3MC syndrome 3

Summary

3MC syndrome 3 (MONDO:0009554) is a disease caused by COLEC10 (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: COLEC10 (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 6

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	3MC syndrome 3
Mondo ID	MONDO:0009554
MeSH	C535704
OMIM	248340
Orphanet	2453
DOID	DOID:0060577
UMLS	C0796032
MedGen	208657
GARD	0008531
Is cancer (heuristic)	no

Also known as: 3MC syndrome 3 · 3MC syndrome caused by mutation in COLEC10 · 3MC syndrome type 3 · 3Mc syndrome type 3 · 3MC3 · COLEC10 3MC syndrome · facial clefting syndrome, Gypsy type · Malpuech Facial clefting syndrome

Data availability: 6 ClinVar variants · 1 GenCC gene-disease record.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › 3MC syndrome › 3MC syndrome 3

Related subtypes (2): 3MC syndrome 1, 3MC syndrome 2

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

6 retrieved; paginated sample, class counts are floors:

4 pathogenic, 1 uncertain significance, 1 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
417733	NM_006438.5(COLEC10):c.25C>T (p.Arg9Ter)	COLEC10	Pathogenic	criteria provided, single submitter
417734	NM_006438.5(COLEC10):c.228del (p.Gly77fs)	COLEC10	Pathogenic	no assertion criteria provided
417735	NM_006438.5(COLEC10):c.528C>G (p.Cys176Trp)	COLEC10	Pathogenic	no assertion criteria provided
992663	NM_006438.5(COLEC10):c.128_129del (p.Thr43fs)	LOC126860480	Pathogenic	criteria provided, single submitter
4081283	NM_006438.5(COLEC10):c.311G>T (p.Gly104Val)	COLEC10	Likely pathogenic	criteria provided, single submitter
3065389	NM_006438.5(COLEC10):c.310G>A (p.Gly104Ser)	COLEC10	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 2 · 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
COLEC10	Strong	Autosomal recessive	3MC syndrome 3	2

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
COLEC10	Orphanet:293843	3MC syndrome

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
COLEC10	HGNC:2220	ENSG00000184374	Q9Y6Z7	Collectin-10	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
COLEC10	Collectin-10	Lectin that binds to various sugars: galactose > mannose = fucose > N-acetylglucosamine > N-acetylgalactosamine.

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)
COLEC10	Other/Unknown	no		C-type_lectin-like, Collagen, C-type_lectin-like/link_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
liver	1
male germ line stem cell (sensu Vertebrata) in testis	1
right lobe of liver	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
COLEC10	91	tissue_specific	marker	right lobe of liver, liver, male germ line stem cell (sensu Vertebrata) in testis

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
COLEC10	839

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
COLEC10	Q9Y6Z7	81.20

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 2. 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
Lectin pathway of complement activation	1	1268.9×	0.002	COLEC10
Initial triggering of complement	1	601.0×	0.002	COLEC10

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
complement activation, lectin pathway	1	1685.2×	0.001	COLEC10
positive regulation of opsonization	1	1685.2×	0.001	COLEC10
cell surface pattern recognition receptor signaling pathway	1	1404.3×	0.001	COLEC10
cranial skeletal system development	1	936.2×	0.001	COLEC10
proteolysis	1	34.2×	0.029	COLEC10

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
COLEC10	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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	COLEC10

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)
COLEC10	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.