Odontogenic cyst

Summary

Odontogenic cyst (MONDO:0006328) is a disease with 1 GWAS associations across 4 studies and 9 clinical trials. A subtype of neoplasm — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• GWAS associations: 1
• Clinical trials: 9

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	odontogenic cyst
Mondo ID	MONDO:0006328
EFO	EFO:1000406
MeSH	D009807
NCIT	C54220
SNOMED CT	235110008
UMLS	C0028879
MedGen	14461
Is cancer (heuristic)	no

Data availability: 1 GWAS association (4 studies).

Disease family

This is a subtype of neoplasm. 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 etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › odontogenic cyst

Related subtypes (47): pre-malignant neoplasm, endocrine gland neoplasm, giant cell tumor, hematopoietic and lymphoid system neoplasm, skin neoplasm, mesenchymal cell neoplasm, epidural spinal canal neoplasm, skeletal muscle neoplasm, trophoblastic neoplasm, cancer, germ cell tumor, benign neoplasm, upper aerodigestive tract neoplasm, histiocytoma, embryonal neoplasm, head and neck neoplasm, epithelial neoplasm, reproductive system neoplasm, non-seminomatous lesion, phosphaturic mesenchymal tumor, thyroglossal duct cyst, hamartoma, mesenchymoma, mesothelial neoplasm, peritoneal neoplasm, virus associated tumor, nail tumor, respiratory tract neoplasm, spindle cell neoplasm, mixed neoplasm, urinary system neoplasm, cystic neoplasm, childhood neoplasm, melanocytic neoplasm, digestive system neoplasm, nervous system neoplasm, neoplasm of thorax, connective tissue neoplasm, bronchial adenomas/carcinoids childhood, diffuse idiopathic pulmonary neuroendocrine cell hyperplasia, erythroplakia, retroperitoneal neoplasm, cardiovascular neoplasm, dermoid or epidermoid cyst of the central nervous system, connective and soft tissue neoplasm, NTRK fusion positive cancer, RET fusion positive cancer

Subtypes (1): dentigerous cyst

Genetics & variants

GWAS landscape

1 GWAS associations across 4 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
rs118037607	6e-09	LINC02949 - LINC02950	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90436277	Zhou W	2018	329	398,136	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90044106	Jiang L	2021	274	456,074	A generalized linear mixed model association tool for biobank-scale data.
GCST90482112	Verma A	2024	232	450,426	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90651407	Liu TY	2025	195	208,919	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.

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
intergenic_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs118037607	8	8437440	A>G		intergenic_variant	LINC02949 - LINC02950	6e-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

No druggable-target or therapeutic data for this disease’s cohort.

Clinical trials & evidence

Clinical trials

Clinical trials: 9.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	9

Top trials by phase / activity

NCT	Phase	Status	Title
NCT06688851	Not specified	RECRUITING	Patient Specific Implants (PSIs) for the Decompression of Odontogenic Cysts
NCT07424716	Not specified	RECRUITING	Bone Regeneration Using PRF After Cyst Enucleation
NCT05253261	Not specified	COMPLETED	Decompression of Odontogenic Cysts Using an Appliance Fabricated With a Fully Digital Workflow
NCT05358275	Not specified	UNKNOWN	The Evaluation of the Effect of Performing Guided Lid Surgery
NCT06071806	Not specified	COMPLETED	Recurrence of Odontogenic Keratocyst
NCT06133764	Not specified	COMPLETED	Risk-Adapted Treatment Strategies for Odontogenic Keratocysts: A Long-Term Randomized Clinical Trial Quantifying Recurrence Reduction
NCT06262802	Not specified	UNKNOWN	Volumetric Changes in Large Cystic Lesions Using Active Decompression and Distraction Sugosteogenesis vs Passive Decompression
NCT06536907	Not specified	COMPLETED	Decompression of Odontogenic Cysts
NCT06833840	Not specified	COMPLETED	Evaluation of the Expression and Prognostic Role of Tumor Stem Cell Marker SOX2 in Odontogenic Cysts and Tumors