Clear cell sarcoma of kidney

Summary

Clear cell sarcoma of kidney (MONDO:0005006) is a cancer with 1 cohort gene (1 CIViC-evidence somatic driver) and 6 clinical trials. Top therapeutic interventions include cyclophosphamide anhydrous, dactinomycin, and dalteparin sodium.

At a glance

• Classification: Cancer
• Cohort genes: 1
• Clinical trials: 6

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	clear cell sarcoma of kidney
Mondo ID	MONDO:0005006
EFO	EFO:0000350
Orphanet	457246
DOID	DOID:4880
NCIT	C4264
UMLS	C0334488
MedGen	90791
GARD	0021905
Anatomy (UBERON)	UBERON:0002113
Is cancer (heuristic)	yes

Also known as: CCSK · childhood clear cell sarcoma of the kidney · childhood kidney clear cell sarcoma · childhood renal clear cell sarcoma · clear cell sarcoma - kidney · clear cell sarcoma of kidney · clear cell sarcoma of the kidney · kidney clear cell sarcoma · paediatric kidney clear cell sarcoma · paediatric renal clear cell sarcoma · pediatric kidney clear cell sarcoma · pediatric renal clear cell sarcoma · renal clear cell sarcoma

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › cancer › sarcoma › soft tissue sarcoma › clear cell sarcoma › clear cell sarcoma of kidney

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

Somatic driver evidence (intOGen + CIViC, cohort fanout)

Gene	intOGen role	Cancer types	CIViC
BCOR	LoF	ACC,AML,CHOL,CLLSLL,COADREAD,GBM,LGGNOS,LUAD,MBL,PAAD,PAST,PGNG,PLMESO,SIC,STAD,THYM,UCEC,UCS	CIViC #12555

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
BCOR	Orphanet:2712	Oculofaciocardiodental syndrome
BCOR	Orphanet:457246	Clear cell sarcoma of kidney
BCOR	Orphanet:520	Acute promyelocytic leukemia
BCOR	Orphanet:568	Microphthalmia, Lenz type

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
civic_only	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
BCOR	HGNC:20893	ENSG00000183337	Q6W2J9	BCL-6 corepressor	civic_evidence

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
BCOR	BCL-6 corepressor	Transcriptional corepressor.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 0 · 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
Scaffold/PPI	1	17.3×	0.058

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
BCOR	Scaffold/PPI	no		Ankyrin_rpt, BCOR, PUFD

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
buccal mucosa cell	1
cortical plate	1
ganglionic eminence	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
BCOR	265	ubiquitous	marker	buccal mucosa cell, ganglionic eminence, cortical plate

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
BCOR	2,188

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
BCOR	Q6W2J9	5

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
specification of axis polarity	1	16852.0×	6e-04	BCOR
negative regulation of tooth mineralization	1	8426.0×	6e-04	BCOR
negative regulation of bone mineralization	1	936.2×	0.004	BCOR
blastocyst hatching	1	543.6×	0.004	BCOR
odontogenesis	1	526.6×	0.004	BCOR
roof of mouth development	1	247.8×	0.007	BCOR
heart development	1	78.8×	0.017	BCOR
chromatin remodeling	1	73.0×	0.017	BCOR
negative regulation of DNA-templated transcription	1	31.6×	0.035	BCOR
negative regulation of transcription by RNA polymerase II	1	17.7×	0.056	BCOR

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
BCOR	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
BCOR	2	Binding:2

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

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)
BCOR	2	—

Clinical trials & evidence

Clinical trials

Clinical trials: 6.

Phase distribution (across all retrieved trials)

Phase	Trials
PHASE2	2
Not specified	2
PHASE1/PHASE2	1
PHASE1	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT00335556	PHASE2	COMPLETED	Combination Chemotherapy, Radiation Therapy, and/or Surgery in Treating Patients With High-Risk Kidney Tumors
NCT01154452	PHASE1/PHASE2	COMPLETED	Vismodegib and Gamma-Secretase/Notch Signalling Pathway Inhibitor RO4929097 in Treating Patients With Advanced or Metastatic Sarcoma
NCT01553539	PHASE2	COMPLETED	Therapeutic Angiotensin-(1-7) in Treating Patients With Metastatic Sarcoma That Cannot Be Removed By Surgery
NCT01061411	PHASE1	COMPLETED	Dalteparin and Sunitinib Malate as First-Line Therapy in Treating Patients With Kidney Cancer That is Metastatic or Cannot Be Removed by Surgery
NCT00898365	Not specified	COMPLETED	Study of Kidney Tumors in Younger Patients
NCT01118078	Not specified	COMPLETED	Biomarkers in Tissue Samples From Patients With High-Risk Wilms Tumor

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
CYCLOPHOSPHAMIDE ANHYDROUS	4	1
DACTINOMYCIN	4	1
DALTEPARIN SODIUM	4	1
VISMODEGIB	4	1
TALFIRASTIDE	2	1
CHEMBL4748391	0	1