Bladder calculus

Summary

Bladder calculus (MONDO:0006678) is a disease with 83 GWAS associations across 8 studies. A subtype of lower urinary tract calculus — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• GWAS associations: 83

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	bladder calculus
Mondo ID	MONDO:0006678
EFO	EFO:1000839
MeSH	D001744
DOID	DOID:11355
SNOMED CT	70650003
UMLS	C0005683
MedGen	14149
MedDRA	10005001
Is cancer (heuristic)	no

Data availability: 83 GWAS associations (8 studies).

Disease family

This is a subtype of lower urinary tract calculus. 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 body system or component › urinary system disorder › urolithiasis › lower urinary tract calculus › bladder calculus

Related subtypes (2): prostate calculus, urethral calculus

Subtypes (1): stone in bladder diverticulum

Genetics & variants

GWAS landscape

83 GWAS associations across 8 studies. Top hits map to 26 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs77924615	5e-93	PDILT	G	0.18
rs56235845	2e-80	RGS14	T	0.14
chr21:37832621	1e-66		G	0.14
rs10051765	1e-62	RGS14 - SLC34A1	T	0.13
rs2231142	4e-53	ABCG2	G	0.17
rs219776	3e-49	LNCTSI, CLDN14	T	0.12
rs149027545	2e-47	ABCG2	G	0.17
rs6127099	5e-44	BCAS1 - CYP24A1	A	0.12
chr22:23366323	7e-36		G	0.09
rs2299905	1e-35	AQP1	A	0.1
rs1772719	6e-32	ALPL	A	0.1
rs9895661	3e-27	BCAS3, TBX2-AS1	C	0.1
rs6003469	3e-27	ATP5PFP2 - RSPH14	A	0.09
rs9897621	4e-27	KANSL1	T	0.1
chr2:234369796	4e-25		G	0.08
rs2241358	1e-23	PTGER1 - GIPC1	C	0.08
chr16:88516940	3e-22		A	0.07
chr4:115624891	4e-22		A	0.09
rs142212375	2e-21	KLK15	C	0.18
chr2:224677354	2e-21		T	0.07
rs2238691	6e-21	GIPR	G	0.08
rs1317983	1e-18	VEGFA - LINC02537	T	0.07
rs838717	2e-18	DGKD	G	0.07
rs12496336	3e-18	CASR	A	0.07
rs2206271	7e-18	TFAP2D - TFAP2B	T	0.07
rs12947281	8e-18	CDK12	G	0.07
rs7584689	1e-17	AP1S3	A	0.06
rs4795384	2e-17	CDK12	C	0.07
chr17:70346698	4e-17		T	0.06
rs13147491	4e-17	UGT8 - CIR1P2	A	0.1

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90476143	Verma A	2024	39,380	394,076	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90436437	Zhou W	2018	6,643	401,005	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90478565	Verma A	2024	5,904	112,267	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90480398	Verma A	2024	5,904	112,267	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90478564	Verma A	2024	4,320	53,566	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90080589	Backman JD	2021	886	387,039	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90084575	Backman JD	2021	886	387,039	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90482221	Verma A	2024	393	6,300	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	3
Tier 2: splice/UTR	2
Tier 3: regulatory	1
Tier 4: intronic/intergenic	44

MAF distribution

Bucket	Variants
common (>=0.05)	46
low_freq (0.01-0.05)	4
rare (<0.01)	0
unknown	0

Functional consequences

Consequence	Count
intron_variant	22
unknown	15
intergenic_variant	5
missense_variant	2
splice_region_variant	1
stop_gained	1
3_prime_UTR_variant	1
regulatory_region_variant	1
synonymous_variant	1
non_coding_transcript_exon_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs77924615	16	20381010	G>A	0.2	intron_variant	PDILT	5e-93	Tier 4: intronic/intergenic
rs56235845	5	177371039	T>G	0.335	splice_region_variant	RGS14	2e-80	Tier 2: splice/UTR
chr21:37832621				0.25			1e-66	Tier 4: intronic/intergenic
rs10051765	5	177372991	T>C	0.361	intergenic_variant	RGS14 - SLC34A1	1e-62	Tier 4: intronic/intergenic
rs2231142	4	88131171	G>A,C,T	0.11	stop_gained	ABCG2	4e-53	Tier 1: coding
rs219776	21	36462537	T>C	0.298	intron_variant	LNCTSI, CLDN14	3e-49	Tier 4: intronic/intergenic
rs149027545	4	88123028	G>A,C,T	0.101	intron_variant	ABCG2	2e-47	Tier 4: intronic/intergenic
rs6127099	20	54114863	A>C,T	0.289	intron_variant	BCAS1 - CYP24A1	5e-44	Tier 4: intronic/intergenic
chr22:23366323				0.303			7e-36	Tier 4: intronic/intergenic
rs2299905	7	30918001	A>C,T	0.289	intron_variant	AQP1	1e-35	Tier 4: intronic/intergenic
rs1772719	1	21577881	A>C	0.197	3_prime_UTR_variant	ALPL	6e-32	Tier 2: splice/UTR
rs9895661	17	61379228	C>A,T	0.184	intron_variant	BCAS3, TBX2-AS1	3e-27	Tier 4: intronic/intergenic
rs6003469	22	23025207	A>C	0.252	intergenic_variant	ATP5PFP2 - RSPH14	3e-27	Tier 4: intronic/intergenic
rs9897621	17	46036026	T>A	0.199	intron_variant	KANSL1	4e-27	Tier 4: intronic/intergenic
chr2:234369796				0.455			4e-25	Tier 4: intronic/intergenic
rs2241358	19	14477664	C>A,G	0.327	regulatory_region_variant	PTGER1 - GIPC1	1e-23	Tier 3: regulatory
chr16:88516940				0.423			3e-22	Tier 4: intronic/intergenic
chr4:115624891				0.186			4e-22	Tier 4: intronic/intergenic
rs142212375	19	50833005	C>T	0.038	intron_variant	KLK15	2e-21	Tier 4: intronic/intergenic
chr2:224677354				0.381			2e-21	Tier 4: intronic/intergenic
rs2238691	19	45675785	G>A	0.206	intron_variant	GIPR	6e-21	Tier 4: intronic/intergenic
rs1317983	6	43838598	T>A,C	0.313	intron_variant	VEGFA - LINC02537	1e-18	Tier 4: intronic/intergenic
rs838717	2	233387798	G>A	0.4	intron_variant	DGKD	2e-18	Tier 4: intronic/intergenic
rs12496336	3	122210603	A>G	0.258	intron_variant	CASR	3e-18	Tier 4: intronic/intergenic
rs2206271	6	50818295	T>A	0.295	intron_variant	TFAP2D - TFAP2B	7e-18	Tier 4: intronic/intergenic
rs12947281	17	39495957	G>A,T	0.277	intron_variant	CDK12	8e-18	Tier 4: intronic/intergenic
rs7584689	2	223801731	A>G	0.408	intron_variant	AP1S3	1e-17	Tier 4: intronic/intergenic
rs4795384	17	39560518	C>G	0.312	intergenic_variant	CDK12	2e-17	Tier 4: intronic/intergenic
chr17:70346698				0.494			4e-17	Tier 4: intronic/intergenic
rs13147491	4	114696462	A>C	0.109	intergenic_variant	UGT8 - CIR1P2	4e-17	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

No druggable-target or therapeutic data for this disease’s cohort.

Clinical trials & evidence

Clinical trials

Clinical trials: 0.