Benign urinary system neoplasm

Summary

Benign urinary system neoplasm (MONDO:0004180) is a cancer (an umbrella term covering 6 Mondo subtypes) with 3 GWAS associations across 5 studies and 1 clinical trial. Top therapeutic interventions include cisplatin, apatorsen, and apatorsen sodium. A subtype of benign neoplasm — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Classification: Cancer
• Umbrella term: 6 Mondo subtypes
• GWAS associations: 3
• Clinical trials: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	benign urinary system neoplasm
Mondo ID	MONDO:0004180
MeSH	D014571
DOID	DOID:731
NCIT	C192667, C4893
SNOMED CT	92468007
UMLS	C0686167
MedGen	146348
Anatomy (UBERON)	UBERON:0001008
Is cancer (heuristic)	yes

Also known as: benign neoplasm of the urinary tract · benign neoplasm of urinary tract · benign tumor of the urinary tract · benign tumor of urinary tract · benign tumour of the urinary tract · benign tumour of urinary tract · benign urinary system neoplasm · benign urinary tract neoplasm · benign urinary tract tumor · benign urinary tract tumour · neoplasm of urinary system · renal system benign neoplasm · tumor of the urinary system · tumor of urinary tract · tumour of the urinary system · tumour of urinary tract · urinary tract neoplasm

Data availability: 3 GWAS associations (5 studies).

Disease family

This is a subtype of benign neoplasm. Genetic, therapeutic, and trial evidence is largely curated at the broader-term level — see the parent page for the associated-gene cohort and molecular evidence.

Classification path: disease › human disease › disease by etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › benign neoplasm › benign urinary system neoplasm

Related subtypes (28): respiratory system benign neoplasm, benign reproductive system neoplasm, benign digestive system neoplasm, benign endocrine neoplasm, cardiovascular organ benign neoplasm, immune system organ benign neoplasm, thoracic benign neoplasm, musculoskeletal system benign neoplasm, nervous system benign neoplasm, peritoneal benign neoplasm, integumentary system benign neoplasm, benign mesothelioma, benign mesenchymoma, benign perivascular tumor, calcifying fibrous tumor, pheochromocytoma, benign mastocytoma, benign neoplasm of oral cavity, benign neoplasm of neck, benign neoplasm of salivary gland, benign neoplasm of lip, benign neoplasm of floor of mouth, benign neoplasm of pharynx, benign neoplasm of buccal mucosa, benign chondrogenic neoplasm, benign epithelial neoplasm, benign phyllodes tumor, germ cell benign neoplasm

Subtypes (6): bladder benign neoplasm, ureter benign neoplasm, benign prostate phyllodes tumor, kidney benign neoplasm, urothelial papilloma, benign urethral neoplasm

Genetics & variants

GWAS landscape

3 GWAS associations across 5 studies. Top hits map to 1 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs17483551	1e-11	SLC2A13	T	2.81
rs75813768	2e-11	WDR11 - RPL19P16	C	1.68
rs149837797	9e-08	GYG1P2 - RNU6-67P	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90477282	Verma A	2024	1,413	446,929	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90651817	Liu TY	2025	465	188,123	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90479848	Verma A	2024	340	120,916	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90481556	Verma A	2024	340	120,916	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90435671	Zhou W	2018	174	371,171	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	0
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	3

MAF distribution

Bucket	Variants
common (>=0.05)	0
low_freq (0.01-0.05)	0
rare (<0.01)	2
unknown	1

Functional consequences

Consequence	Count
intron_variant	2
intergenic_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs17483551	12	40081458	T>C	0	intron_variant	SLC2A13	1e-11	Tier 4: intronic/intergenic
rs75813768	10	120977606	C>T	0.002	intron_variant	WDR11 - RPL19P16	2e-11	Tier 4: intronic/intergenic
rs149837797	13	83264839	C>A,T		intergenic_variant	GYG1P2 - RNU6-67P	9e-08	Tier 4: intronic/intergenic

Genes & proteins

No associated-gene cohort resolved for this disease. Atlas builds the molecular and therapeutic sections — associated genes, protein families, druggability, pathways, interactions, and drug associations — by aggregating over a disease’s associated genes (resolved via GWAS / GenCC / ClinVar / CIViC), and none resolved here. This is expected for antibody-mediated, autoimmune, or otherwise non-gene-defined conditions; the curated evidence for this disease is its clinical features, GWAS susceptibility, and clinical trials (above).

Function

No pathway enrichment — requires an associated-gene cohort.

Therapeutics

Drugs indicated or in trials for this disease

2 approved drugs — disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

Drug	Status
Atezolizumab	Approved (phase 4)
Enfortumab Vedotin	Approved (phase 4)

Clinical trials & evidence

Clinical trials

Clinical trials: 1.

Phase distribution (across all retrieved trials)

Phase	Trials
PHASE2	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT01454089	PHASE2	COMPLETED	A Phase 2 Study Comparing Chemotherapy in Combination With OGX-427 or Placebo in Patients With Bladder Cancer

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
CISPLATIN	4	1
APATORSEN	2	1
APATORSEN SODIUM	-1	1