Stomatitis

Summary

Stomatitis (MONDO:0004842) is a disease (an umbrella term covering 7 Mondo subtypes) with 10 GWAS associations across 26 studies and 207 clinical trials. Top therapeutic interventions include benzydamine, palifermin, and chlorhexidine. A subtype of mucositis — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Umbrella term: 7 Mondo subtypes
• GWAS associations: 10
• Clinical trials: 207

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	stomatitis
Mondo ID	MONDO:0004842
EFO	EFO:0009688
MeSH	D013280
DOID	DOID:9637
NCIT	C26887
SNOMED CT	61170000
UMLS	C0038362
MedGen	52511
Is cancer (heuristic)	no

Also known as: inflammation of mouth mucosa · mouth mucosa inflammation · mucositis oral · oral mucositis

Data availability: 10 GWAS associations (26 studies).

Disease family

This is a subtype of mucositis. 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 developmental or physiological process › inflammatory disease › mucositis › stomatitis

Related subtypes (5): gastrointestinal mucositis, endometritis, rhinitis, epiglottitis, tracheitis

Subtypes (7): gingivitis, aphthous stomatitis, ulcerative stomatitis, canker sore, chemotherapy-induced oral mucositis, herpes simplex virus gingivostomatitis, denture stomatitis

Genetics & variants

GWAS landscape

10 GWAS associations across 26 studies. Top hits map to 7 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs368732611	4e-12	SLC4A8	A	3.42
rs901895588	1e-11	PWRN1	A	3.09
rs536922999	3e-11	NTRK3	T	3.54
rs2239141	2e-09	VWF	?
rs12029003	4e-07	TMIGD3	?	3
rs12433034	5e-07	LINC02332	?	2.8
rs141748690	5e-07	LINC02214 - RPL35AP15	?	3.7
rs143685874	9e-07	LINC02504	?	3.5
rs1233378	1e-06	SUMO2P1 - MOG	?	2.4
rs139761439	2e-06	ITLN1 - ITLN2	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90652237	Liu TY	2025	5,562	215,085	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90473764	UK Biobank Whole-Genome Sequencing Consortium	2025	4,234	454,206	Whole-genome sequencing of 490,640 UK Biobank participants.
GCST90651342	Liu TY	2025	3,888	215,085	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90726978	Kim HI	2026	2,001	42,025	Exome sequencing and analysis of 44,028 British South Asians enriched for high autozygosity.
GCST90080179	Backman JD	2021	1,778	382,114	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90084165	Backman JD	2021	1,778	382,114	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90478306	Verma A	2024	1,710	444,108	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90079555	Backman JD	2021	1,312	386,618	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083541	Backman JD	2021	1,312	386,618	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90080178	Backman JD	2021	770	385,531	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	0
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	10

MAF distribution

Bucket	Variants
common (>=0.05)	5
low_freq (0.01-0.05)	0
rare (<0.01)	3
unknown	2

Functional consequences

Consequence	Count
intron_variant	9
non_coding_transcript_exon_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs368732611	12	51416407	A>G	0	intron_variant	SLC4A8	4e-12	Tier 4: intronic/intergenic
rs901895588	15	24779338	A>C	0	intron_variant	PWRN1	1e-11	Tier 4: intronic/intergenic
rs536922999	15	88019982	T>A,C	0	intron_variant	NTRK3	3e-11	Tier 4: intronic/intergenic
rs2239141	12	6091212	T>A		intron_variant	VWF	2e-09	Tier 4: intronic/intergenic
rs12029003	1	111529398	C>T	0.05	intron_variant	TMIGD3	4e-07	Tier 4: intronic/intergenic
rs12433034	14	22557405	T>A,C	0.05	non_coding_transcript_exon_variant	LINC02332	5e-07	Tier 4: intronic/intergenic
rs141748690	5	116796980	T>C	0.05	intron_variant	LINC02214 - RPL35AP15	5e-07	Tier 4: intronic/intergenic
rs143685874	4	171295973	CATGT>C	0.05	intron_variant	LINC02504	9e-07	Tier 4: intronic/intergenic
rs1233378	6	29636347	G>A	0.05	intron_variant	SUMO2P1 - MOG	1e-06	Tier 4: intronic/intergenic
rs139761439	1	160939870	A>G		intron_variant	ITLN1 - ITLN2	2e-06	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, 13 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

