Ovarian cyst

Summary

Ovarian cyst (MONDO:0003282) is a disease with 1 cohort gene and 46 clinical trials. Top therapeutic interventions include cetrorelix, danazol, and desflurane.

At a glance

• Cohort genes: 1
• ClinVar variants: 2
• Clinical trials: 46

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	ovarian cyst
Mondo ID	MONDO:0003282
MeSH	D010048
DOID	DOID:5119
SNOMED CT	79883001
UMLS	C0029927
MedGen	14540
Is cancer (heuristic)	no

Also known as: corpus luteum cyst · corpus luteum cysts · cyst, corpus luteum · cyst, ovarian · cysts, corpus luteum · cysts, ovarian · ovarian cyst · ovarian cyst (disease)

Data availability: 2 ClinVar variants · 1 HPO phenotype.

Disease family

An umbrella term covering 3 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › reproductive system disorder › gonadal disorder › ovarian disorder › ovarian cyst

Related subtypes (10): ovarian dysfunction, anovulation, ovarian stromal hyperthecosis, luteoma of pregnancy, ovarian endometriosis, oophoritis, ovarian hyperstimulation syndrome, ovarian neoplasm, ovarian remnant syndrome, ovarian ectopic pregnancy

Subtypes (3): corpus luteum cyst, malignant ovarian cyst, neonatal ovarian cyst

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

2 retrieved; paginated sample, class counts are floors:

2 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
267851	46;XX;ins(5;6)(p13;p24p25)dn		Pathogenic	criteria provided, single submitter
90577	NM_000251.3(MSH2):c.1226_1227del (p.Gln409fs)	MSH2	Pathogenic	reviewed by expert panel

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 2 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
MSH2	Orphanet:144	Lynch syndrome
MSH2	Orphanet:252202	Constitutional mismatch repair deficiency 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
MSH2	HGNC:7325	ENSG00000095002	P43246	DNA mismatch repair protein Msh2	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
MSH2	DNA mismatch repair protein Msh2	Component of the post-replicative DNA mismatch repair system (MMR).

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)
MSH2	Other/Unknown	no		DNA_mismatch_repair_MutS_C, DNA_mismatch_repair_MutS-lik_N, DNA_mismatch_repair_MutS_core

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
oocyte	1
secondary oocyte	1
ventricular zone	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
MSH2	278	ubiquitous	marker	secondary oocyte, oocyte, ventricular zone

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
MSH2	4,537

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
MSH2	P43246	30

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 15. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).

Pathways 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.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Defective Mismatch Repair Associated With MSH3	1	5710.0×	0.001	MSH2
Defective Mismatch Repair Associated With MSH6	1	5710.0×	0.001	MSH2
Defective Mismatch Repair Associated With MSH2	1	3806.7×	0.001	MSH2
Mismatch Repair	1	2855.0×	0.001	MSH2
Diseases of Mismatch Repair (MMR)	1	2855.0×	0.001	MSH2
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)	1	815.7×	0.003	MSH2
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)	1	815.7×	0.003	MSH2
Diseases of DNA repair	1	571.0×	0.003	MSH2
TP53 Regulates Transcription of DNA Repair Genes	1	181.3×	0.009	MSH2
DNA Repair	1	98.5×	0.015	MSH2
Transcriptional Regulation by TP53	1	62.1×	0.022	MSH2
RNA Polymerase II Transcription	1	22.5×	0.055	MSH2
Gene expression (Transcription)	1	17.8×	0.065	MSH2
Generic Transcription Pathway	1	15.1×	0.071	MSH2
Disease	1	13.1×	0.076	MSH2

