Esophageal disorder

Summary

Esophageal disorder (MONDO:0003749) is a disease (an umbrella term covering 20 Mondo subtypes) with 55 GWAS associations across 52 studies and 1 clinical trial. A subtype of upper digestive tract disorder — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Umbrella term: 20 Mondo subtypes
• GWAS associations: 55
• Clinical trials: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	esophageal disorder
Mondo ID	MONDO:0003749
EFO	EFO:0009544
MeSH	D004935
DOID	DOID:6050
ICD-11	1594312948
NCIT	C3027
SNOMED CT	30811009, 37657006
UMLS	C0014852
MedGen	8693
Anatomy (UBERON)	UBERON:0001043
Is cancer (heuristic)	no

Also known as: disease of esophagus · disease of oesophagus · disease or disorder of esophagus · disease or disorder of oesophagus · disorder of esophagus · disorder of oesophagus · esophageal disorder · esophageal ulcer · esophagus disease · esophagus disease or disorder · oesophagus disease · oesophagus disease or disorder

Data availability: 55 GWAS associations (52 studies).

Disease family

This is a subtype of upper digestive tract 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 body system or component › digestive system disorder › upper digestive tract disorder › esophageal disorder

Related subtypes (1): internal hirudiniasis

Subtypes (20): esophageal atresia, esophageal varices, esophagitis, megaesophagus, esophageal tuberculosis, esophageal leukoplakia, dyskinesia of esophagus, esophageal diverticulosis, gastroesophageal reflux disease, esophageal atresia/tracheoesophageal fistula, achalasia, Barrett esophagus, esophageal duplication cyst, tubular duplication of the esophagus, laryngotracheoesophageal cleft, isolated tracheo-esophageal fistula, congenital esophageal diverticulum, neoplasm of esophagus, esophageal ulcer, congenital esophageal stenosis

Genetics & variants

GWAS landscape

55 GWAS associations across 52 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
rs9673356	7e-21	AKTIP - RPGRIP1L	A	0.04
chr9:128660676	2e-19		G	0.04
chr9:96586175	4e-18		G	0.04
rs3094503	3e-16	DDX52 - HNF1B	C	1.75
rs2891698	3e-16	KLHL26 - CRTC1	G	0.03
rs4766578	4e-16	ATXN2	T	0.03
chr6:34603350	8e-16		G	0.05
chr11:32492265	3e-13		A	0.03
rs10987077	3e-13	PBX3 - MVB12B	G	0.04
rs11863156	4e-13	AKTIP - RPGRIP1L	C	0.03
rs6499626	7e-13	AKTIP - RPGRIP1L	T	0.03
chr11:32507733	9e-13		A	0.03
chr3:183403556	1e-12		C	0.03
chr6:65125567	1e-12		T	0.03
chr12:78252709	3e-12		G	0.03
chr2:200152198	3e-12		A	0.03
chr2:67812176	3e-12		G	0.03
rs429358	4e-12	APOE	T	0.04
chr13:36150308	8e-12		C	0.03
rs566890996	8e-12	FYB2	C	3.51
chr2:52990318	1e-11		T	0.03
rs13107325	2e-11	SLC39A8	C	0.05
chr6:43700705	2e-11		C	0.26
rs10404696	2e-11	CRTC1	G	0.03
chr2:233597196	4e-11		G	0.03
chr13:81191213	4e-11		C	0.04
rs8046904	2e-10	LINC00917 - FENDRR	G	1.47
chr11:62671644	3e-09		C	1.85
chr19:18600515	8e-09		T	0.11
chr4:4148369	8e-09		G	1.36

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90476045	Verma A	2024	189,441	223,867	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90476046	Verma A	2024	185,368	228,046	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90478313	Verma A	2024	46,915	63,027	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90480294	Verma A	2024	46,915	63,027	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90478316	Verma A	2024	45,951	64,111	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90480291	Verma A	2024	45,951	64,111	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90691969	Karczewski KJ	2025	42,944	371,349	Pan-UK Biobank genome-wide association analyses enhance discovery and resolution of ancestry-enriched effects.
GCST90693094	Karczewski KJ	2025	42,944	371,349	Pan-UK Biobank genome-wide association analyses enhance discovery and resolution of ancestry-enriched effects.
GCST90691970	Karczewski KJ	2025	40,018	371,349	Pan-UK Biobank genome-wide association analyses enhance discovery and resolution of ancestry-enriched effects.
GCST90693095	Karczewski KJ	2025	40,018	371,349	Pan-UK Biobank genome-wide association analyses enhance discovery and resolution of ancestry-enriched effects.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	2
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	35