Drug	Development status
Palifermin	Approved (phase 4)
Avasopasem Manganese	Phase 3 (in late-stage trials)
Benzydamine	Phase 3 (in late-stage trials)
Bifidobacterium Spp.	Phase 3 (in late-stage trials)
Cisplatin	Phase 3 (in late-stage trials)
Curcumin	Phase 3 (in late-stage trials)
Diphenhydramine	Phase 3 (in late-stage trials)
Glutamine	Phase 3 (in late-stage trials)
Lactobacillus Acidophilus	Phase 3 (in late-stage trials)
Lidocaine	Phase 3 (in late-stage trials)
Nepidermin	Phase 3 (in late-stage trials)
Nystatin	Phase 3 (in late-stage trials)
Thalidomide	Phase 3 (in late-stage trials)
Ulinastatin	Phase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Acetylcysteine, Aluminum Hydroxide, Amlexanox, Ascorbic Acid, Celecoxib, Chamomile, Chlorhexidine, Clazakizumab, Clonidine, Dexpanthenol, Dusquetide, Etanercept, Magnesium, Meclocycline Sulfosalicylate, Miconazole, Morphine, Nibrozetone, OMEGA-3-ACID ETHYL ESTERS, Povidone-Iodine, Sodium Chloride, Vitamin E, Wax, Emulsifying, Zinc Acetate Anhydrous.

Clinical trials & evidence

Clinical trials

Clinical trials: 207.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	91
PHASE2	54
PHASE3	26
PHASE4	11
PHASE1	11
PHASE2/PHASE3	6
PHASE1/PHASE2	4
EARLY_PHASE1	4

