Mineral metabolism disease

Summary

Mineral metabolism disease (MONDO:0000226) is a disease (an umbrella term covering 13 Mondo subtypes) with 17 GWAS associations across 19 studies and 1 clinical trial. A subtype of metabolic disease — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Umbrella term: 13 Mondo subtypes
• GWAS associations: 17
• Clinical trials: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	mineral metabolism disease
Mondo ID	MONDO:0000226
EFO	EFO:0009556
ICD-10-CM	E83
SNOMED CT	45744005
UMLS	C0154260
MedGen	509562
Is cancer (heuristic)	no

Also known as: disease of mineral metabolism · disorder of mineral metabolism

Data availability: 17 GWAS associations (19 studies).

Disease family

This is a subtype of metabolic 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

Related subtypes (36): glutaric aciduria, xanthinuria, chondrocalcinosis, ochronosis disorder, glucose metabolism disease, diabetic kidney disease, xanthoma, diabetic retinopathy, hypertriglyceridemia, gout, lactic acidosis, acquired metabolic disease, lipodystrophy, developmental anomaly of metabolic origin, dopa-responsive dystonia, hypoalphalipoproteinemia, steroid dehydrogenase deficiency-dental anomalies syndrome, inborn errors of metabolism, vitamin B12 deficiency, proteostasis deficiencies, hyperlipidemia, disorder of GPI anchor biosynthesis, bilirubin metabolism disease, hyperlipoproteinemia, carbohydrate metabolism disease, porphyrin metabolism disease, purine metabolism disease, amino acid metabolism disease, pyrimidine metabolism disease, disorder of acid-base balance, disorder of glutamate decarboxylase, tumor lysis syndrome, collagenous sprue, steroid metabolism disease, disorder of organic acid metabolism, skeletal fluorosis

Subtypes (13): iron metabolism disease, phosphorus metabolism disease, potassium deficiency disease, calcium metabolic 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

Genetics & variants

GWAS landscape

17 GWAS associations across 19 studies. Top hits map to 3 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs79220007	7e-193	HFE, H2BC4	T	0.51
rs73885319	3e-14	APOL1	A	0.15
chr9:5073770	5e-14		T	1.38
chr6:87541048	4e-09		A	1.72
chr12:34950932	1e-08		T	0.9
chr14:20833423	1e-08		G	0.13
rs117573981	2e-08	RPL7AP67 - ZNF24TR	?
chrX:66229416	2e-08		G	2.42
chr20:24687490	2e-08		T	2.59
chr21:34959203	2e-08		TA	3.01
chr5:67448022	2e-08		G	2.24
chr6:119569383	2e-08		T	3.32
chr6:85234182	2e-08		A	1.68
chr6:26092913	inf		A	0.83

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90475742	Verma A	2024	24,136	403,344	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90473225	UK Biobank Whole-Genome Sequencing Consortium	2025	10,191	448,249	Whole-genome sequencing of 490,640 UK Biobank participants.
GCST90667897	UK Biobank Whole-Genome Sequencing Consortium	2025	10,191	448,249	Whole-genome sequencing of 490,640 UK Biobank participants.
GCST90475741	Verma A	2024	7,832	107,043	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90479941	Verma A	2024	7,832	107,043	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90297601	Auwerx C	2024	5,196	321,402	Rare copy-number variants as modulators of common disease susceptibility.
GCST90297655	Auwerx C	2024	5,196	321,402	Rare copy-number variants as modulators of common disease susceptibility.
GCST90297751	Auwerx C	2024	5,196	321,402	Rare copy-number variants as modulators of common disease susceptibility.
GCST90079772	Backman JD	2021	3,300	383,907	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083758	Backman JD	2021	3,300	383,907	Exome sequencing and analysis of 454,787 UK Biobank participants.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	1
Tier 2: splice/UTR	1
Tier 3: regulatory	0
Tier 4: intronic/intergenic	12

MAF distribution

Bucket	Variants
common (>=0.05)	2
low_freq (0.01-0.05)	0
rare (<0.01)	0
unknown	12

Functional consequences

Consequence	Count
unknown	11
3_prime_UTR_variant	1
missense_variant	1
intergenic_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
chr6:26092913								Tier 4: intronic/intergenic
rs79220007	6	26098246	T>C	0.065	3_prime_UTR_variant	HFE, H2BC4	7e-193	Tier 2: splice/UTR
rs73885319	22	36265860	A>G	0.224	missense_variant	APOL1	3e-14	Tier 1: coding
chr9:5073770							5e-14	Tier 4: intronic/intergenic
chr6:87541048							4e-09	Tier 4: intronic/intergenic
chr12:34950932							1e-08	Tier 4: intronic/intergenic
chr14:20833423							1e-08	Tier 4: intronic/intergenic
rs117573981	18	35402396	A>G		intergenic_variant	RPL7AP67 - ZNF24TR	2e-08	Tier 4: intronic/intergenic
chrX:66229416							2e-08	Tier 4: intronic/intergenic
chr20:24687490							2e-08	Tier 4: intronic/intergenic
chr21:34959203							2e-08	Tier 4: intronic/intergenic
chr5:67448022							2e-08	Tier 4: intronic/intergenic
chr6:119569383							2e-08	Tier 4: intronic/intergenic
chr6:85234182							2e-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: 1.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT01772927	Not specified	UNKNOWN	Clinical Tolerance of Numeta 13%