MAF distribution

Bucket	Variants
common (>=0.05)	27
low_freq (0.01-0.05)	0
rare (<0.01)	2
unknown	8

Functional consequences

Consequence	Count
unknown	22
intergenic_variant	7
intron_variant	6
missense_variant	2

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs9673356	16	53530276	A>C,G	0.344	intergenic_variant	AKTIP - RPGRIP1L	7e-21	Tier 4: intronic/intergenic
chr9:128660676				0.354			2e-19	Tier 4: intronic/intergenic
chr9:96586175				0.435			4e-18	Tier 4: intronic/intergenic
rs3094503	17	37670407	A>C,G,T	0.05	intron_variant	DDX52 - HNF1B	3e-16	Tier 4: intronic/intergenic
rs2891698	19	18677171	G>A,C	0.477	intergenic_variant	KLHL26 - CRTC1	3e-16	Tier 4: intronic/intergenic
rs4766578	12	111466567	T>A	0.495	intron_variant	ATXN2	4e-16	Tier 4: intronic/intergenic
chr6:34603350				0.189			8e-16	Tier 4: intronic/intergenic
chr11:32492265				0.368			3e-13	Tier 4: intronic/intergenic
rs10987077	9	125980899	G>A,C	0.296	intergenic_variant	PBX3 - MVB12B	3e-13	Tier 4: intronic/intergenic
rs11863156	16	53522178	C>A,G,T	0.4	intergenic_variant	AKTIP - RPGRIP1L	4e-13	Tier 4: intronic/intergenic
rs6499626	16	53531054	T>C	0.395	intergenic_variant	AKTIP - RPGRIP1L	7e-13	Tier 4: intronic/intergenic
chr11:32507733				0.351			9e-13	Tier 4: intronic/intergenic
chr3:183403556				0.254			1e-12	Tier 4: intronic/intergenic
chr6:65125567				0.253			1e-12	Tier 4: intronic/intergenic
chr12:78252709				0.49			3e-12	Tier 4: intronic/intergenic
chr2:200152198				0.296			3e-12	Tier 4: intronic/intergenic
chr2:67812176				0.274			3e-12	Tier 4: intronic/intergenic
rs429358	19	44908684	T>C	0.14	missense_variant	APOE	4e-12	Tier 1: coding
chr13:36150308				0.412			8e-12	Tier 4: intronic/intergenic
rs566890996	1	56783783	C>G	0	intron_variant	FYB2	8e-12	Tier 4: intronic/intergenic
chr2:52990318				0.375			1e-11	Tier 4: intronic/intergenic
rs13107325	4	102267552	C>A,T	0.083	missense_variant	SLC39A8	2e-11	Tier 1: coding
chr6:43700705				0.003			2e-11	Tier 4: intronic/intergenic
rs10404696	19	18693485	G>T	0.409	intron_variant	CRTC1	2e-11	Tier 4: intronic/intergenic
chr2:233597196				0.449			4e-11	Tier 4: intronic/intergenic
chr13:81191213				0.198			4e-11	Tier 4: intronic/intergenic
rs8046904	16	86373131	C>G,T	0.05	intergenic_variant	LINC00917 - FENDRR	2e-10	Tier 4: intronic/intergenic
chr11:62671644							3e-09	Tier 4: intronic/intergenic
chr19:18600515							8e-09	Tier 4: intronic/intergenic
chr4:4148369							8e-09	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

2 approved, 1 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

Drug	Development status
Budesonide	Approved (phase 4)
Dupilumab	Approved (phase 4)
Pantoprazole	Phase 3 (in late-stage trials)

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
NCT03645070	Not specified	COMPLETED	Randomized Study on the Effect of Oesophageal Temperature on the Incidence of Esophageal Lesions After AF Ablation