Lower urinary tract calculus

Summary

Lower urinary tract calculus (MONDO:0004828) is a disease with 8 GWAS associations across 12 studies. A subtype of urolithiasis — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• GWAS associations: 8

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	lower urinary tract calculus
Mondo ID	MONDO:0004828
DOID	DOID:9590
ICD-10-CM	N21.9
SNOMED CT	79509009
UMLS	C0156264
MedGen	510219
Anatomy (UBERON)	UBERON:0001556
Is cancer (heuristic)	no

Also known as: lower urinary tract urolithiasis · urolithiasis of lower urinary tract

Data availability: 8 GWAS associations (12 studies).

Disease family

This is a subtype of urolithiasis. 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

Related subtypes (1): nephrolithiasis

Subtypes (3): prostate calculus, urethral calculus, bladder calculus

Genetics & variants

GWAS landscape

8 GWAS associations across 12 studies. Top hits map to 5 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs77924615	2e-20	PDILT	G	0.29
rs572335259	3e-12	RGS17	C	2.76
rs574680540	7e-12	WRN	C	2.91
rs576332594	2e-11	HMGB1P38 - OSBPL9P1	G	2.29
rs566403614	2e-11	RBM47	G	3.89
rs113448569	2e-11	RNU6-793P - RPL6P17	G	2.43
rs141094127	1e-08	SLC23A4P	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90691977	Karczewski KJ	2025	7,593	411,207	Pan-UK Biobank genome-wide association analyses enhance discovery and resolution of ancestry-enriched effects.
GCST90476146	Verma A	2024	3,051	445,408	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90474184	UK Biobank Whole-Genome Sequencing Consortium	2025	1,875	456,565	Whole-genome sequencing of 490,640 UK Biobank participants.
GCST90080590	Backman JD	2021	979	386,821	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90084576	Backman JD	2021	979	386,821	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90436439	Zhou W	2018	778	401,005	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90651507	Liu TY	2025	649	217,244	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90480396	Verma A	2024	436	121,043	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90482224	Verma A	2024	436	121,043	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90482223	Verma A	2024	281	59,393	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	0
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	7

MAF distribution

Bucket	Variants
common (>=0.05)	1
low_freq (0.01-0.05)	0
rare (<0.01)	5
unknown	1

Functional consequences

Consequence	Count
intron_variant	6
intergenic_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs77924615	16	20381010	G>A	0.174	intron_variant	PDILT	2e-20	Tier 4: intronic/intergenic
rs572335259	6	153130037	C>T	0.001	intron_variant	RGS17	3e-12	Tier 4: intronic/intergenic
rs574680540	8	31052367	C>T	0.001	intron_variant	WRN	7e-12	Tier 4: intronic/intergenic
rs576332594	3	79987935	G>A	0.001	intergenic_variant	HMGB1P38 - OSBPL9P1	2e-11	Tier 4: intronic/intergenic
rs566403614	4	40493713	G>A	0	intron_variant	RBM47	2e-11	Tier 4: intronic/intergenic
rs113448569	6	14932632	G>A	0	intron_variant	RNU6-793P - RPL6P17	2e-11	Tier 4: intronic/intergenic
rs141094127	7	135297057	G>A		intron_variant	SLC23A4P	1e-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

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

Clinical trials & evidence

Clinical trials

Clinical trials: 0.