spondyloepimetaphyseal dysplasia, Li-Shao-Li type

disease

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Summary

spondyloepimetaphyseal dysplasia, Li-Shao-Li type (MONDO:0976230) 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	spondyloepimetaphyseal dysplasia, Li-Shao-Li type
Mondo ID	MONDO:0976230
OMIM	621099
DOID	DOID:0051046
UMLS	C6012697
MedGen	1876456
GARD	0027434
Is cancer (heuristic)	no

Data availability: 1 ClinVar variant.

Disease family

Classification path: disease › human disease › disease by body system or component › musculoskeletal system disorder › skeletal system disorder › bone disorder › bone development disease › osteochondrodysplasia › spondyloepimetaphyseal dysplasia › spondyloepimetaphyseal dysplasia, Li-Shao-Li 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

ClinVar germline variants

1 retrieved; paginated sample, class counts are floors:

1 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
3629449	NM_001901.4(CCN2):c.65G>C (p.Arg22Pro)	CCN2	Pathogenic	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
CCN2	Orphanet:220393	Diffuse cutaneous systemic sclerosis
CCN2	Orphanet:220402	Limited cutaneous systemic sclerosis

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
CCN2	HGNC:2500	ENSG00000118523	P29279	CCN family member 2	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
CCN2	CCN family member 2	Major connective tissue mitoattractant secreted by vascular endothelial cells.

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)
CCN2	Other/Unknown	no		IGFBP-like, TSP1_rpt, VWF_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
ascending aorta	1
thoracic aorta	1
tibia	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
CCN2	270	ubiquitous	marker	tibia, ascending aorta, thoracic aorta

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
CCN2	3,887

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
CCN2	P29279	78.43

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 6. 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
RUNX3 regulates YAP1-mediated transcription	1	1427.5×	0.004	CCN2
YAP1- and WWTR1 (TAZ)-stimulated gene expression	1	761.3×	0.004	CCN2
Transcriptional regulation by RUNX3	1	271.9×	0.007	CCN2
RNA Polymerase II Transcription	1	22.5×	0.066	CCN2
Gene expression (Transcription)	1	17.8×	0.066	CCN2
Generic Transcription Pathway	1	15.1×	0.066	CCN2

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
regulation of chondrocyte differentiation	1	1404.3×	0.008	CCN2
chondrocyte proliferation	1	1053.2×	0.008	CCN2
DNA biosynthetic process	1	802.5×	0.008	CCN2
cartilage condensation	1	766.0×	0.008	CCN2
tissue homeostasis	1	561.7×	0.008	CCN2
reactive oxygen species metabolic process	1	468.1×	0.008	CCN2
positive regulation of stress fiber assembly	1	312.1×	0.009	CCN2
chondrocyte differentiation	1	300.9×	0.009	CCN2
fibroblast growth factor receptor signaling pathway	1	285.6×	0.009	CCN2
positive regulation of cell differentiation	1	267.5×	0.009	CCN2
response to wounding	1	221.7×	0.009	CCN2
epidermis development	1	210.7×	0.009	CCN2
lung development	1	198.3×	0.009	CCN2
cell-matrix adhesion	1	163.6×	0.009	CCN2
positive regulation of JNK cascade	1	163.6×	0.009	CCN2
integrin-mediated signaling pathway	1	160.5×	0.009	CCN2
osteoblast differentiation	1	121.2×	0.011	CCN2
positive regulation of ERK1 and ERK2 cascade	1	85.1×	0.015	CCN2
negative regulation of gene expression	1	69.1×	0.018	CCN2
angiogenesis	1	62.4×	0.018	CCN2
cell migration	1	61.5×	0.018	CCN2
cell adhesion	1	37.5×	0.028	CCN2
signal transduction	1	16.1×	0.062	CCN2

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
CCN2	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
CCN2	16	Binding:16

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	CCN2

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)
CCN2	16	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: CCN2