial colorectal cancer Type X
RAD51D	Orphanet:1331	Familial prostate cancer
RAD51D	Orphanet:145	Hereditary breast and/or ovarian cancer syndrome

Cohort genes → proteins

3 cohort genes, 3 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	3

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
TP53	HGNC:11998	ENSG00000141510	P04637	Cellular tumor antigen p53	clinvar
MUTYH	HGNC:7527	ENSG00000132781	Q9UIF7	Adenine DNA glycosylase	clinvar
RAD51D	HGNC:9823	ENSG00000185379	O75771	DNA repair protein RAD51 homolog 4	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
TP53	Cellular tumor antigen p53	Multifunctional transcription factor that induces cell cycle arrest, DNA repair or apoptosis upon binding to its target DNA sequence.
MUTYH	Adenine DNA glycosylase	Involved in oxidative DNA damage repair.
RAD51D	DNA repair protein RAD51 homolog 4	Involved in the homologous recombination repair (HRR) pathway of double-stranded DNA breaks arising during DNA replication or induced by DNA-damaging agents.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 2 · Druggable fraction: 0.0

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
Transcription factor	1	2.8×	0.587
Other/Unknown	2	1.2×	0.587

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
TP53	Transcription factor	no		p53_tumour_suppressor, p53-like_TF_DNA-bd_sf, p53_tetrameristn
MUTYH	Other/Unknown	no		NUDIX_hydrolase_dom, HhH_motif, HhH-GPD_domain
RAD51D	Other/Unknown	no		AAA+_ATPase, Rad51_C, DNA_recomb/repair_RecA-like

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)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	3
unknown	0

Top tissues across cohort

Tissue	Cohort genes
ganglionic eminence	1
tendon of biceps brachii	1
ventricular zone	1
cerebellar cortex	1
cerebellar hemisphere	1
right hemisphere of cerebellum	1
male germ cell	1
oocyte	1
sperm	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
TP53	223	ubiquitous	marker	ventricular zone, ganglionic eminence, tendon of biceps brachii
MUTYH	134	ubiquitous	marker	cerebellar hemisphere, cerebellar cortex, right hemisphere of cerebellum
RAD51D	187	ubiquitous	yes	sperm, male germ cell, oocyte

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
TP53	22,736
RAD51D	3,089
MUTYH	1,815

Structural data

PDB: 3 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
TP53	P04637	313
RAD51D	O75771	17
MUTYH	Q9UIF7	3

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 60. Enrichment computed across 3 evidence-associated genes (3 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 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Defective MUTYH substrate binding	1	3806.7×	0.004	MUTYH
Defective MUTYH substrate processing	1	3806.7×	0.004	MUTYH
Loss of function of TP53 in cancer due to loss of tetramerization ability	1	3806.7×	0.004	TP53
TP53 Regulates Transcription of DNA Repair Genes	2	120.8×	0.004	TP53, RAD51D
Regulation of TP53 Expression	1	1903.3×	0.006	TP53
Transcriptional activation of cell cycle inhibitor p21	1	951.7×	0.011	TP53
Activation of NOXA and translocation to mitochondria	1	634.4×	0.013	TP53
RUNX3 regulates CDKN1A transcription	1	543.8×	0.013	TP53
PI5P Regulates TP53 Acetylation	1	423.0×	0.013	TP53
Activation of PUMA and translocation to mitochondria	1	380.7×	0.013	TP53
Displacement of DNA glycosylase by APEX1	1	346.1×	0.013	MUTYH
TP53 Regulates Transcription of Caspase Activators and Caspases	1	317.2×	0.013	TP53
TP53 Regulates Transcription of Death Receptors and Ligands	1	317.2×	0.013	TP53
Urea cycle	1	292.8×	0.013	TP53
Regulation of TP53 Activity through Association with Co-factors	1	271.9×	0.013	TP53
TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain	1	253.8×	0.013	TP53
Stabilization of p53	1	253.8×	0.013	TP53
TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest	1	237.9×	0.013	TP53
Formation of Senescence-Associated Heterochromatin Foci (SAHF)	1	223.9×	0.013	TP53
Zygotic genome activation (ZGA)	1	223.9×	0.013	TP53
Regulation of NF-kappa B signaling	1	211.5×	0.013	TP53
TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest	1	200.3×	0.013	TP53
SUMOylation of transcription factors	1	190.3×	0.013	TP53
TP53 Regulates Transcription of Genes Involved in Cytochrome C Release	1	181.3×	0.013	TP53
Regulation of TP53 Activity through Methylation	1	181.3×	0.013	TP53
TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain	1	173.0×	0.013	TP53
Regulation of TP53 Activity through Acetylation	1	152.3×	0.013	TP53
Impaired BRCA2 binding to PALB2	1	152.3×	0.013	RAD51D
Pyroptosis	1	141.0×	0.013	TP53
Defective homologous recombination repair (HRR) due to BRCA1 loss of function	1	141.0×	0.013	RAD51D

