Calcium metabolic disease

Summary

Calcium metabolic disease (MONDO:0005557) is a disease with 3 GWAS associations across 8 studies. A subtype of mineral metabolism disease — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• GWAS associations: 3

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	calcium metabolic disease
Mondo ID	MONDO:0005557
EFO	EFO:0005769
MeSH	D002128
DOID	DOID:10575
SNOMED CT	71638002
UMLS	C0006705
MedGen	714
Is cancer (heuristic)	no

Also known as: disorder of calcium metabolism

Data availability: 3 GWAS associations (8 studies).

Disease family

This is a subtype of mineral metabolism disease. 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 developmental or physiological process › metabolic disease › mineral metabolism disease › calcium metabolic disease

Related subtypes (12): iron metabolism disease, phosphorus metabolism disease, potassium deficiency disease, spondyloepiphyseal dysplasia with congenital joint dislocations, diastrophic dysplasia, multiple epiphyseal dysplasia type 4, atelosteogenesis type II, achondrogenesis type IB, chondrodysplasia with joint dislocations, gPAPP type, spondyloepimetaphyseal dysplasia, PAPSS2 type, acquired mineral metabolism disease, sulfur metabolism disease

Subtypes (4): hypercalcemia disease, calcinosis, autosomal dominant hypocalcemia, calcium-alkali syndrome

Genetics & variants

GWAS landscape

3 GWAS associations across 8 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
rs60910145	4e-22	APOL1	T	0.3
rs9622362	8e-22	APOL1	A	0.27
rs113657392	1e-07	LINC01899 - CBLN2	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90477395	Verma A	2024	6,769	433,174	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90475745	Verma A	2024	2,717	115,696	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90479939	Verma A	2024	2,717	115,696	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90079771	Backman JD	2021	1,603	386,117	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083757	Backman JD	2021	1,603	386,117	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90435767	Zhou W	2018	1,204	406,834	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90477394	Verma A	2024	1,025	57,557	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90651861	Liu TY	2025	344	235,993	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

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

MAF distribution

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

Functional consequences

Consequence	Count
missense_variant	1
intron_variant	1
intergenic_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs60910145	22	36265988	T>C,G	0.044	missense_variant	APOL1	4e-22	Tier 1: coding
rs9622362	22	36260398	A>C	0.473	intron_variant	APOL1	8e-22	Tier 4: intronic/intergenic
rs113657392	18	72232628	G>A,T	0.05	intergenic_variant	LINC01899 - CBLN2	1e-07	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.