Metaphyseal acroscyphodysplasia

Summary

Metaphyseal acroscyphodysplasia (MONDO:0009592) is a disease with 1 cohort gene.

At a glance

• Cohort genes: 1
• ClinVar variants: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	metaphyseal acroscyphodysplasia
Mondo ID	MONDO:0009592
MeSH	C537350
OMIM	250215
Orphanet	1240
ICD-11	1994645064
UMLS	C1855243
MedGen	344453
GARD	0003519
Is cancer (heuristic)	no

Also known as: Bellini Chiumello Rimoldi syndrome · Bellini syndrome · intellectual disability-short stature-wedge-shaped epiphyses of knees syndrome · metaphyseal acroscyphodysplasia · wedge-shaped epiphyses of knees · wedge-shaped epiphyses of the knees with intellectual disability and short stature · wedge-shaped epiphyses of the knees with mental retardation and short stature

Data availability: 1 ClinVar variant.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › skeletal dysplasia › metaphyseal acroscyphodysplasia

Related subtypes (118): osteochondrodysplasia, diaphyseal medullary stenosis-bone malignancy syndrome, fibular aplasia-ectrodactyly syndrome, cerebrocostomandibular syndrome, cleidorhizomelic syndrome, dyschondrosteosis-nephritis syndrome, dysplasia epiphysealis hemimelica, carpotarsal osteochondromatosis, Camurati-Engelmann disease, genochondromatosis, autosomal dominant osteosclerosis, Worth type, coxopodopatellar syndrome, Lenz-Majewski hyperostotic dwarfism, delayed membranous cranial ossification, metaphyseal dysplasia-maxillary hypoplasia-brachydacty syndrome, oculodentodigital dysplasia, Ollier disease, osteoglophonic dysplasia, parietal foramina with cleidocranial dysplasia, chondromalacia patellae, Currarino triad, Proteus syndrome, brachydactyly-elbow wrist dysplasia syndrome, tricho-dento-osseous syndrome, bird headed-dwarfism, Montreal type, Yunis-Varon syndrome, split hand-foot malformation 1 with sensorineural hearing loss, ghosal hematodiaphyseal dysplasia, hyperostosis corticalis generalisata, Larsen-like syndrome, B3GAT3 type, mesomelic dwarfism-cleft palate-camptodactyly syndrome, metaphyseal dysostosis-intellectual disability-conductive deafness syndrome, familial osteodysplasia, Anderson type, pseudodiastrophic dysplasia, rhizomelic syndrome, Urbach type, Richieri Costa-Pereira syndrome, craniometadiaphyseal dysplasia, wormian bone type, Weaver syndrome, SHOX-related short stature, craniofrontonasal syndrome, Eiken syndrome, 2q37 microdeletion syndrome, skeletal dysplasia-epilepsy-short stature syndrome, rhizomelic dysplasia, Patterson-Lowry type, pelvic dysplasia-arthrogryposis of lower limbs syndrome, Marshall-Smith syndrome, baby rattle pelvis dysplasia, metaphyseal dysplasia, Braun-Tinschert type, genitopatellar syndrome, osteofibrous dysplasia, Larsen-like osseous dysplasia-short stature syndrome, pancreatic insufficiency-anemia-hyperostosis syndrome, microcephalic primordial dwarfism due to ZNF335 deficiency, Hartsfield-Bixler-Demyer syndrome, colobomatous microphthalmia-rhizomelic dysplasia syndrome, Tatton-Brown-Rahman overgrowth syndrome, tall stature-scoliosis-macrodactyly of the great toes syndrome, Catel-Manzke syndrome, cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome, skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome, complex lethal osteochondrodysplasia, amniotic band syndrome, metaphyseal anadysplasia, syndromic craniosynostosis, thin ribs-tubular bones-dysmorphism syndrome, dysplasia of head of femur, Meyer type, epimetaphyseal skeletal dysplasia, melorheostosis with osteopoikilosis, Cole-Carpenter syndrome, spondylometaphyseal dysplasia, omodysplasia, Bruck syndrome, osteopetrosis, congenital absence of upper arm and forearm with hand present, congenital absence of thigh and lower leg with foot present, congenital absence of both forearm and hand, congenital absence of both lower leg and foot, acheiria, apodia, chondroectodermal dysplasia with night blindness, TRPV4-related bone disorder, adactyly of foot, short stature-advanced bone age-early-onset osteoarthritis syndrome, McCune-Albright syndrome, parietal foramina, Sotos syndrome, dysspondyloenchondromatosis, autosomal recessive cutis laxa type 2, FGFR3-related chondrodysplasia, filamin-related bone disorder, short rib dysplasia, spondylodysplastic dysplasia, acromelic dysplasia, bent bone dysplasia, chondrodysplasia punctata, primary osteolysis, non-syndromic limb reduction defect, Robinow syndrome, synpolydactyly, acrocoxomesomelic dysplasia, bone dysplasia Moore type, bone dysplasia corpus callosum agenesis, type 2 collagenopathy, LRP5-related primary osteoporosis, SLC26A2-related skeletal dysplasia, COMP-related skeletal dysplasia, primordial dwarfism and slender bone disorder, polydactyly-syndactyly-triphalangism, lysosomal storage disease with skeletal involvement, abnormal mineralization disorder, calvarial doughnut lesions with bone fragility and spondylometaphyseal dysplasia, de la Chapelle dysplasia, mesomelic dysplasia-digital anomalies-intellectual disability syndrome, proximal femoral focal deficiency, rhizomelic dysplasia, Ain-Naz type, craniotubular dysplasia, Ikegawa type, TRIP11-related skeletal dysplasia, FAM111A-related skeletal dysplasia

