Disorder of pharynx

Summary

Disorder of pharynx (MONDO:0020592) is a disease (an umbrella term covering 10 Mondo subtypes) with 34 GWAS associations across 3 studies and 7 clinical trials. Top therapeutic interventions include rabeprazole sodium and remimazolam. A subtype of respiratory system disorder — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Umbrella term: 10 Mondo subtypes
• GWAS associations: 34
• Clinical trials: 7

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	disorder of pharynx
Mondo ID	MONDO:0020592
NCIT	C26850
SNOMED CT	75860007
UMLS	C0031345
MedGen	10691
Anatomy (UBERON)	UBERON:0001042
Is cancer (heuristic)	no

Also known as: chordate pharynx disease · chordate pharynx disease or disorder · disease of chordate pharynx · disease or disorder of chordate pharynx · disorder of chordate pharynx · pharyngeal disease · pharyngeal disorder

Data availability: 34 GWAS associations (3 studies).

Disease family

This is a subtype of respiratory system 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 › respiratory system disorder › disorder of pharynx

Related subtypes (58): lower respiratory tract disorder, respiratory system cancer, respiratory system benign neoplasm, allergic respiratory disease, paranasal sinus disorder, upper respiratory tract disorder, pertussis, severe acute respiratory syndrome, sleep apnea syndrome, diaphragm disorder, pulmonary tuberculosis, altitude sickness, perinatal asphyxia, pulmonary nodular lymphoid hyperplasia, tracheobronchopathia osteochondroplastica, Williams-Campbell syndrome, cystic fibrosis, growth delay-hydrocephaly-lung hypoplasia syndrome, laryngo-onycho-cutaneous syndrome, congenital pulmonary lymphangiectasia, familial primary pulmonary hypoplasia, Mounier-Kuhn syndrome, Young syndrome, lung agenesis-heart defect-thumb anomalies syndrome, sudden infant death-dysgenesis of the testes syndrome, alpha 1-antitrypsin deficiency, hereditary sclerosing poikiloderma with tendon and pulmonary involvement, autoimmune interstitial lung disease-arthritis syndrome, mucopolysaccharidosis-plus syndrome, congenital bronchobiliary fistula, bronchogenic cyst, primary ciliary dyskinesia, congenital pulmonary airway malformation, transient hyperammonemia of the newborn, congenital pulmonary sequestration, Siegler-Brewer-Carey syndrome, tracheal agenesis, 16q24.1 microdeletion syndrome, staphylococcal necrotizing pneumonia, pulmonary veno-occlusive disease and/or pulmonary capillary haemangiomatosis, plastic bronchitis, recurrent respiratory papillomatosis, IgG4-related mediastinitis, bronchopulmonary dysplasia, infantile apnea, diffuse alveolar hemorrhage, respiratory or thoracic malformation, pulmonary agenesis, eosinophilic granuloma, respiratory tract neoplasm, pulmonary alveolar proteinosis with hypogammaglobulinemia, respiratory tract infectious disorder, Middle East respiratory syndrome, reactive airway disease, acinar dysplasia, pulmonary hypoplasia, isolated left bronchial isomerism, bronchiectasis and nasal polyposis

Subtypes (10): oropharyngeal anthrax, tonsillitis, nasopharyngeal disorder, pharynx cancer, epiglottitis, peritonsillar abscess, Takayasu arteritis, tonsil neoplasm, neoplasm of hypopharynx, neoplasm of oropharynx

