Bone development disease

Summary

Bone development disease (MONDO:0005497) is a disease (an umbrella term covering 9 Mondo subtypes) with 1 cohort gene.

At a glance

• Umbrella term: 9 Mondo subtypes
• Cohort genes: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	bone development disease
Mondo ID	MONDO:0005497
EFO	EFO:0005541
DOID	DOID:0080006
SNOMED CT	371521007
UMLS	C0005941
MedGen	2309
Is cancer (heuristic)	no

Also known as: bone development disease · bone development disease or disorder · disease of bone development · disease or disorder of bone development · disorder of bone development

Data availability: 1 GenCC gene-disease record.

Disease family

An umbrella term covering 9 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › musculoskeletal system disorder › skeletal system disorder › bone disorder › bone development disease

Related subtypes (26): bone remodeling disease, disease of bone structure, mucopolysaccharidosis type 1, bone inflammation disease, Baastrup syndrome, periostitis, osteonecrosis, ainhum, cervical rib disease, coxoauricular syndrome, metachondromatosis, mucopolysaccharidosis type 9, Sagliker syndrome, mixed sclerosing bone dystrophy with extra-skeletal manifestations, GM1 gangliosidosis, skeletal dysplasia, autosomal dominant myopia-midfacial retrusion-sensorineural hearing loss-rhizomelic dysplasia syndrome, mucopolysaccharidosis type 3, bone neoplasm, skull disorder, Duane anomaly-myopathy-scoliosis syndrome, mueller-weiss syndrome, SLC10A7-congenital disorder of glycosylation, metabolic bone disorder, proteoglycan-related bone disorder, ACAN-related short stature spectrum

Subtypes (9): developmental dysplasia of the hip, osteochondrodysplasia, brachydactyly-elbow wrist dysplasia syndrome, spondylocarpotarsal synostosis syndrome, odontoid hypoplasia, dysostosis, segmental odontomaxillary dysplasia, angioosteohypotrophic syndrome, microcephalic osteodysplastic dysplasia, Saul-Wilson type

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

No tiered GWAS variants or ClinVar records for this disease.

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 4 · 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
ABL1	Limited	Autosomal recessive	bone development disease	5

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
ABL1	Orphanet:521	Chronic myeloid leukemia
ABL1	Orphanet:585909	B-lymphoblastic leukemia/lymphoma with t(9;22)(q34.1;q11.2)
ABL1	Orphanet:643503	Marfanoid habitus-facial dysmorphism-skeletal abnormality-heart defect syndrome
ABL1	Orphanet:99861	Precursor T-cell acute lymphoblastic leukemia

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
ABL1	HGNC:76	ENSG00000097007	P00519	Tyrosine-protein kinase ABL1	gencc

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
ABL1	Tyrosine-protein kinase ABL1	Non-receptor tyrosine-protein kinase that plays a role in many key processes linked to cell growth and survival such as cytoskeleton remodeling in response to extracellular stimuli, cell motility and adhesion, receptor endocytosis, autopha…

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
Kinase	1	27.7×	0.036

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
ABL1	Kinase	yes	2.7.10.2	Prot_kinase_dom, SH2, Ser-Thr/Tyr_kinase_cat_dom

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
frontal pole	1
middle frontal gyrus	1
paraflocculus	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
ABL1	283	ubiquitous	marker	frontal pole, paraflocculus, middle frontal gyrus

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
ABL1	6,937

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
ABL1	P00519	85

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 53. 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
Role of ABL in ROBO-SLIT signaling	1	1268.9×	0.012	ABL1
RUNX2 regulates bone development	1	815.7×	0.012	ABL1
DNA Double Strand Break Response	1	475.8×	0.012	ABL1
RUNX2 regulates osteoblast differentiation	1	456.8×	0.012	ABL1
G1 Phase	1	393.8×	0.012	ABL1
Myogenesis	1	380.7×	0.012	ABL1
Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells	1	356.9×	0.012	ABL1
Parasite infection	1	346.1×	0.012	ABL1
Leishmania phagocytosis	1	346.1×	0.012	ABL1
RHO GTPases Activate WASPs and WAVEs	1	317.2×	0.012	ABL1
Homology Directed Repair	1	308.6×	0.012	ABL1
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)	1	308.6×	0.012	ABL1
Response of endothelial cells to shear stress	1	300.5×	0.012	ABL1
HDR through Single Strand Annealing (SSA)	1	292.8×	0.012	ABL1
Fcgamma receptor (FCGR) dependent phagocytosis	1	278.5×	0.012	ABL1
Cellular responses to mechanical stimuli	1	259.6×	0.012	ABL1
Transcriptional regulation by RUNX2	1	253.8×	0.012	ABL1
DNA Double-Strand Break Repair	1	248.3×	0.012	ABL1
Cyclin D associated events in G1	1	233.1×	0.012	ABL1
Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes	1	215.5×	0.012	ABL1
Epigenetic regulation of gene expression by MLL3 and MLL4 complexes	1	196.9×	0.012	ABL1
FCGR3A-mediated phagocytosis	1	187.2×	0.012	ABL1
Regulation of actin dynamics for phagocytic cup formation	1	184.2×	0.012	ABL1
Mitotic G1 phase and G1/S transition	1	184.2×	0.012	ABL1
Leishmania infection	1	163.1×	0.012	ABL1
Parasitic Infection Pathways	1	163.1×	0.012	ABL1
Epigenetic regulation by WDR5-containing histone modifying complexes	1	154.3×	0.012	ABL1
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks	1	146.4×	0.012	ABL1
Transcriptional regulation by RUNX1	1	146.4×	0.012	ABL1
Signaling by ROBO receptors	1	124.1×	0.014	ABL1