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 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
4687864	NM_001104631.2(PDE4D):c.673C>T (p.Pro225Ser)	PDE4D	Likely pathogenic	criteria provided, single submitter

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
PDE4D	Orphanet:439822	PDE4D haploinsufficiency syndrome
PDE4D	Orphanet:950	Acrodysostosis

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
PDE4D	HGNC:8783	ENSG00000113448	Q08499	3’,5’-cyclic-AMP phosphodiesterase 4D	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
PDE4D	3’,5’-cyclic-AMP phosphodiesterase 4D	Hydrolyzes the second messenger cAMP, which is a key regulator of many important physiological processes.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0

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
Enzyme (other)	1	12.0×	0.083

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
PDE4D	Enzyme (other)	yes	3.1.4.53	PDEase_catalytic_dom, PDEase, PDEase_CS

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
biceps brachii	1
gluteal muscle	1
skeletal muscle tissue of rectus abdominis	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
PDE4D	283	ubiquitous	marker	gluteal muscle, biceps brachii, skeletal muscle tissue of rectus abdominis

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
PDE4D	1,533

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
PDE4D	Q08499	122

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 3. 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
DARPP-32 events	1	475.8×	0.004	PDE4D
Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells	1	356.9×	0.004	PDE4D
G alpha (s) signalling events	1	73.2×	0.014	PDE4D

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 relaxation of cardiac muscle	1	8426.0×	0.002	PDE4D
negative regulation of heart contraction	1	4213.0×	0.002	PDE4D
cAMP catabolic process	1	1872.4×	0.002	PDE4D
adrenergic receptor signaling pathway	1	1872.4×	0.002	PDE4D
regulation of cell communication by electrical coupling involved in cardiac conduction	1	1872.4×	0.002	PDE4D
negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway	1	1685.2×	0.002	PDE4D
regulation of calcium ion transmembrane transport via high voltage-gated calcium channel	1	1685.2×	0.002	PDE4D
positive regulation of interleukin-5 production	1	1404.3×	0.002	PDE4D
cellular response to epinephrine stimulus	1	1296.3×	0.002	PDE4D
regulation of cardiac muscle cell contraction	1	1123.5×	0.002	PDE4D
establishment of endothelial barrier	1	766.0×	0.002	PDE4D
positive regulation of heart rate	1	702.2×	0.002	PDE4D
regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	1	674.1×	0.002	PDE4D
negative regulation of cAMP/PKA signal transduction	1	601.9×	0.002	PDE4D
regulation of heart rate	1	468.1×	0.003	PDE4D
positive regulation of interleukin-2 production	1	468.1×	0.003	PDE4D
cellular response to cAMP	1	290.6×	0.004	PDE4D
positive regulation of type II interferon production	1	224.7×	0.005	PDE4D
T cell receptor signaling pathway	1	151.8×	0.007	PDE4D

