Canker sore

Summary

Canker sore (MONDO:0005318) is a disease with 1 cohort gene (1 GWAS associations across 3 studies) and 11 clinical trials.

At a glance

• Cohort genes: 1
• GWAS associations: 1
• ClinVar variants: 2
• Clinical trials: 11

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	canker sore
Mondo ID	MONDO:0005318
EFO	EFO:0003938
MeSH	D013281
NCIT	C62546
SNOMED CT	427617000
UMLS	C2937365
MedGen	445425
Anatomy (UBERON)	UBERON:0003343
Is cancer (heuristic)	no

Also known as: aphthous ulcer · canker sore

Data availability: 2 ClinVar variants · 1 GWAS association (3 studies) · 1 HPO phenotype.

Disease family

Classification path: disease › human disease › disease by developmental or physiological process › inflammatory disease › mucositis › stomatitis › canker sore

Related subtypes (6): gingivitis, aphthous stomatitis, ulcerative stomatitis, chemotherapy-induced oral mucositis, herpes simplex virus gingivostomatitis, denture stomatitis

Genetics & variants

GWAS landscape

1 GWAS associations across 3 studies. Top hits map to 0 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs186496805	4e-07	BIN1 - NIFKP9	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90652106	Liu TY	2025	1,770	215,085	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90482122	Verma A	2024	653	447,900	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90436291	Zhou W	2018	85	403,323	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.

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	1

MAF distribution

Bucket	Variants
common (>=0.05)	0
low_freq (0.01-0.05)	0
rare (<0.01)	0
unknown	1

Functional consequences

Consequence	Count
intron_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs186496805	2	127130364	T>G		intron_variant	BIN1 - NIFKP9	4e-07	Tier 4: intronic/intergenic

ClinVar germline variants

2 retrieved; paginated sample, class counts are floors:

1 pathogenic/likely pathogenic, 1 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
374163	NM_152564.5(VPS13B):c.4545del (p.Ser1516fs)	VPS13B	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
56635	NM_152564.5(VPS13B):c.11239C>T (p.Gln3747Ter)	VPS13B	Pathogenic	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 1 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
VPS13B	Orphanet:193	Cohen syndrome

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
VPS13B	HGNC:2183	ENSG00000132549	Q7Z7G8	Intermembrane lipid transfer protein VPS13B	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
VPS13B	Intermembrane lipid transfer protein VPS13B	Mediates the transfer of lipids between membranes at organelle contact sites.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

Family	Genes	Fold	FDR
Other/Unknown	1	1.8×	0.558

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
VPS13B	Other/Unknown	no		VPS13_VAB, VPS13_N, VPS13B

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
bronchial epithelial cell	1
nipple	1
sural nerve	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
VPS13B	291	ubiquitous	marker	sural nerve, nipple, bronchial epithelial cell

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
VPS13B	1,950

Structural data

PDB: 0 · AlphaFold-only: 1 · No structure: 0

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
VPS13B	Q7Z7G8

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 1 evidence-associated genes (0 with Reactome annotation).

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
slow endocytic recycling	1	8426.0×	0.002	VPS13B
Golgi reassembly	1	3370.4×	0.002	VPS13B
maintenance of lens transparency	1	2106.5×	0.002	VPS13B
head morphogenesis	1	2106.5×	0.002	VPS13B
dentate gyrus development	1	624.1×	0.005	VPS13B
acrosome assembly	1	455.5×	0.006	VPS13B
adipose tissue development	1	401.2×	0.006	VPS13B
social behavior	1	271.8×	0.007	VPS13B
lipid transport	1	263.3×	0.007	VPS13B
memory	1	183.2×	0.009	VPS13B
muscle organ development	1	166.8×	0.009	VPS13B
multicellular organism growth	1	137.0×	0.010	VPS13B
Golgi organization	1	133.8×	0.010	VPS13B
neuron projection development	1	122.1×	0.010	VPS13B
central nervous system development	1	115.4×	0.010	VPS13B
vesicle-mediated transport	1	96.3×	0.011	VPS13B
nervous system development	1	45.9×	0.022	VPS13B

Therapeutics

Drugs indicated for this disease

No approved or late-stage (phase ≥3) drug is indicated for this disease; the following are in earlier-phase trials only.

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Colchicine, Diphenhydramine, Ibuprofen, Prednisolone, Zinc Sulfate.

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1

Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
VPS13B	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	VPS13B

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
VPS13B	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 11.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	8
PHASE4	1
PHASE1	1
EARLY_PHASE1	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT06819033	PHASE4	RECRUITING	Effects of Photobiomodulation (PBM) on Pain After Presentation of Aphthous Ulcers in Pediatric Dental Patients
NCT05392842	PHASE1	COMPLETED	Corchorus Olitorius Buccal Films for the Treatment of Recurrent Minor Aphthous Ulcerations
NCT06960278	EARLY_PHASE1	COMPLETED	Effect of Alum Stone Containing Mucosal Adhesive Patches on Healing of Recurrent Aphthous Stomatitis
NCT07141758	Not specified	RECRUITING	Salivary E-cadherin, Calprotectin, and Matrix Metalloproteinase-9 Levels in Recurrent Aphthous Stomatitis
NCT00556686	Not specified	WITHDRAWN	Salivary Catecholamines in Aphthous Stomatitis (Canker Sores)
NCT04385979	Not specified	COMPLETED	Curcumin and Nanocurcumin in Oral Aphthous Ulcer
NCT04914533	Not specified	WITHDRAWN	Luminance RED for Canker Sores
NCT05959824	Not specified	UNKNOWN	Devintec OR-AT0222 Oral Gel for the Treatment of Canker Sores: A Double Blind, Randomized, Placebo Controlled Clinical Investigation
NCT06013202	Not specified	UNKNOWN	The Efficacy of Nigella Sativa Oil Mouth Rinse in the Management of Recurrent Minor Aphthous Ulcer
NCT07121361	Not specified	COMPLETED	Effectiveness of Recurrent Aphthous Stomatitis Mouthwash System for the Treatment of Oral Ulcers
NCT07322666	Not specified	COMPLETED	Non-Thermal Plasma vs. Low-Level Laser Therapy for Recurrent Oral Ulcers

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
CHEMBL443232	0	1