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
somatic recombination of immunoglobulin genes involved in immune response	1	16852.0×	0.001	MSH2
somatic recombination of immunoglobulin gene segments	1	4213.0×	0.001	MSH2
B cell mediated immunity	1	4213.0×	0.001	MSH2
maintenance of DNA repeat elements	1	3370.4×	0.001	MSH2
mitotic recombination	1	2808.7×	0.001	MSH2
positive regulation of isotype switching to IgA isotypes	1	2808.7×	0.001	MSH2
response to UV-B	1	1872.4×	0.002	MSH2
DNA damage tolerance	1	1685.2×	0.002	MSH2
positive regulation of isotype switching to IgG isotypes	1	1532.0×	0.002	MSH2
oxidative phosphorylation	1	1404.3×	0.002	MSH2
negative regulation of DNA recombination	1	1123.5×	0.002	MSH2
somatic hypermutation of immunoglobulin genes	1	1053.2×	0.002	MSH2
mitotic intra-S DNA damage checkpoint signaling	1	936.2×	0.002	MSH2
response to X-ray	1	887.0×	0.002	MSH2
isotype switching	1	842.6×	0.002	MSH2
mismatch repair	1	648.1×	0.002	MSH2
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	1	495.6×	0.003	MSH2
germ cell development	1	455.5×	0.003	MSH2
determination of adult lifespan	1	432.1×	0.003	MSH2
B cell differentiation	1	218.9×	0.006	MSH2
double-strand break repair	1	203.0×	0.006	MSH2
male gonad development	1	156.0×	0.007	MSH2
negative regulation of neuron apoptotic process	1	110.9×	0.010	MSH2
in utero embryonic development	1	72.0×	0.014	MSH2
DNA repair	1	63.8×	0.016	MSH2

Therapeutics

Drugs indicated or in trials for this disease

No drug has an approved disease-direct ChEMBL indication for this disease.

1 drug in clinical trials for this disease (phase 2–3, investigational): efficacy not established — a trial record, not an indication.

Drug	Highest phase
Ropivacaine	Phase 3

Drug target analysis

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

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
MSH2	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