Therapeutics

Drug target analysis

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

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

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

Symbol	Example approved molecule
PDE4D	INAMRINONE

Top cohort targets by molecule count

Symbol	Molecules	Max phase
PDE4D	269	4

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
INAMRINONE	4	PDE4D
THEOPHYLLINE	4	PDE4D
VARDENAFIL	4	PDE4D
MILRINONE	4	PDE4D
LOSARTAN	4	PDE4D
SILDENAFIL	4	PDE4D
ROFLUMILAST	4	PDE4D
ENOXIMONE	4	PDE4D
ENSIFENTRINE	4	PDE4D
CRISABOROLE	4	PDE4D
APREMILAST	4	PDE4D
PENTOXIFYLLINE	4	PDE4D
TADALAFIL	4	PDE4D
DIPYRIDAMOLE	4	PDE4D
CANDESARTAN CILEXETIL	4	PDE4D
TELMISARTAN	4	PDE4D
SIMVASTATIN	4	PDE4D
MORICIZINE	4	PDE4D
AMLEXANOX	4	PDE4D
AMOXAPINE	4	PDE4D
PONATINIB	4	PDE4D
RUCAPARIB	4	PDE4D
CELECOXIB	4	PDE4D
VILANTEROL	4	PDE4D
TIOCONAZOLE	4	PDE4D
UNOPROSTONE ISOPROPYL	4	PDE4D
OLMESARTAN MEDOXOMIL	4	PDE4D
HYDROXYPROGESTERONE CAPROATE	4	PDE4D
NORGESTIMATE	4	PDE4D
THIOTHIXENE	4	PDE4D

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

Symbol	Assays	Type breakdown
PDE4D	863	Binding:805, Functional:33, ADMET:23, Toxicity:2

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
PDE4D	3.1.4.53	3’,5’-cyclic-AMP phosphodiesterase

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

Symbol	ChEMBL assays
PDE4D	863

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

30 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.

Compound	Max phase	Cohort target (bioactivity)
INAMRINONE	4	PDE4D
THEOPHYLLINE	4	PDE4D
VARDENAFIL	4	PDE4D
MILRINONE	4	PDE4D
LOSARTAN	4	PDE4D
SILDENAFIL	4	PDE4D
ROFLUMILAST	4	PDE4D
ENOXIMONE	4	PDE4D
ENSIFENTRINE	4	PDE4D
CRISABOROLE	4	PDE4D
APREMILAST	4	PDE4D
PENTOXIFYLLINE	4	PDE4D
TADALAFIL	4	PDE4D
DIPYRIDAMOLE	4	PDE4D
CANDESARTAN CILEXETIL	4	PDE4D
TELMISARTAN	4	PDE4D
SIMVASTATIN	4	PDE4D
MORICIZINE	4	PDE4D
AMLEXANOX	4	PDE4D
AMOXAPINE	4	PDE4D
PONATINIB	4	PDE4D
RUCAPARIB	4	PDE4D
CELECOXIB	4	PDE4D
VILANTEROL	4	PDE4D
TIOCONAZOLE	4	PDE4D
UNOPROSTONE ISOPROPYL	4	PDE4D
OLMESARTAN MEDOXOMIL	4	PDE4D
HYDROXYPROGESTERONE CAPROATE	4	PDE4D
NORGESTIMATE	4	PDE4D
THIOTHIXENE	4	PDE4D

Druggability pyramid

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

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	1	PDE4D
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	0

Undrugged target profiles

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

Clinical trials & evidence

Clinical trials

Clinical trials: 0.