Epiphyseal dysplasia, multiple, 7

Summary

Epiphyseal dysplasia, multiple, 7 (MONDO:0054680) is a disease with 1 cohort gene.

At a glance

• Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
• Cohort genes: 1
• ClinVar variants: 17

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

Type	Class	Value	Geography	Validation
Cases/families		2	Worldwide	Validated
Point prevalence	<1 / 1 000 000		Worldwide	Validated

Identifiers

Disease identifiers

Field	Value
Canonical name	epiphyseal dysplasia, multiple, 7
Mondo ID	MONDO:0054680
OMIM	617719
Orphanet	647676
DOID	DOID:0070302
UMLS	C4540251
MedGen	1620874
GARD	0025960
Is cancer (heuristic)	no

Also known as: EDM7 · epiphyseal dysplasia, multiple, 7 · multiple epiphyseal dysplasia type 7

Data availability: 17 ClinVar variants.

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 › multiple epiphyseal dysplasia › epiphyseal dysplasia, multiple, 7

Related subtypes (9): multiple epiphyseal dysplasia type 1, multiple epiphyseal dysplasia, Beighton type, multiple epiphyseal dysplasia type 4, multiple epiphyseal dysplasia, Lowry type, multiple epiphyseal dysplasia type 5, multiple epiphyseal dysplasia, Al-Gazali type, multiple epiphyseal dysplasia, with severe proximal femoral dysplasia, multiple epiphyseal dysplasia, with miniepiphyses, multiple epiphyseal dysplasia due to collagen 9 anomaly

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

17 retrieved; paginated sample, class counts are floors:

6 likely pathogenic, 5 pathogenic/likely pathogenic, 4 conflicting classifications of pathogenicity, 1 uncertain significance, 1 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
1324008	NM_001159773.2(CANT1):c.71dup (p.Leu25fs)	CANT1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
197369	NM_001159773.2(CANT1):c.836-9G>A	CANT1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
2838791	NM_001159773.2(CANT1):c.188del (p.Arg63fs)	CANT1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
31014	NM_001159773.2(CANT1):c.228dup (p.Trp77fs)	CANT1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
31018	NM_001159773.2(CANT1):c.676G>A (p.Val226Met)	CANT1	Pathogenic	criteria provided, multiple submitters, no conflicts
452497	NM_001159773.2(CANT1):c.734C>T (p.Pro245Leu)	CANT1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
31016	NM_001159773.2(CANT1):c.671T>C (p.Leu224Pro)	CANT1	Likely pathogenic	criteria provided, single submitter
3583085	NM_001159773.2(CANT1):c.632-5_661dup	CANT1	Likely pathogenic	criteria provided, single submitter
3583087	NM_001159773.2(CANT1):c.267del (p.Asp89fs)	CANT1	Likely pathogenic	criteria provided, single submitter
441248	NM_001159773.2(CANT1):c.511A>T (p.Ile171Phe)	CANT1	Likely pathogenic	criteria provided, single submitter
4819343	NM_001159773.2(CANT1):c.1111G>C (p.Ala371Pro)	CANT1	Likely pathogenic	criteria provided, single submitter
929439	NM_001159773.2(CANT1):c.739T>C (p.Trp247Arg)	CANT1	Likely pathogenic	criteria provided, multiple submitters, no conflicts
282	NM_001159773.2(CANT1):c.374G>A (p.Trp125Ter)	CANT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
3251620	NM_001159773.2(CANT1):c.340G>A (p.Asp114Asn)	CANT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
548509	NM_001159773.2(CANT1):c.1112C>T (p.Ala371Val)	CANT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
892010	NM_001159773.2(CANT1):c.513T>G (p.Ile171Met)	CANT1	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1446552	NM_001159773.2(CANT1):c.622G>A (p.Val208Met)	CANT1	Uncertain significance	criteria provided, multiple submitters, no conflicts

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
CANT1	Orphanet:1425	Desbuquois syndrome
CANT1	Orphanet:647676	Multiple epiphyseal dysplasia type 7

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
CANT1	HGNC:19721	ENSG00000171302	Q8WVQ1	Soluble calcium-activated nucleotidase 1	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
CANT1	Soluble calcium-activated nucleotidase 1	Calcium-dependent nucleotidase with a preference for UDP.

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)
CANT1	Enzyme (other)	yes	3.6.1.5	Apyrase, Apyrase_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
colonic mucosa	1
mucosa of transverse colon	1
pancreatic ductal cell	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
CANT1	280	ubiquitous	marker	pancreatic ductal cell, mucosa of transverse colon, colonic mucosa

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
CANT1	1,231

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
CANT1	Q8WVQ1	4

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
Innate Immune System	1	25.5×	0.065	CANT1
Neutrophil degranulation	1	23.1×	0.065	CANT1
Immune System	1	13.0×	0.077	CANT1

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
proteoglycan biosynthetic process	1	842.6×	0.002	CANT1
positive regulation of canonical NF-kappaB signal transduction	1	72.6×	0.014	CANT1

Therapeutics

Drug target analysis

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

Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
CANT1	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
CANT1	3.6.1.5	apyrase

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	1	CANT1
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	0

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)
CANT1	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.