Genetics & variants

GWAS landscape

34 GWAS associations across 3 studies. Top hits map to 24 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs573841223	5e-29	TNFRSF13B	G	1.42
rs10849448	2e-22	LTBR	G	0.9
rs1045267	1e-20	MIR4435-2HG	G	0.91
rs713875	7e-18	HORMAD2 - LIF-AS1	G	1.08
rs189411872	3e-15	ADAM23	G	1.4
rs5860793	4e-13	RNU6-351P - TET2	GC	1.08
rs1980080	3e-12	SLC12A8	T	0.93
6p21.32	2e-11		?	1.16
rs4648051	4e-11	NFKB1	G	0.94
rs1019689682	4e-11	PIM3 - IL17REL	G	1.08
rs12128267	2e-10	LINC01705	G	1.1
rs12082271	2e-10	LINC01714	T	0.94
rs9542155	2e-10	KLHL1	C	0.94
rs950529388	3e-10	ABO	A	0.94
rs74178437	2e-09	ZBTB7A	A	1.07
rs6565189	2e-09	ITGAL	G	0.94
rs2286521	6e-09	RSKR, FOXN1	T	1.1
rs774674736	7e-09	ZNF417	A	1.94
rs55935382	8e-09	SPMIP7 - IKZF1	A	0.94
rs73150891	1e-08	CCDC188 - LINC02891	A	0.92
rs6824923	2e-08	FAM241A - AP1AR-DT	C	0.93
rs2491199	2e-08	RNU6-320P - LINC00892	A	0.96
rs73631760	3e-08	SLC20A2	C	1.09
rs117556162	3e-08	CARMIL2	A	0.88
rs192569879	5e-08	IL23R - RNU4ATAC4P	A	0.69
rs551502318	1e-07	ADSS1	?	1.96
rs112672184	2e-07	FBXO33 - LINC02315	?	1.72
rs35668054	2e-07	DYSF - RPS20P10	?	1.09
rs187688516	5e-07	LINC00882	?	0.83
rs2089081	6e-07	ARNT	?	0.95

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90269785	Saarentaus EC	2023	33,157	199,208	Inflammatory and infectious upper respiratory diseases associate with 41 genomic loci and type 2 inflammation.
GCST90080123	Backman JD	2021	682	386,581	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90084109	Backman JD	2021	682	386,581	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	3
Tier 2: splice/UTR	4
Tier 3: regulatory	1
Tier 4: intronic/intergenic	26

MAF distribution

Bucket	Variants
common (>=0.05)	24
low_freq (0.01-0.05)	3
rare (<0.01)	2
unknown	5

