Germinoma

Summary

Germinoma (MONDO:0002598) is a disease with 1 cohort gene and 6 clinical trials. Top therapeutic interventions include etoposide phosphate and ifosfamide.

At a glance

• Cohort genes: 1
• ClinVar variants: 1
• Clinical trials: 6

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	germinoma
Mondo ID	MONDO:0002598
MeSH	D018237
DOID	DOID:3304
NCIT	C3753
UMLS	C0206660
MedGen	64626
GARD	0023182
Is cancer (heuristic)	no

Also known as: germinoma · germinoma (disease)

Data availability: 1 ClinVar variant · 1 HPO phenotype.

Disease family

An umbrella term covering 1 Mondo subtype.

Classification path: disease › human disease › disease by etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › cancer › malignant germ cell tumor › germinoma

Related subtypes (12): seminoma, dysgerminoma, extragonadal germ cell cancer, pulmonary artery choriocarcinoma, malignant testicular germ cell tumor, malignant teratoma, malignant childhood germ cell neoplasm, mixed germ cell tumor, vaginal germ cell malignant tumor, malignant germ cell tumor of corpus uteri, malignant germ cell tumor of cervix uteri, malignant germ cell tumor of ovary

Subtypes (1): extragonadal germinoma

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 conflicting classifications of pathogenicity

ClinVar	Variant (HGVS)	Gene	Classification	Review
453775	NM_000264.5(PTCH1):c.1234G>A (p.Ala412Thr)	PTCH1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 9 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
PTCH1	Orphanet:220386	Semilobar holoprosencephaly
PTCH1	Orphanet:2353	Schilbach-Rott syndrome
PTCH1	Orphanet:280195	Septopreoptic holoprosencephaly
PTCH1	Orphanet:280200	Microform holoprosencephaly
PTCH1	Orphanet:377	Gorlin syndrome
PTCH1	Orphanet:77301	Monosomy 9q22.3 syndrome
PTCH1	Orphanet:93924	Lobar holoprosencephaly
PTCH1	Orphanet:93925	Alobar holoprosencephaly
PTCH1	Orphanet:93926	Midline interhemispheric variant of holoprosencephaly

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
PTCH1	HGNC:9585	ENSG00000185920	Q13635	Protein patched homolog 1	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
PTCH1	Protein patched homolog 1	Acts as a receptor for sonic hedgehog (SHH), indian hedgehog (IHH) and desert hedgehog (DHH).

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 1 · 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
Other/Unknown	1	1.8×	0.558

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
PTCH1	Other/Unknown	no		SSD, TM_rcpt_patched, HMGCR/SNAP/NPC1-like_SSD

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
dorsal root ganglion	1
tibia	1
trigeminal ganglion	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
PTCH1	275	ubiquitous	marker	tibia, dorsal root ganglion, trigeminal ganglion

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
PTCH1	3,368

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
PTCH1	Q13635	16

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 6. 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
GLI proteins bind promoters of Hh responsive genes to promote transcription	1	1631.4×	0.002	PTCH1
Ligand-receptor interactions	1	1427.5×	0.002	PTCH1
Activation of SMO	1	634.4×	0.003	PTCH1
Class B/2 (Secretin family receptors)	1	190.3×	0.006	PTCH1
Hedgehog ‘off’ state	1	178.4×	0.006	PTCH1
Hedgehog ‘on’ state	1	158.6×	0.006	PTCH1

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
response to chlorate	1	8426.0×	0.002	PTCH1
neural plate axis specification	1	8426.0×	0.002	PTCH1
cell proliferation involved in metanephros development	1	8426.0×	0.002	PTCH1
cell differentiation involved in kidney development	1	5617.3×	0.002	PTCH1
epidermal cell fate specification	1	3370.4×	0.003	PTCH1
neural tube patterning	1	2808.7×	0.003	PTCH1
hindlimb morphogenesis	1	2808.7×	0.003	PTCH1
negative regulation of cell division	1	2407.4×	0.003	PTCH1
mammary gland duct morphogenesis	1	2407.4×	0.003	PTCH1
positive regulation of epidermal cell differentiation	1	2106.5×	0.003	PTCH1
metanephric collecting duct development	1	1685.2×	0.003	PTCH1
response to alkaloid	1	1532.0×	0.003	PTCH1
prostate gland development	1	1404.3×	0.003	PTCH1
mammary gland epithelial cell differentiation	1	1203.7×	0.003	PTCH1
negative regulation of multicellular organism growth	1	1123.5×	0.003	PTCH1
somite development	1	1123.5×	0.003	PTCH1
limb morphogenesis	1	1053.2×	0.003	PTCH1
smooth muscle tissue development	1	1053.2×	0.003	PTCH1
commissural neuron axon guidance	1	991.3×	0.003	PTCH1
cell fate determination	1	936.2×	0.003	PTCH1
spinal cord motor neuron differentiation	1	936.2×	0.003	PTCH1
cellular response to cholesterol	1	842.6×	0.003	PTCH1
negative regulation of stem cell proliferation	1	842.6×	0.003	PTCH1
dorsal/ventral neural tube patterning	1	802.5×	0.003	PTCH1
pharyngeal system development	1	802.5×	0.003	PTCH1
negative regulation of keratinocyte proliferation	1	702.2×	0.003	PTCH1
regulation of smoothened signaling pathway	1	624.1×	0.003	PTCH1
positive regulation of cholesterol efflux	1	624.1×	0.003	PTCH1
keratinocyte proliferation	1	581.1×	0.003	PTCH1
liver regeneration	1	510.7×	0.004	PTCH1

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
PTCH1	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

Symbol	Assays	Type breakdown
PTCH1	4	Binding:4

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).

Chemical tractability of cohort targets

0 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.

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	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	PTCH1

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)
PTCH1	4	—

Clinical trials & evidence

Clinical trials

Clinical trials: 6.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	4
PHASE3	1
PHASE2	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT02375204	PHASE3	ACTIVE_NOT_RECRUITING	Standard-Dose Combination Chemotherapy or High-Dose Combination Chemotherapy and Stem Cell Transplant in Treating Patients with Relapsed or Refractory Germ Cell Tumors
NCT06368817	PHASE2	RECRUITING	A Study of Lower Radiotherapy Dose to Treat Children With CNS Germinoma
NCT04648462	Not specified	RECRUITING	Proton Therapy Research Infrastructure- ProTRAIT- Neuro-oncology
NCT05564026	Not specified	RECRUITING	Molecular Epidemiology of Pediatric Germ Cell Tumors
NCT07589361	Not specified	NOT_YET_RECRUITING	Safety and Efficacy of Vertebral Body-Sparing Craniospinal Irradiation With Proton Therapy in Pediatric Tumors
NCT01445288	Not specified	COMPLETED	Exploratory Study of Effects of Radiation Therapy in Pediatric Patients With Central Nervous System Tumors

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
ETOPOSIDE PHOSPHATE	4	1
IFOSFAMIDE	4	1