vitamin B deficiency

Summary

vitamin B deficiency (MONDO:0042976) is a disease with 39 GWAS associations across 14 studies. A subtype of vitamin deficiency disorder — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• GWAS associations: 39

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	vitamin B deficiency
Mondo ID	MONDO:0042976
MeSH	D014804
NCIT	C35129
SNOMED CT	47903000
UMLS	C0042850
MedGen	22669
Is cancer (heuristic)	no

Also known as: deficiencies, vitamin B · deficiency, vitamin B · vitamin B deficiencies

Data availability: 39 GWAS associations (14 studies).

Disease family

This is a subtype of vitamin deficiency disorder. 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 › vitamin B deficiency

Related subtypes (7): nutritional biotin deficiency, vitamin K deficiency hemorrhagic disease, inborn vitamin metabolic disorder, vitamin A deficiency, scurvy, vitamin D deficiency, vitamin deficiency related neuropathy

Subtypes (3): pyridoxine deficiency anemia, beriberi, vitamin B12 deficiency

Genetics & variants

GWAS landscape

39 GWAS associations across 14 studies. Top hits map to 10 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs503644	1e-140	TCN1 - OOSP3	T	1.08
rs34324219	4e-131	TCN1	C	0.34
rs1801222	7e-110	CUBN	A	0.22
rs516246	2e-94	FUT2	C	0.19
rs679574	2e-84	FUT2	C	0.19
rs1131603	6e-46	TCN2	T	0.38
rs9463476	5e-36	EEF1A1P42 - MMUT	A	0.12
chr11:59855905	3e-31		A	0.35
chr6:49419864	2e-30		A	0.11
rs41281112	2e-26	CLYBL	C	0.29
rs8101963	3e-26	CD320	G	0.19
rs281377	2e-20	FUT2	?	1.29
rs2270655	3e-18	MMAA	G	0.17
chr19:49206145	1e-16		G	0.18
chr16:79728049	4e-16		T	0.09
rs17855739	4e-16	FUT6	C	0.15
chr4:146549505	1e-14		C	0.16
chr19:8366064	4e-13		C	0.22
chr4:145661037	1e-12		T	0.18
chr10:17104653	3e-12		A	0.16
rs79193369	9e-12	LINC01229, MAFTRR	G	0.07
chr6:49264412	3e-11		C	0.16
chr22:30622988	5e-11		C	0.36
chr19:48703160	7e-10		G	0.12
chr7:157715944	2e-08		G	3.2
chr14:74253048	2e-08		CA	0.12
chr18:11434939	2e-08		T	2.53
chr3:187560273	3e-08		C	2.9
chr8:136145255	3e-08		G	3.65
chr9:74845217	3e-08		A	3.29

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90475702	Verma A	2024	21,840	415,740	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90473200	UK Biobank Whole-Genome Sequencing Consortium	2025	4,792	453,648	Whole-genome sequencing of 490,640 UK Biobank participants.
GCST90667752	UK Biobank Whole-Genome Sequencing Consortium	2025	4,792	453,648	Whole-genome sequencing of 490,640 UK Biobank participants.
GCST90475701	Verma A	2024	4,527	114,072	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90479910	Verma A	2024	4,527	114,072	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90477363	Verma A	2024	2,161	56,384	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90079758	Backman JD	2021	1,552	384,821	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083744	Backman JD	2021	1,552	384,821	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90079757	Backman JD	2021	1,075	386,854	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083743	Backman JD	2021	1,075	386,854	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	7
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	23

MAF distribution

Bucket	Variants
common (>=0.05)	14
low_freq (0.01-0.05)	5
rare (<0.01)	0
unknown	11

Functional consequences

Consequence	Count
unknown	17
missense_variant	6
intron_variant	4
intergenic_variant	2
stop_gained	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs503644	11	59873981	T>A,C	0.022	intergenic_variant	TCN1 - OOSP3	1e-140	Tier 4: intronic/intergenic
rs34324219	11	59855905	C>A	0.113	missense_variant	TCN1	4e-131	Tier 1: coding
rs1801222	10	17114152	A>C,G,T	0.304	missense_variant	CUBN	7e-110	Tier 1: coding
rs516246	19	48702915	C>A,G,T	0.475	intron_variant	FUT2	2e-94	Tier 4: intronic/intergenic
rs679574	19	48702851	C>A,G	0.484	intron_variant	FUT2	2e-84	Tier 4: intronic/intergenic
rs1131603	22	30622988	T>C	0.04	missense_variant	TCN2	6e-46	Tier 1: coding
rs9463476	6	49417034	A>G	0.358	intergenic_variant	EEF1A1P42 - MMUT	5e-36	Tier 4: intronic/intergenic
chr11:59855905							3e-31	Tier 4: intronic/intergenic
chr6:49419864				0.364			2e-30	Tier 4: intronic/intergenic
rs41281112	13	99866380	C>A,G,T	0.022	stop_gained	CLYBL	2e-26	Tier 1: coding
rs8101963	19	8304495	G>A	0.113	intron_variant	CD320	3e-26	Tier 4: intronic/intergenic
rs281377	19	48703346	C>G,T	0.05	missense_variant	FUT2	2e-20	Tier 1: coding
rs2270655	4	145655266	G>C	0.048	missense_variant	MMAA	3e-18	Tier 1: coding
chr19:49206145				0.497			1e-16	Tier 4: intronic/intergenic
chr16:79728049				0.349			4e-16	Tier 4: intronic/intergenic
rs17855739	19	5831829	C>G,T	0.094	missense_variant	FUT6	4e-16	Tier 1: coding
chr4:146549505				0.051			1e-14	Tier 4: intronic/intergenic
chr19:8366064				0.033			4e-13	Tier 4: intronic/intergenic
chr4:145661037							1e-12	Tier 4: intronic/intergenic
chr10:17104653							3e-12	Tier 4: intronic/intergenic
rs79193369	16	79691119	G>A,C	0.266	intron_variant	LINC01229, MAFTRR	9e-12	Tier 4: intronic/intergenic
chr6:49264412				0.255			3e-11	Tier 4: intronic/intergenic
chr22:30622988							5e-11	Tier 4: intronic/intergenic
chr19:48703160							7e-10	Tier 4: intronic/intergenic
chr7:157715944							2e-08	Tier 4: intronic/intergenic
chr14:74253048							2e-08	Tier 4: intronic/intergenic
chr18:11434939							2e-08	Tier 4: intronic/intergenic
chr3:187560273							3e-08	Tier 4: intronic/intergenic
chr8:136145255							3e-08	Tier 4: intronic/intergenic
chr9:74845217							3e-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

Drugs indicated for this disease

1 approved. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

Drug	Development status
Cyanocobalamin	Approved (phase 4)

Clinical trials & evidence

Clinical trials

Clinical trials: 0.