Vitamin deficiency disorder

Summary

Vitamin deficiency disorder (MONDO:0024298) is a disease (an umbrella term covering 8 Mondo subtypes) with 17 GWAS associations across 6 studies and 18 clinical trials. Top therapeutic interventions include cholecalciferol and cyanocobalamin. A subtype of nutritional deficiency disease — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Umbrella term: 8 Mondo subtypes
• GWAS associations: 17
• Clinical trials: 18

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	vitamin deficiency disorder
Mondo ID	MONDO:0024298
MeSH	D001361
NCIT	C35772
SNOMED CT	85670002
UMLS	C1510471
MedGen	267607
Is cancer (heuristic)	no

Also known as: Avitaminoses · avitaminosis · deficiencies, vitamin · deficiency, vitamin · vitamin deficiencies · vitamin deficiency · vitamin deficiency disorder

Data availability: 17 GWAS associations (6 studies).

Disease family

This is a subtype of nutritional deficiency 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 etiologic mechanism › nutritional disorder › nutritional deficiency disease › vitamin deficiency disorder

Related subtypes (13): Keshan disease, acquired night blindness, iron deficiency anemia, protein-energy malnutrition, folic acid deficiency anemia, ariboflavinosis, choline deficiency disease, endemic goiter, magnesium deficiency, potassium deficiency, pernicious anemia, Wernicke-Korsakoff syndrome, pellagra

Subtypes (8): nutritional biotin deficiency, vitamin K deficiency hemorrhagic disease, inborn vitamin metabolic disorder, vitamin A deficiency, scurvy, vitamin B deficiency, vitamin D deficiency, vitamin deficiency related neuropathy

Genetics & variants

GWAS landscape

17 GWAS associations across 6 studies. Top hits map to 6 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs4588	2e-166	GC	G	0.15
rs1352846	5e-161	GC	A	0.15
chr11:14864214	3e-131		A	0.13
rs12794714	4e-111	CYP2R1	G	0.11
rs4944957	6e-26	NADSYN1	A	0.05
chr11:71187294	3e-25		G	0.06
chr19:49207792	4e-24		G	0.05
rs584768	2e-22	FUT2 - MAMSTR	G	0.05
rs34324219	7e-22	TCN1	C	0.08
rs1801222	6e-19	CUBN	A	0.05
chr4:72639282	2e-17		C	0.15
rs503644	2e-14	TCN1 - OOSP3	T	0.2
rs1131603	4e-12	TCN2	T	0.09

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90475700	Verma A	2024	90,650	318,995	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90475699	Verma A	2024	34,360	74,016	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90479913	Verma A	2024	34,360	74,016	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90475698	Verma A	2024	14,673	39,046	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90477362	Verma A	2024	1,309	4,924	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90435740	Zhou W	2018	1,208	406,492	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	4
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	9

MAF distribution

Bucket	Variants
common (>=0.05)	12
low_freq (0.01-0.05)	1
rare (<0.01)	0
unknown	0

Functional consequences

Consequence	Count
missense_variant	4
unknown	4
intron_variant	2
intergenic_variant	2
synonymous_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs4588	4	71752606	G>A,C,T	0.244	missense_variant	GC	2e-166	Tier 1: coding
rs1352846	4	71752058	A>C,G	0.282	intron_variant	GC	5e-161	Tier 4: intronic/intergenic
chr11:14864214				0.461			3e-131	Tier 4: intronic/intergenic
rs12794714	11	14892029	G>A	0.375	synonymous_variant	CYP2R1	4e-111	Tier 4: intronic/intergenic
rs4944957	11	71456989	A>C,G	0.325	intron_variant	NADSYN1	6e-26	Tier 4: intronic/intergenic
chr11:71187294				0.259			3e-25	Tier 4: intronic/intergenic
chr19:49207792				0.49			4e-24	Tier 4: intronic/intergenic
rs584768	19	48710027	G>A,T	0.48	intergenic_variant	FUT2 - MAMSTR	2e-22	Tier 4: intronic/intergenic
rs34324219	11	59855905	C>A	0.113	missense_variant	TCN1	7e-22	Tier 1: coding
rs1801222	10	17114152	A>C,G,T	0.344	missense_variant	CUBN	6e-19	Tier 1: coding
chr4:72639282				0.224			2e-17	Tier 4: intronic/intergenic
rs503644	11	59873981	T>A,C	0.032	intergenic_variant	TCN1 - OOSP3	2e-14	Tier 4: intronic/intergenic
rs1131603	22	30622988	T>C	0.05	missense_variant	TCN2	4e-12	Tier 1: coding

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: 18.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	12
PHASE4	3
PHASE3	1
PHASE2/PHASE3	1
PHASE2	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT07021170	PHASE4	RECRUITING	Trial Comparing Elan Specialized Bariatric Supplements With Standard Multivitamins in Patients Undergoing Bariatric Procedures
NCT01263288	PHASE4	COMPLETED	Effect of Vitamin D Supplementation on Muscular Strength, Musculoskeletal Pain and Headache
NCT01609387	PHASE4	COMPLETED	Postoperative Vitamin Supplementation in Morbidly Obese Patient (VITAAL Study)
NCT01419262	PHASE3	COMPLETED	DO IT Trial: Vitamin D Outcomes and Interventions In Toddlers
NCT02272842	PHASE2/PHASE3	UNKNOWN	Vitamin B12, Neurodevelopment and Growth in Nepal
NCT01630720	PHASE2	COMPLETED	Vitamin Therapy in JGH Patients
NCT06323538	Not specified	RECRUITING	Cohort Study on Plant-based Diets (COPLANT Study)
NCT00212147	Not specified	COMPLETED	Interaction of Cobalamin Status With Nitrous Oxide in Relation to Postoperative Cognitive Changes in the Elderly
NCT01653353	Not specified	COMPLETED	Swiss Study on Vitamin D and Calcium in Nursing Homes
NCT02686905	Not specified	UNKNOWN	Vitamin Supplementation After Bariatric Surgery
NCT03004807	Not specified	COMPLETED	Role of Centrum® Silver® in Improving Micronutrient Status in Older Men
NCT03146273	Not specified	COMPLETED	Study of Absorption Characteristics of Two Multivitamin Mineral Formulations (Gel vs. Tablet/Capsule)
NCT03360435	Not specified	COMPLETED	Absorption of Transdermal Vitamins in Post Bariatric Surgery Patients
NCT03542591	Not specified	COMPLETED	Supplementation of Critical Nutrients in a Plant-based Diet
NCT04054505	Not specified	COMPLETED	Effectiveness of a Nutraceutical in Raising Circulating Serum Vitamin, Mineral and Amino Acid Levels in Patients.
NCT04587076	Not specified	COMPLETED	Evaluation of Protein Intake and Micronutrient Supplementation After Bariatric Surgery
NCT04673721	Not specified	COMPLETED	PROSPective Evaluation of Fortified Eggs Related to Improvement in The Biomarker Profile for Your Health
NCT06870786	Not specified	COMPLETED	Effect of Vitamin D Deficiency on the Structure of Titanium Platelet-Rich Fibrin

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
CHOLECALCIFEROL	4	1
CYANOCOBALAMIN	4	1
CHEMBL4303681	0	1
VITAMIN B12	0	1