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
negative regulation of helicase activity	1	5617.3×	0.004	TP53
cellular response to actinomycin D	1	5617.3×	0.004	TP53
regulation of intrinsic apoptotic signaling pathway by p53 class mediator	1	5617.3×	0.004	TP53
negative regulation of G1 to G0 transition	1	5617.3×	0.004	TP53
positive regulation of mitochondrial membrane permeability	1	2808.7×	0.004	TP53
oligodendrocyte apoptotic process	1	2808.7×	0.004	TP53
negative regulation of glucose catabolic process to lactate via pyruvate	1	2808.7×	0.004	TP53
negative regulation of pentose-phosphate shunt	1	2808.7×	0.004	TP53
obsolete homolactic fermentation	1	1872.4×	0.004	TP53
signal transduction by p53 class mediator	1	1872.4×	0.004	TP53
negative regulation of miRNA processing	1	1872.4×	0.004	TP53
intrinsic apoptotic signaling pathway in response to hypoxia	1	1872.4×	0.004	TP53
regulation of fibroblast apoptotic process	1	1872.4×	0.004	TP53
T cell proliferation involved in immune response	1	1404.3×	0.004	TP53
DNA strand invasion	1	1404.3×	0.004	RAD51D
depurination	1	1404.3×	0.004	MUTYH
positive regulation of programmed necrotic cell death	1	1404.3×	0.004	TP53
oxidative stress-induced premature senescence	1	1404.3×	0.004	TP53
B cell lineage commitment	1	1123.5×	0.004	TP53
T cell lineage commitment	1	1123.5×	0.004	TP53
mRNA transcription	1	1123.5×	0.004	TP53
positive regulation of RNA polymerase II transcription preinitiation complex assembly	1	1123.5×	0.004	TP53
positive regulation of thymocyte apoptotic process	1	1123.5×	0.004	TP53
cellular response to UV-C	1	1123.5×	0.004	TP53
regulation of cell cycle	2	49.7×	0.004	TP53, RAD51D
DNA repair	2	42.6×	0.004	MUTYH, RAD51D
regulation of mitochondrial membrane permeability involved in apoptotic process	1	936.2×	0.005	TP53
viral process	1	802.5×	0.005	TP53
mitochondrial DNA repair	1	802.5×	0.005	TP53
regulation of cell cycle G2/M phase transition	1	802.5×	0.005	TP53

Therapeutics

Drug target analysis

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

Druggability breadth: 2 of 3 evidence-associated genes (67%) 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.

Symbol	Example approved molecule
TP53	NITROFURANTOIN

Top cohort targets by molecule count

Symbol	Molecules	Max phase
TP53	196	4
MUTYH	0	0
RAD51D	0	0

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
NITROFURANTOIN	4	TP53
DIOSMIN	4	TP53
VERTEPORFIN	4	TP53
CANDESARTAN CILEXETIL	4	TP53
DIENESTROL	4	TP53
CLOTRIMAZOLE	4	TP53
COLCHICINE	4	TP53
NABUMETONE	4	TP53
SALMETEROL XINAFOATE	4	TP53
AMIODARONE HYDROCHLORIDE	4	TP53
FURAZOLIDONE	4	TP53
AMOXAPINE	4	TP53
RALOXIFENE HYDROCHLORIDE	4	TP53
NICARDIPINE HYDROCHLORIDE	4	TP53
SULCONAZOLE NITRATE	4	TP53
PYRITHIONE ZINC	4	TP53
LACTIC ACID	4	TP53
OXYMETHOLONE	4	TP53
CHLOROXINE	4	TP53
PROPIOLACTONE	4	TP53
CLOMIPRAMINE HYDROCHLORIDE	4	TP53
PHENYL AMINOSALICYLATE	4	TP53
THIORIDAZINE HYDROCHLORIDE	4	TP53
AMITRIPTYLINE HYDROCHLORIDE	4	TP53
ETHOPROPAZINE HYDROCHLORIDE	4	TP53
MECHLORETHAMINE HYDROCHLORIDE	4	TP53
ECONAZOLE NITRATE	4	TP53
TRIFLUPROMAZINE HYDROCHLORIDE	4	TP53
PROCHLORPERAZINE EDISYLATE	4	TP53
DEQUALINIUM CHLORIDE	4	TP53

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

Symbol	Assays	Type breakdown
TP53	869	Binding:775, ADMET:83, Functional:10, Toxicity:1
MUTYH	1	Functional:1

Cohort genes with high screening signal

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

Symbol	ChEMBL assays
TP53	869

Pharmacogenomics

Cohort genes with a PharmGKB record: 3; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

30 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Compound	Max phase	Cohort target (bioactivity)
NITROFURANTOIN	4	TP53
DIOSMIN	4	TP53
VERTEPORFIN	4	TP53
CANDESARTAN CILEXETIL	4	TP53
DIENESTROL	4	TP53
CLOTRIMAZOLE	4	TP53
COLCHICINE	4	TP53
NABUMETONE	4	TP53
SALMETEROL XINAFOATE	4	TP53
AMIODARONE HYDROCHLORIDE	4	TP53
FURAZOLIDONE	4	TP53
AMOXAPINE	4	TP53
RALOXIFENE HYDROCHLORIDE	4	TP53
NICARDIPINE HYDROCHLORIDE	4	TP53
SULCONAZOLE NITRATE	4	TP53
PYRITHIONE ZINC	4	TP53
LACTIC ACID	4	TP53
OXYMETHOLONE	4	TP53
CHLOROXINE	4	TP53
PROPIOLACTONE	4	TP53
CLOMIPRAMINE HYDROCHLORIDE	4	TP53
PHENYL AMINOSALICYLATE	4	TP53
THIORIDAZINE HYDROCHLORIDE	4	TP53
AMITRIPTYLINE HYDROCHLORIDE	4	TP53
ETHOPROPAZINE HYDROCHLORIDE	4	TP53
MECHLORETHAMINE HYDROCHLORIDE	4	TP53
ECONAZOLE NITRATE	4	TP53
TRIFLUPROMAZINE HYDROCHLORIDE	4	TP53
PROCHLORPERAZINE EDISYLATE	4	TP53
DEQUALINIUM CHLORIDE	4	TP53

Druggability pyramid

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

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	1	TP53
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	2	MUTYH, RAD51D

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
MUTYH	1	—
RAD51D	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.