Chromosome 3q29 microduplication syndrome

Summary

Chromosome 3q29 microduplication syndrome (MONDO:0012761) is a disease with 1 cohort gene.

At a glance

• Prevalence: Unknown (Worldwide)
• Cohort genes: 1
• ClinVar variants: 1
• Phenotypes (HPO): 30

Clinical features

Signs & symptoms

Clinical features (HPO)

30 HPO clinical features (Orphanet curated; top 30 by frequency):

HPO ID	Term	Frequency
HP:0000164	Abnormality of the dentition	Frequent (30-79%)
HP:0000252	Microcephaly	Frequent (30-79%)
HP:0000494	Downslanted palpebral fissures	Frequent (30-79%)
HP:0001249	Intellectual disability	Frequent (30-79%)
HP:0001252	Hypotonia	Frequent (30-79%)
HP:0001263	Global developmental delay	Frequent (30-79%)
HP:0001513	Obesity	Frequent (30-79%)
HP:0000175	Cleft palate	Occasional (5-29%)
HP:0000218	High palate	Occasional (5-29%)
HP:0000239	Large fontanelles	Occasional (5-29%)
HP:0000256	Macrocephaly	Occasional (5-29%)
HP:0000348	High forehead	Occasional (5-29%)
HP:0000365	Hearing impairment	Occasional (5-29%)
HP:0000369	Low-set ears	Occasional (5-29%)
HP:0000431	Wide nasal bridge	Occasional (5-29%)
HP:0000470	Short neck	Occasional (5-29%)
HP:0000518	Cataract	Occasional (5-29%)
HP:0000526	Aniridia	Occasional (5-29%)
HP:0000568	Microphthalmia	Occasional (5-29%)
HP:0000612	Iris coloboma	Occasional (5-29%)
HP:0000647	Sclerocornea	Occasional (5-29%)
HP:0001250	Seizure	Occasional (5-29%)
HP:0001363	Craniosynostosis	Occasional (5-29%)
HP:0001629	Ventricular septal defect	Occasional (5-29%)
HP:0001770	Toe syndactyly	Occasional (5-29%)
HP:0001836	Camptodactyly of toe	Occasional (5-29%)
HP:0001852	Sandal gap	Occasional (5-29%)
HP:0002002	Deep philtrum	Occasional (5-29%)
HP:0004397	Ectopic anus	Occasional (5-29%)
HP:0004422	Biparietal narrowing	Occasional (5-29%)

Identifiers

Disease identifiers

Field	Value
Canonical name	chromosome 3q29 microduplication syndrome
Mondo ID	MONDO:0012761
MeSH	C567626
OMIM	611936
Orphanet	251038
DOID	DOID:0060459
SNOMED CT	717973004
UMLS	C2749873
MedGen	440897
GARD	0010360
Is cancer (heuristic)	no

Also known as: 3q29 microduplication syndrome · trisomy 3q29

Data availability: 1 ClinVar variant.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › chromosomal disorder › syndrome caused by partial chromosomal duplication › partial duplication of chromosome 3 › partial duplication of the long arm of chromosome 3 › chromosome 3q29 microduplication syndrome

Related subtypes (1): 3q26 microduplication syndrome

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 not provided

ClinVar	Variant (HGVS)	Gene	Classification	Review
4279951	GRCh37/hg19 3q29(chr3:194814799-197817520)x3	ACAP2	not provided	no classification provided

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 0 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

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
ACAP2	HGNC:16469	ENSG00000114331	Q15057	Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
ACAP2	Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2	GTPase-activating protein (GAP) for ADP ribosylation factor 6 (ARF6).

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 0 · 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
Scaffold/PPI	1	17.3×	0.058

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
ACAP2	Scaffold/PPI	no		ArfGAP_dom, PH_domain, Ankyrin_rpt

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
bone marrow cell	1
epithelium of nasopharynx	1
superficial temporal artery	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
ACAP2	288	ubiquitous	marker	epithelium of nasopharynx, bone marrow cell, superficial temporal artery

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
ACAP2	1,288

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
ACAP2	Q15057	1

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 1 evidence-associated genes (0 with Reactome annotation).

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
actin filament-based process	1	8426.0×	4e-04	ACAP2
cellular response to nerve growth factor stimulus	1	468.1×	0.003	ACAP2
endocytic recycling	1	267.5×	0.004	ACAP2

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
ACAP2	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	ACAP2

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)
ACAP2	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.