Patent ductus arteriosus 3

Summary

Patent ductus arteriosus 3 (MONDO:0024266) is a disease caused by PRDM6 (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: PRDM6 (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 12

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	patent ductus arteriosus 3
Mondo ID	MONDO:0024266
OMIM	617039
UMLS	C4310753
MedGen	934720
GARD	0018490
Is cancer (heuristic)	no

Also known as: patent ductus arteriosus 3 · patent ductus arteriosus caused by mutation in PRDM6 · PDA3 · PRDM6 patent ductus arteriosus

Data availability: 12 ClinVar variants · 3 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › cardiovascular disorder › vascular disorder › patent ductus arteriosus › patent ductus arteriosus 3

Related subtypes (3): Char syndrome, patent ductus arteriosus 2, PDA1

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

12 retrieved; paginated sample, class counts are floors:

5 uncertain significance, 3 pathogenic, 3 likely benign, 1 conflicting classifications of pathogenicity

ClinVar	Variant (HGVS)	Gene	Classification	Review
243049	NM_001136239.4(PRDM6):c.1646G>A (p.Arg549Gln)	PRDM6	Pathogenic	no assertion criteria provided
243050	NM_001136239.4(PRDM6):c.788G>C (p.Cys263Ser)	PRDM6	Pathogenic	no assertion criteria provided
243051	NM_001136239.4(PRDM6):c.1385A>G (p.Gln462Arg)	PRDM6	Pathogenic	no assertion criteria provided
4628354	NM_001136239.4(PRDM6):c.985G>T (p.Ala329Ser)	PRDM6	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1031874	NM_001136239.4(PRDM6):c.1781T>G (p.Val594Gly)	PRDM6	Uncertain significance	criteria provided, single submitter
2435237	NM_001136239.4(PRDM6):c.233C>G (p.Ser78Cys)	PRDM6	Uncertain significance	criteria provided, multiple submitters, no conflicts
3377116	NM_001136239.4(PRDM6):c.1697_1699dup (p.Phe566_Thr567insIle)	PRDM6	Uncertain significance	criteria provided, single submitter
3892175	NM_001136239.4(PRDM6):c.328G>T (p.Ala110Ser)	PRDM6	Uncertain significance	criteria provided, single submitter
992789	NM_001136239.4(PRDM6):c.1031C>T (p.Ser344Leu)	PRDM6	Uncertain significance	criteria provided, single submitter
3892177	NC_000006.12:g.122104728_122104730dup		Likely benign	criteria provided, single submitter
3892176	NM_001136239.4(PRDM6):c.997G>A (p.Gly333Arg)	PRDM6	Likely benign	criteria provided, single submitter
4819410	NM_001136239.4(PRDM6):c.453TGG[4] (p.Gly158_Glu159insGly)	PRDM6	Likely benign	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 4 · Orphanet: 1 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

Gene	Classification	Inheritance	Disease	Records
PRDM6	Strong	Autosomal dominant	patent ductus arteriosus 3	4

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
PRDM6	Orphanet:466729	Familial patent arterial duct

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
PRDM6	HGNC:9350	ENSG00000061455	Q9NQX0	Putative histone-lysine N-methyltransferase PRDM6	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
PRDM6	Putative histone-lysine N-methyltransferase PRDM6	Putative histone methyltransferase that acts as a transcriptional repressor of smooth muscle gene expression.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 0 · 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
Transcription factor	1	8.3×	0.121

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
PRDM6	Transcription factor	no		SET_dom, Znf_C2H2_type, Znf_C2H2_sf

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
ascending aorta	1
descending thoracic aorta	1
thoracic aorta	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
PRDM6	176	broad	marker	descending thoracic aorta, thoracic aorta, ascending aorta

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
PRDM6	847

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
PRDM6	Q9NQX0	57.72

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
negative regulation of smooth muscle cell differentiation	1	1872.4×	0.003	PRDM6
neurogenesis	1	208.1×	0.010	PRDM6
methylation	1	170.2×	0.010	PRDM6
regulation of gene expression	1	83.4×	0.015	PRDM6
negative regulation of transcription by RNA polymerase II	1	17.7×	0.056	PRDM6

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
PRDM6	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
PRDM6	1	Binding:1

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	PRDM6

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)
PRDM6	1	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.