Top trials by phase / activity

NCT	Phase	Status	Title
NCT07357597	PHASE4	NOT_YET_RECRUITING	An Open-label, Single-arm Study of Prophylaxis for Datopotamab Deruxtecan (Dato-DXd) -Related Stomatitis in Eligible Patients With Metastatic or Inoperable Locally Recurrent Breast Cancer or Locally Advanced or Metastatic Epidermal Growth Factor Receptor-Mutated Non-small Cell Lung Cancer.
NCT01115049	PHASE4	COMPLETED	Hexetidine and Chlorobutanol for Lesions Due to Prostheses
NCT01283906	PHASE4	COMPLETED	A Study to Evaluate the Efficacy of MuGard for the Amelioration of Oral Mucositis in Head and Neck Cancer Patients
NCT01288625	PHASE4	WITHDRAWN	Prospective Study of Head and Neck Cancer Radiation Treatment With or Without Amifostine
NCT01876407	PHASE4	UNKNOWN	Effectiveness of Low Energy Laser Treatment in Oral Mucositis Induced by Chemotherapy and Radiotherapy in Head and Neck Cancer
NCT02407834	PHASE4	COMPLETED	Effectiveness of Hygiene Solutions on Denture Biofilm
NCT02662374	PHASE4	UNKNOWN	Oral Hygiene Regimen in Patients on HCT
NCT03490396	PHASE4	TERMINATED	Gelclair at Conditioning or After Oral Mucositis Diagnosed vs. Magic Mouth Wash in Stem Cell Transplant Recipients
NCT03867214	PHASE4	UNKNOWN	Effects of Oral Care With Glutamine on Oral Health, Oral Flora and Incidence of Pneumonia After Neurosurgery With Microbiome Analysis
NCT05211622	PHASE4	UNKNOWN	OZOCLO_MUCOSITIS: a New Protocol for Prevention of Oral Mucositis
NCT05818007	PHASE4	COMPLETED	Is Hyaluronic Acid Gel Effective on Oral Mucositis in Children Who Receiving Chemotherapy
NCT03983369	PHASE3	RECRUITING	Low-level Laser Therapy in the Prevention of Chemotherapy-induced Mucositis in Children and Young Adults
NCT06071637	PHASE3	RECRUITING	Low Power Laser Therapy As Prevention Of Oral Mucositis And Oropharyngeal Pain In Patients Undergoing Allogenetic HSCT
NCT07325383	PHASE3	ACTIVE_NOT_RECRUITING	Safety and Efficacy of N-Acetylcysteine Mouthwash in Prevention of Mucositis in HSCT Patients
NCT07543978	PHASE3	NOT_YET_RECRUITING	Traditional Chinese Medicine for the Prevention of Radiotherapy-Induced Oral Mucositis (RTOM)
NCT00001812	PHASE3	COMPLETED	A Randomized, Double-Blind, Placebo Controlled Trial Evaluating the Impact of Nystatin on the Development of Oral Irritation in Patients Receiving High Dose Intravenous Interleukin-2
NCT00041665	PHASE3	COMPLETED	Recombinant Human Keratinocyte Growth Factor to Reduce Oral Mucositis in Hematologic Malignancy Patients Undergoing Peripheral Blood Stem Cell Transplantation After Radiation and High-dose Chemotherapy
NCT00051441	PHASE3	COMPLETED	Safety & Efficacy Study of Benzydamine Oral Rinse for the Treatment of Oral Mucositis (Mouth Sores) Resulting From Radiation Therapy for Cancer of the Oral Cavity, Oropharynx, or Nasopharynx
NCT00101582	PHASE3	COMPLETED	Palifermin for the Reduction of Oral Mucositis in Patients With Locally Advanced Head and Neck Cancer
NCT00293462	PHASE3	COMPLETED	GM-CSF Mouthwash for Preventing and Treating Mucositis in Patients Undergoing Radiation Therapy for Head and Neck Cancer
NCT00574860	PHASE3	TERMINATED	EN3285 for the Prevention or Delay of Oral Mucositis in Patients With Head and Neck Cancer
NCT00790322	PHASE3	COMPLETED	Efficacy and Safety Study of SBG vs Placebo in Head and Neck Cancer Patients Undergoing Radiation Therapy
NCT01007617	PHASE2/PHASE3	UNKNOWN	Low-energy Laser Therapy for Prevention of Oral Mucositis in Children
NCT01099891	PHASE3	UNKNOWN	The Clinical Study for Evaluation of Efficacy and Safety of EGF on Oral Mucositis in Radiation Therapy Patients
NCT01837446	PHASE2/PHASE3	COMPLETED	Morphine Mouthwash for Management of Oral Mucositis in Patients With Head and Neck Cancer
NCT02020928	PHASE3	UNKNOWN	Laser Therapy Prevents Mucositis Oral in Chemotherapy for Bone Marrow Transplantation?
NCT02539342	PHASE3	TERMINATED	Caphosol Study: Prevention of Oral Mucositis in Children, Adolescents and Young Adults Receiving Chemotherapy
NCT02555501	PHASE3	COMPLETED	Oral Mucositis and Laser Therapy Associated With Photodynamic Therapy
NCT02762019	PHASE3	COMPLETED	Laser for Oral Mucositis in Pediatric Onco-hematology
NCT02868151	PHASE2/PHASE3	COMPLETED	Effect of Oral Vitamin C in Assessing the Severity of Oral Mucositis in Chemoradiation of Head and Neck Cancers
NCT03237325	PHASE3	COMPLETED	DOM-INNATE: Study of SGX942 for the Treatment of Oral Mucositis in Patients With Concomitant Chemoradiation Therapy for Head and Neck Cancer
NCT03689712	PHASE3	COMPLETED	ROMAN: Phase 3 Trial Investigating the Effects of GC4419 on Radiation Induced Oral Mucositis in Head/Neck Cancer Patients
NCT04080622	PHASE3	COMPLETED	Evaluate the Efficacy of Selenium for the Prevention of Chemotherapy-induced Mucositis During Autologous Stem Cell Transplantation.
NCT04187222	PHASE3	COMPLETED	Effect of Probiotic Use Bifidobacterium Animalis Subsp. Lactis in Peri-implant Mucositis
NCT04303312	PHASE3	UNKNOWN	Treatment of Chemotherapy and Radiotherapy Induced Oral Mucositis
NCT04685395	PHASE3	UNKNOWN	Comparative Efficacy of Rebamipide Gargle And Benzydamine HCL Gargle in Prevention and Management of Chemo- and Radio-therapy-induced Oral Mucositis
NCT04896164	PHASE3	UNKNOWN	Randomized Trial of Curcumin to Reduce Mucositis in Autologous Transplant Setting
NCT04995354	PHASE2/PHASE3	UNKNOWN	Efficacy of EGF-loaded Self Healing Gel in Treatment of Oral Mucositis
NCT05214495	PHASE2/PHASE3	COMPLETED	Omega-3 Hydrogel and Prevention of Oral Mucositis
NCT05878405	PHASE3	COMPLETED	Methylene Blue Mouthwash for the Treatment of Oral Mucositis Pain in Patients With Cancer

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
BENZYDAMINE	4	4
PALIFERMIN	4	4
CHLORHEXIDINE	4	3
GLUTAMINE	4	3
METHYLENE BLUE CATION	4	3
NYSTATIN	4	2
SODIUM BICARBONATE	4	2
ZINC ACETATE ANHYDROUS	4	2
ALFACALCIDOL	4	1
AMIFOSTINE	4	1
AMLEXANOX	4	1
ASCORBIC ACID	4	1
DIPHENHYDRAMINE	4	1
FOLIC ACID	4	1
HEXETIDINE	4	1
HYALURONIC ACID	4	1
METHADONE HYDROCHLORIDE	4	1
OLIVE OIL	4	1
OXYCODONE HYDROCHLORIDE	4	1
PHENYLEPHRINE	4	1
PROCAINE	4	1
SARGRAMOSTIM	4	1
VALACYCLOVIR	4	1
HONEY	3	6
PROPOLIS WAX	3	5
AVASOPASEM MANGANESE	3	2
CURCUMIN	3	2
DUSQUETIDE	3	2
NIBROZETONE	3	2
OZONE	3	2