Functional consequences

Consequence	Count
intron_variant	18
intergenic_variant	6
5_prime_UTR_variant	2
missense_variant	2
non_coding_transcript_exon_variant	1
splice_polypyrimidine_tract_variant	1
unknown	1
regulatory_region_variant	1
splice_region_variant	1
frameshift_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs573841223	17	16939881	C>G,T	0.025	intron_variant	TNFRSF13B	5e-29	Tier 4: intronic/intergenic
rs10849448	12	6384185	A>G	0.245	5_prime_UTR_variant	LTBR	2e-22	Tier 2: splice/UTR
rs1045267	2	111429464	A>C,G,T	0.34	non_coding_transcript_exon_variant	MIR4435-2HG	1e-20	Tier 4: intronic/intergenic
rs713875	22	30196498	C>A,G,T	0.479	intron_variant	HORMAD2 - LIF-AS1	7e-18	Tier 4: intronic/intergenic
rs189411872	2	206557414	A>G	0.013	splice_polypyrimidine_tract_variant	ADAM23	3e-15	Tier 2: splice/UTR
rs5860793	4	105129809	G>GC	0.284	intergenic_variant	RNU6-351P - TET2	4e-13	Tier 4: intronic/intergenic
rs1980080	3	125192997	C>A,T	0.347	intron_variant	SLC12A8	3e-12	Tier 4: intronic/intergenic
6p21.32							2e-11	Tier 4: intronic/intergenic
rs4648051	4	102593836	A>G	0.32	intron_variant	NFKB1	4e-11	Tier 4: intronic/intergenic
rs1019689682	22	49976339	C>G,T	0.236	regulatory_region_variant	PIM3 - IL17REL	4e-11	Tier 3: regulatory
rs12128267	1	221915660	A>G	0.122	intron_variant	LINC01705	2e-10	Tier 4: intronic/intergenic
rs12082271	1	8189495	G>A,C,T	0.302	intron_variant	LINC01714	2e-10	Tier 4: intronic/intergenic
rs9542155	13	70005395	T>C,G	0.357	intron_variant	KLHL1	2e-10	Tier 4: intronic/intergenic
rs950529388	9	133261662		0.436	intron_variant	ABO	3e-10	Tier 4: intronic/intergenic
rs74178437	19	4056862	G>A,C,T	0.262	5_prime_UTR_variant	ZBTB7A	2e-09	Tier 2: splice/UTR
rs6565189	16	30495944	T>A,C,G	0.291	intron_variant	ITGAL	2e-09	Tier 4: intronic/intergenic
rs2286521	17	28534546	C>G,T	0.085	splice_region_variant	RSKR, FOXN1	6e-09	Tier 2: splice/UTR
rs774674736	19	57910050	ACT>A	0.002	frameshift_variant	ZNF417	7e-09	Tier 1: coding
rs55935382	7	50250073	C>A,G	0.314	intron_variant	SPMIP7 - IKZF1	8e-09	Tier 4: intronic/intergenic
rs73150891	22	20181899	G>A	0.137	intergenic_variant	CCDC188 - LINC02891	1e-08	Tier 4: intronic/intergenic
rs6824923	4	112220279	T>C	0.166	intergenic_variant	FAM241A - AP1AR-DT	2e-08	Tier 4: intronic/intergenic
rs2491199	X	136591724	G>A,T	0.488	intergenic_variant	RNU6-320P - LINC00892	2e-08	Tier 4: intronic/intergenic
rs73631760	8	42424332	G>A,C,T	0.094	intron_variant	SLC20A2	3e-08	Tier 4: intronic/intergenic
rs117556162	16	67646903	G>A,T	0.047	missense_variant	CARMIL2	3e-08	Tier 1: coding
rs192569879	1	67266351	G>A	0.005	intergenic_variant	IL23R - RNU4ATAC4P	5e-08	Tier 4: intronic/intergenic
rs551502318	14	104740994	G>A,T		intron_variant	ADSS1	1e-07	Tier 4: intronic/intergenic
rs112672184	14	39920670	A>G,T		intron_variant	FBXO33 - LINC02315	2e-07	Tier 4: intronic/intergenic
rs35668054	2	71827707	C>A,T	0.05	intergenic_variant	DYSF - RPS20P10	2e-07	Tier 4: intronic/intergenic
rs187688516	3	106701452	G>T		intron_variant	LINC00882	5e-07	Tier 4: intronic/intergenic
rs2089081	1	150827641	T>C	0.05	intron_variant	ARNT	6e-07	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: 7.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	5
PHASE4	1
PHASE2	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT06507202	PHASE4	RECRUITING	Comparison of Remimazolam and Propofol for Recovery of Ambulatory Upper Airway Surgery
NCT04409873	PHASE2	TERMINATED	Antiseptic Mouthwash / Pre-Procedural Rinse on SARS-CoV-2 Load (COVID-19)
NCT04124198	Not specified	ACTIVE_NOT_RECRUITING	Quality of Life After Primary TORS vs IMRT for Patients With Early-stage Oropharyngeal Squamous Cell Carcinoma
NCT00614536	Not specified	COMPLETED	Study of Changes in Reflux Symptoms and Reflux Finding Score According to Rabeprazole Treatment Period
NCT01276418	Not specified	COMPLETED	ENT FiberLase CO2 Study
NCT02482896	Not specified	UNKNOWN	The Lolland-Falster Health Study
NCT06061250	Not specified	WITHDRAWN	Effect of Gum Chewing on Sore Throat After Double-lumen Tube Intubation

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
RABEPRAZOLE SODIUM	4	1
REMIMAZOLAM	4	1