Deficiency anemia

Summary

Deficiency anemia (MONDO:0001639) is a disease with 23 GWAS associations across 16 studies. A subtype of anemia — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• GWAS associations: 23

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	deficiency anemia
Mondo ID	MONDO:0001639
DOID	DOID:13121
SNOMED CT	267513007
UMLS	C0041782
MedGen	508256
GARD	0022980
Is cancer (heuristic)	no

Also known as: deficiency anemias · unspecified deficiency anaemia · unspecified deficiency anemia

Data availability: 23 GWAS associations (16 studies).

Disease family

This is a subtype of anemia. 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 › hematologic disorder › anemia › deficiency anemia

Related subtypes (18): congenital anemia, neonatal anemia, microcytic anemia, hypochromic anemia, pancytopenia, pure red-cell aplasia, macrocytic anemia, normocytic anemia, sideroblastic anemia, aplastic anemia, hemoglobin C disease, hemoglobin E disease, beta-thalassemia and related diseases, hemoglobinopathy Toms River, hereditary methemoglobinemia, hemoglobin D disease, anemia due to enzyme disorder, anemia due to chronic disorder

Subtypes (3): protein-deficiency anemia, hereditary anemia, acquired deficiency anemia

Genetics & variants

GWAS landscape

23 GWAS associations across 16 studies. Top hits map to 8 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs34324219	1e-53	TCN1	C	0.25
rs503644	2e-49	TCN1 - OOSP3	T	0.77
rs1801222	3e-35	CUBN	A	0.14
rs9389269	7e-32	HBS1L - MYB	T	0.29
chr6:135419039	8e-29		C	0.3
chr19:49206462	1e-27		C	0.12
rs1131603	6e-22	TCN2	T	0.28
chr6:49428755	1e-14		G	0.09
rs765132976	6e-14	RFC3 - VDAC1P12	T	3.35
rs144445234	7e-13	CXXC1 - RNA5SP458	A	2.92
rs148603992	1e-12	KCNIP4	C	3
rs143366287	1e-12	GPRIN3 - SNCA	A	1.08
rs551690531	2e-12	ZNF717 - ROBO2	C	3.24
rs181869483	2e-12	RNU6-1059P - RNU6-34P	C	1.88
chr19:8386056	9e-12		G	0.15
rs116187676	1e-11	LINC02462 - EEF1A1P35	A	1.65
chr19:5839746	2e-11		G	0.15
rs186948048	2e-11	PTPRN2	G	2.42
rs1801133	3e-11	MTHFR	G	0.29
rs139864875	3e-11	CEP83	G	3.6
rs73140592	2e-07	RNA5SP158 - TLR10	?
rs78691998	3e-07	LRRC43	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90475772	Verma A	2024	17,244	418,381	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90475771	Verma A	2024	4,486	113,046	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90480951	Verma A	2024	4,486	113,046	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90475777	Verma A	2024	3,401	441,667	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90477447	Verma A	2024	1,845	56,436	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90435796	Zhou W	2018	1,133	390,026	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90477452	Verma A	2024	1,081	118,777	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90479964	Verma A	2024	1,081	118,777	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90477451	Verma A	2024	903	449,159	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90479963	Verma A	2024	450	120,910	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	4
Tier 2: splice/UTR	1
Tier 3: regulatory	0
Tier 4: intronic/intergenic	17

MAF distribution

Bucket	Variants
common (>=0.05)	11
low_freq (0.01-0.05)	1
rare (<0.01)	9
unknown	1

Functional consequences

Consequence	Count
intergenic_variant	6
unknown	5
intron_variant	5
missense_variant	4
non_coding_transcript_exon_variant	1
splice_polypyrimidine_tract_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs34324219	11	59855905	C>A	0.113	missense_variant	TCN1	1e-53	Tier 1: coding
rs503644	11	59873981	T>A,C	0.032	intergenic_variant	TCN1 - OOSP3	2e-49	Tier 4: intronic/intergenic
rs1801222	10	17114152	A>C,G,T	0.343	missense_variant	CUBN	3e-35	Tier 1: coding
rs9389269	6	135106021	T>C	0.221	intergenic_variant	HBS1L - MYB	7e-32	Tier 4: intronic/intergenic
chr6:135419039				0.253			8e-29	Tier 4: intronic/intergenic
chr19:49206462				0.487			1e-27	Tier 4: intronic/intergenic
rs1131603	22	30622988	T>C	0.05	missense_variant	TCN2	6e-22	Tier 1: coding
chr6:49428755				0.366			1e-14	Tier 4: intronic/intergenic
rs765132976	13	34026654	T>C	0	intron_variant	RFC3 - VDAC1P12	6e-14	Tier 4: intronic/intergenic
rs144445234	18	50294179	A>G	0.001	intergenic_variant	CXXC1 - RNA5SP458	7e-13	Tier 4: intronic/intergenic
rs148603992	4	21616729	C>T	0	intron_variant	KCNIP4	1e-12	Tier 4: intronic/intergenic
rs143366287	4	89584053	A>C	0.009	non_coding_transcript_exon_variant	GPRIN3 - SNCA	1e-12	Tier 4: intronic/intergenic
rs551690531	3	75896522	C>A,T	0.001	intron_variant	ZNF717 - ROBO2	2e-12	Tier 4: intronic/intergenic
rs181869483	4	95972465	C>G	0.001	intergenic_variant	RNU6-1059P - RNU6-34P	2e-12	Tier 4: intronic/intergenic
chr19:8386056				0.41			9e-12	Tier 4: intronic/intergenic
rs116187676	4	134913939	A>G	0.003	intergenic_variant	LINC02462 - EEF1A1P35	1e-11	Tier 4: intronic/intergenic
chr19:5839746				0.481			2e-11	Tier 4: intronic/intergenic
rs186948048	7	158227061	G>A	0.001	intron_variant	PTPRN2	2e-11	Tier 4: intronic/intergenic
rs1801133	1	11796321	G>A,C,T	0.291	missense_variant	MTHFR	3e-11	Tier 1: coding
rs139864875	12	94416972	G>A	0	intron_variant	CEP83	3e-11	Tier 4: intronic/intergenic
rs73140592	4	38764771	C>T	0.05	intergenic_variant	RNA5SP158 - TLR10	2e-07	Tier 4: intronic/intergenic
rs78691998	12	122200733	C>G,T		splice_polypyrimidine_tract_variant	LRRC43	3e-07	Tier 2: splice/UTR

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.