PDA1

Summary

PDA1 (MONDO:0024560) is a disease with 1 cohort gene and 5 clinical trials. Top therapeutic interventions include acetaminophen.

At a glance

• Cohort genes: 1
• ClinVar variants: 1
• Clinical trials: 5

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	PDA1
Mondo ID	MONDO:0024560
OMIM	607411
UMLS	C4282128
MedGen	924232
GARD	0007342
Is cancer (heuristic)	no

Also known as: patent ductus arteriosus, susceptibility to · PDA · PDA1

Data availability: 1 ClinVar variant.

Disease family

Classification path: disease › human disease › disease by body system or component › cardiovascular disorder › vascular disorder › patent ductus arteriosus › PDA1

Related subtypes (3): Char syndrome, patent ductus arteriosus 2, patent ductus arteriosus 3

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

1 retrieved; paginated sample, class counts are floors:

1 uncertain significance

ClinVar	Variant (HGVS)	Gene	Classification	Review
1703209	NM_001200.4(BMP2):c.721A>T (p.Lys241Ter)	BMP2	Uncertain significance	no assertion criteria provided

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
BMP2	Orphanet:261295	20p12.3 microdeletion syndrome
BMP2	Orphanet:93396	Brachydactyly type A2

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
BMP2	HGNC:1069	ENSG00000125845	P12643	Bone morphogenetic protein 2	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
BMP2	Bone morphogenetic protein 2	Growth factor of the TGF-beta superfamily that plays essential roles in many developmental processes, including cardiogenesis, neurogenesis, and osteogenesis.

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)
BMP2	Other/Unknown	no		TGF-b_propeptide, TGF-b_C, TGF-beta-like

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
cartilage tissue	1
pancreatic ductal cell	1
pigmented layer of retina	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
BMP2	238	broad	marker	cartilage tissue, pancreatic ductal cell, pigmented layer of retina

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
BMP2	3,131

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
BMP2	P12643	21

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 11. 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
Signaling by BMP	1	356.9×	0.011	BMP2
Elastic fibre formation	1	335.9×	0.011	BMP2
Molecules associated with elastic fibres	1	308.6×	0.011	BMP2
Transcriptional regulation by RUNX2	1	253.8×	0.011	BMP2
Regulation of RUNX2 expression and activity	1	181.3×	0.012	BMP2
Signaling by TGFB family members	1	115.3×	0.016	BMP2
Extracellular matrix organization	1	63.1×	0.025	BMP2
RNA Polymerase II Transcription	1	22.5×	0.061	BMP2
Gene expression (Transcription)	1	17.8×	0.068	BMP2
Generic Transcription Pathway	1	15.1×	0.073	BMP2
Signal Transduction	1	10.2×	0.098	BMP2

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
negative regulation of calcium-independent cell-cell adhesion	1	16852.0×	0.002	BMP2
endodermal-mesodermal cell signaling	1	8426.0×	0.002	BMP2
cardiac atrium formation	1	8426.0×	0.002	BMP2
cardiocyte differentiation	1	8426.0×	0.002	BMP2
mesenchymal cell proliferation involved in ureteric bud development	1	8426.0×	0.002	BMP2
positive regulation of extracellular matrix constituent secretion	1	5617.3×	0.002	BMP2
embryonic heart tube anterior/posterior pattern specification	1	5617.3×	0.002	BMP2
corticotropin hormone secreting cell differentiation	1	5617.3×	0.002	BMP2
positive regulation of bone mineralization involved in bone maturation	1	5617.3×	0.002	BMP2
cardiac jelly development	1	5617.3×	0.002	BMP2
positive regulation of phosphatase activity	1	4213.0×	0.002	BMP2
negative regulation of aldosterone biosynthetic process	1	4213.0×	0.002	BMP2
atrioventricular canal morphogenesis	1	4213.0×	0.002	BMP2
negative regulation of cortisol biosynthetic process	1	4213.0×	0.002	BMP2
aortic valve development	1	3370.4×	0.002	BMP2
negative regulation of steroid biosynthetic process	1	3370.4×	0.002	BMP2
positive regulation of odontogenesis	1	3370.4×	0.002	BMP2
telencephalon regionalization	1	2808.7×	0.002	BMP2
thyroid-stimulating hormone-secreting cell differentiation	1	2808.7×	0.002	BMP2
regulation of odontogenesis of dentin-containing tooth	1	2407.4×	0.002	BMP2
mesenchyme development	1	2407.4×	0.002	BMP2
positive regulation of odontoblast differentiation	1	2407.4×	0.002	BMP2
negative regulation of cardiac muscle cell differentiation	1	2407.4×	0.002	BMP2
heart induction	1	2106.5×	0.002	BMP2
ameloblast differentiation	1	2106.5×	0.002	BMP2
negative regulation of insulin-like growth factor receptor signaling pathway	1	2106.5×	0.002	BMP2
mesenchymal cell differentiation	1	2106.5×	0.002	BMP2
proteoglycan metabolic process	1	1872.4×	0.002	BMP2
pericardium development	1	1872.4×	0.002	BMP2
positive regulation of peroxisome proliferator activated receptor signaling pathway	1	1685.2×	0.002	BMP2

Therapeutics

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
BMP2	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
BMP2	22	Binding:18, Functional:4

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	BMP2

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)
BMP2	22	—

Clinical trials & evidence

Clinical trials

Clinical trials: 5.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	3
PHASE3	1
PHASE1/PHASE2	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT01755728	PHASE3	COMPLETED	Paracetamol (Acetaminophen) for Closure of PDA in Preterm Infants
NCT01149564	PHASE1/PHASE2	UNKNOWN	Comparison of Oral and Intravenous Ibuprofen for PDA Treatment in Premature Infants
NCT02396004	Not specified	COMPLETED	NIRS in PDA VLBW Infants
NCT04379843	Not specified	COMPLETED	The Efficacy of Implementing a Treatment Algorithm in Managing Patent Ductus Arteriosus (PDA) in the Extremely Low Birth Weight Neonatal Population.
NCT05321849	Not specified	COMPLETED	Echocardiography-guided Percutaneous Patent Ductus Arteriosus Closure

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
ACETAMINOPHEN	4	1