Symbol	Assays	Type breakdown
MSH2	9	Binding:9

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	MSH2

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)
MSH2	9	—

Clinical trials & evidence

Clinical trials

Clinical trials: 46.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	34
PHASE4	6
PHASE3	4
PHASE2/PHASE3	1
PHASE1/PHASE2	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT00713778	PHASE4	COMPLETED	The Impact of Electrocoagulation on Ovarian Reserve After Laparoscopic Excision of Ovarian Cyst
NCT00746278	PHASE4	COMPLETED	A Random Clinical Trial (RCT) of the Impact of Electrocoagulation on Ovarian Reserve
NCT01631253	PHASE4	UNKNOWN	The Impact on Ovarian Reserve After Single-port, Two-port, or Four-port Access Laparoscopic Ovarian Cyst Enucleation
NCT01779232	PHASE4	COMPLETED	Danazol Treatment in Endometriosis Women Before IVF
NCT01999569	PHASE4	COMPLETED	The Role of Estrogen in Luteinizing Hormone Surge and Ovulation
NCT04993924	PHASE4	UNKNOWN	GnRH Antagonist Pre-treatment in the Early Follicular Phase for Resolution of a Baseline Functional Ovarian Cyst
NCT00865488	PHASE3	SUSPENDED	Evaluation of Adhexil Safety and Efficacy in Prevention and/or Reduction of Adhesions in Gynecological Surgery
NCT01142622	PHASE3	COMPLETED	Intraperitoneal Ropivacaine Nebulization for Pain Control After Gynecologic Laparoscopic Surgery
NCT01288599	PHASE3	COMPLETED	Single Versus Conventional Laparoscopy for Benign Adnexal Disease
NCT01857466	PHASE3	COMPLETED	Ovarian Reserve After Ovarian Hemostasis by Floseal Matrix
NCT06227676	PHASE2/PHASE3	COMPLETED	Effect of ‘Cramp Bites’ on Period Cramps in Women Aged 18-25
NCT01431612	PHASE1/PHASE2	COMPLETED	Effects of Adrenergic Drugs on the Fluid Balance During Surgery
NCT05763511	Not specified	RECRUITING	Improved Diagnosis of Ovarian Cancer by Use of Circulating Tumor DNA as a Biomarker
NCT05842629	Not specified	RECRUITING	Improved Diagnosis of Ovarian Cancer
NCT06583395	Not specified	ENROLLING_BY_INVITATION	Quest to Analyze One Thousand Humans Meditating
NCT06638593	Not specified	RECRUITING	MIRRORS-FROZEN - Comparing Open Vs Robotic Surgery in the Management of Women with Complex Pelvic Adnexal Masses ≤ 8cm.
NCT06828419	Not specified	NOT_YET_RECRUITING	A Clinical Study on the Feasibility and Safety of Abdominal Endoscopic Single-port Surgery System to Assist Gynecological Day Surgery
NCT06913335	Not specified	RECRUITING	Comparison Between Electrosurgical Energy and Hemostatic Sealants on Hemostasis in Laparoscopic Ovarian Cystectomy
NCT06964594	Not specified	NOT_YET_RECRUITING	A Randomized Controlled Trial Study Comparing Adnexal Surgery by vNOTES or Laparoscopy
NCT07248553	Not specified	RECRUITING	Timing of LNG-IUD Insertion and Ovarian Cyst Formation
NCT00222066	Not specified	COMPLETED	Effect of Fetal Ovarian Cyst Aspiration to Prevent Torsion
NCT01379313	Not specified	COMPLETED	The Effect of Different I:E Ratio on Gas Exchange of Patients Undergoing Gynecologic Laparoscopic Surgery With Trendelenburg Position
NCT01698632	Not specified	UNKNOWN	International Ovarian Tumour Analysis (IOTA) Phase 5
NCT01937104	Not specified	COMPLETED	ONSD According to the Position During Laparoscopy
NCT02086318	Not specified	UNKNOWN	A New Algorithm to Predict Ovarian Age
NCT02129036	Not specified	COMPLETED	Ovarian Clear Cell Adenocarcinoma Review
NCT02218502	Not specified	TERMINATED	Study Into a New Diagnostic Tool (Simple Ultrasound-based Rules) in Patients With Adnexal Masses
NCT02482467	Not specified	TERMINATED	Prognosis and Long Term Pubertal Outcome of Girls Previously Diagnosed With a Prenatal Ovarian Cyst
NCT02831556	Not specified	COMPLETED	Point of Care 3D Ultrasound for Various Applications: A Pilot Study
NCT02835391	Not specified	COMPLETED	PerClot Compared to Usual Care in Gynaecology Procedures
NCT02852447	Not specified	COMPLETED	The Effect of Surgery for Non Endometriosic Ovarian Cysts on Ovarian Reserve
NCT02890914	Not specified	COMPLETED	Transvaginal Ultrasound Training for Obstetrics and Gynecology Residents
NCT03189316	Not specified	TERMINATED	Anti-inflammatory Cells in Peritoneal Cavity
NCT03370952	Not specified	COMPLETED	Laparoscopy-assisted Ovarian Cystectomy: NEW APPROCH
NCT03440931	Not specified	UNKNOWN	Monitoring Ovarian Cysts in Pregnancy
NCT04142203	Not specified	COMPLETED	Implementation of 23 Hour Surgery Model in a Tertiary Hospital
NCT04188652	Not specified	COMPLETED	Diagnosing Ovarian Cysts - the DOC Study
NCT04355312	Not specified	COMPLETED	Using INDOcyanine Green to Analyse Ovarian Vascularization After Ovarian Laparoscopic CYStectomy
NCT05054946	Not specified	COMPLETED	The Effect of Laparoscopic Surgery on Ovarian Reserve According to Cyst Types
NCT05342298	Not specified	UNKNOWN	Assessment of Ovarian Cysts Using Machine Learning

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
CETRORELIX	4	2
DANAZOL	4	1
DESFLURANE	4	1
ESMOLOL	4	1
LETROZOLE	4	1
PHENYLEPHRINE	4	1
CELLULOSE, OXIDIZED	-1	1