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
protein localization to cytoplasmic microtubule plus-end	1	16852.0×	0.002	ABL1
transitional one stage B cell differentiation	1	8426.0×	0.002	ABL1
phospholipase C-inhibiting G protein-coupled receptor signaling pathway	1	8426.0×	0.002	ABL1
DNA conformation change	1	8426.0×	0.002	ABL1
podocyte apoptotic process	1	8426.0×	0.002	ABL1
DN4 thymocyte differentiation	1	8426.0×	0.002	ABL1
cerebellum morphogenesis	1	5617.3×	0.002	ABL1
neuropilin signaling pathway	1	5617.3×	0.002	ABL1
response to epinephrine	1	5617.3×	0.002	ABL1
regulation of modification of synaptic structure	1	5617.3×	0.002	ABL1
B-1 B cell homeostasis	1	4213.0×	0.002	ABL1
microspike assembly	1	4213.0×	0.002	ABL1
negative regulation of ubiquitin-protein transferase activity	1	4213.0×	0.002	ABL1
regulation of postsynaptic specialization assembly	1	4213.0×	0.002	ABL1
positive regulation of extracellular matrix organization	1	4213.0×	0.002	ABL1
positive regulation of establishment of T cell polarity	1	4213.0×	0.002	ABL1
platelet-derived growth factor receptor-beta signaling pathway	1	3370.4×	0.002	ABL1
vascular endothelial cell response to oscillatory fluid shear stress	1	3370.4×	0.002	ABL1
positive regulation of phospholipase C/protein kinase C signal transduction	1	3370.4×	0.002	ABL1
B cell proliferation involved in immune response	1	2808.7×	0.002	ABL1
positive regulation of blood vessel branching	1	2808.7×	0.002	ABL1
mitochondrial depolarization	1	2407.4×	0.002	ABL1
cellular response to dopamine	1	2407.4×	0.002	ABL1
alpha-beta T cell differentiation	1	1872.4×	0.002	ABL1
activated T cell proliferation	1	1872.4×	0.002	ABL1
positive regulation of Wnt signaling pathway, planar cell polarity pathway	1	1872.4×	0.002	ABL1
Bergmann glial cell differentiation	1	1532.0×	0.002	ABL1
neuroepithelial cell differentiation	1	1532.0×	0.002	ABL1
regulation of hematopoietic stem cell differentiation	1	1532.0×	0.002	ABL1
regulation of Cdc42 protein signal transduction	1	1404.3×	0.003	ABL1

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
ABL1	PONATINIB

Top cohort targets by molecule count

Symbol	Molecules	Max phase
ABL1	122	4

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
PONATINIB	4	ABL1
AFATINIB	4	ABL1
FEDRATINIB	4	ABL1
TIVOZANIB	4	ABL1
LENVATINIB	4	ABL1
AXITINIB	4	ABL1
SORAFENIB	4	ABL1
DASATINIB ANHYDROUS	4	ABL1
IMATINIB MESYLATE	4	ABL1
RUXOLITINIB	4	ABL1
NERATINIB	4	ABL1
INFIGRATINIB PHOSPHATE	4	ABL1
INFIGRATINIB	4	ABL1
IBRUTINIB	4	ABL1
REGORAFENIB	4	ABL1
ENTRECTINIB	4	ABL1
DABRAFENIB	4	ABL1
TOFACITINIB CITRATE	4	ABL1
AFATINIB DIMALEATE	4	ABL1
CABOZANTINIB	4	ABL1
TOFACITINIB	4	ABL1
CERITINIB	4	ABL1
VANDETANIB	4	ABL1
NILOTINIB	4	ABL1
BOSUTINIB	4	ABL1
FILGOTINIB	4	ABL1
TOVORAFENIB	4	ABL1
BRIGATINIB	4	ABL1
ASCIMINIB	4	ABL1
PAZOPANIB	4	ABL1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

Symbol	Assays	Type breakdown
ABL1	3,282	Binding:3254, ADMET:16, Functional:10, Toxicity:2

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
ABL1	2.7.10.2	non-specific protein-tyrosine kinase

Cohort genes with high screening signal

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

Symbol	ChEMBL assays
ABL1	3,282

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)
PONATINIB	4	ABL1
AFATINIB	4	ABL1
FEDRATINIB	4	ABL1
TIVOZANIB	4	ABL1
LENVATINIB	4	ABL1
AXITINIB	4	ABL1
SORAFENIB	4	ABL1
DASATINIB ANHYDROUS	4	ABL1
IMATINIB MESYLATE	4	ABL1
RUXOLITINIB	4	ABL1
NERATINIB	4	ABL1
INFIGRATINIB PHOSPHATE	4	ABL1
INFIGRATINIB	4	ABL1
IBRUTINIB	4	ABL1
REGORAFENIB	4	ABL1
ENTRECTINIB	4	ABL1
DABRAFENIB	4	ABL1
TOFACITINIB CITRATE	4	ABL1
AFATINIB DIMALEATE	4	ABL1
CABOZANTINIB	4	ABL1
TOFACITINIB	4	ABL1
CERITINIB	4	ABL1
VANDETANIB	4	ABL1
NILOTINIB	4	ABL1
BOSUTINIB	4	ABL1
FILGOTINIB	4	ABL1
TOVORAFENIB	4	ABL1
BRIGATINIB	4	ABL1
ASCIMINIB	4	ABL1
PAZOPANIB	4	ABL1

Druggability pyramid

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

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	1	ABL1
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.