Partial deletion of the short arm of chromosome 3

Summary

Partial deletion of the short arm of chromosome 3 (MONDO:0016885) is a disease with 2 cohort genes.

At a glance

• Cohort genes: 2

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	partial deletion of the short arm of chromosome 3
Mondo ID	MONDO:0016885
Orphanet	261875
ICD-11	551346575
UMLS	C5679666
MedGen	1826020
Is cancer (heuristic)	no

Also known as: partial deletion of chromosome 3p · partial deletion of the short arm of chromosome type 3 · partial monosomy of chromosome 3p · partial monosomy of the short arm of chromosome 3

Data availability: 1 GenCC gene-disease record.

Disease family

An umbrella term covering 2 Mondo subtypes.

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › chromosomal disorder › syndrome caused by partial chromosomal deletion › partial deletion of chromosome 3 › partial deletion of the short arm of chromosome 3

Related subtypes (2): partial deletion of the long arm of chromosome 3, blepharophimosis-ptosis-epicanthus inversus syndrome plus

Subtypes (2): 3p- syndrome, 3p25.3 microdeletion 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

No tiered GWAS variants or ClinVar records for this disease.

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 9 · 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
CHL1	Limited	Autosomal dominant	partial deletion of the short arm of chromosome 3	2
DDX11	Limited	Autosomal dominant	partial deletion of the short arm of chromosome 3	7

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
DDX11	Orphanet:280558	Warsaw breakage syndrome

Cohort genes → proteins

2 cohort genes, 2 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	2

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
CHL1	HGNC:1939	ENSG00000134121	O00533	Neural cell adhesion molecule L1-like protein	gencc
DDX11	HGNC:2736	ENSG00000013573	Q96FC9	ATP-dependent DNA helicase DDX11	gencc

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
CHL1	Neural cell adhesion molecule L1-like protein	Extracellular matrix and cell adhesion protein that plays a role in nervous system development and in synaptic plasticity.
DDX11	ATP-dependent DNA helicase DDX11	DNA-dependent ATPase and ATP-dependent DNA helicase that participates in various functions in genomic stability, including DNA replication, DNA repair and heterochromatin organization as well as in ribosomal RNA synthesis.

Protein-family classification

Druggable: 2 · 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
Antibody/Immunoglobulin	1	14.6×	0.135
Enzyme (other)	1	6.0×	0.160

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
CHL1	Antibody/Immunoglobulin	yes		Ig_sub2, Ig_sub, FN3_dom
DDX11	Enzyme (other)	yes	3.6.4.12	Helicase-like_DEXD_c2, ATP-dep_Helicase_C, RAD3-like_helicase_DEAD

Expression context

Cohort genes with no expression data: 0.

2 cohort genes 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)	2
unknown	0

Top tissues across cohort

Tissue	Cohort genes
Brodmann (1909) area 23	1
cortical plate	1
endothelial cell	1
body of pancreas	1
lower esophagus mucosa	1
mucosa of transverse colon	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
CHL1	263	broad	marker	cortical plate, Brodmann (1909) area 23, endothelial cell
DDX11	201	ubiquitous	marker	lower esophagus mucosa, mucosa of transverse colon, body of pancreas

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
DDX11	2,096
CHL1	1,196

Structural data

PDB: 0 · AlphaFold-only: 2 · No structure: 0

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
CHL1	O00533	78.37
DDX11	Q96FC9	71.77

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 6. Enrichment computed across 2 evidence-associated genes (2 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 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
CHL1 interactions	1	634.4×	0.009	CHL1
XBP1(S) activates chaperone genes	1	107.7×	0.028	DDX11
L1CAM interactions	1	60.1×	0.033	CHL1
Axon guidance	1	22.6×	0.055	CHL1
Nervous system development	1	21.5×	0.055	CHL1
Developmental Biology	1	7.2×	0.134	CHL1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 2 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
establishment of sister chromatid cohesion	1	4213.0×	0.003	DDX11
nucleolar chromatin organization	1	4213.0×	0.003	DDX11
cellular response to bleomycin	1	2808.7×	0.003	DDX11
positive regulation of sister chromatid cohesion	1	1685.2×	0.003	DDX11
cellular response to cisplatin	1	1685.2×	0.003	DDX11
positive regulation of chromatin binding	1	1404.3×	0.003	DDX11
positive regulation of transcription of nucleolar large rRNA by RNA polymerase I	1	766.0×	0.004	DDX11
cellular response to hydroxyurea	1	702.2×	0.004	DDX11
sister chromatid cohesion	1	383.0×	0.006	DDX11
exploration behavior	1	324.1×	0.006	CHL1
negative regulation of protein binding	1	312.1×	0.006	DDX11
replication fork processing	1	210.7×	0.009	DDX11
positive regulation of double-strand break repair	1	172.0×	0.010	DDX11
adult locomotory behavior	1	150.5×	0.010	CHL1
cognition	1	142.8×	0.010	CHL1
neuron migration	1	66.9×	0.020	CHL1
negative regulation of neuron apoptotic process	1	55.4×	0.023	CHL1
axon guidance	1	45.3×	0.027	CHL1
DNA repair	1	31.9×	0.036	DDX11
DNA damage response	1	26.8×	0.041	DDX11
cell adhesion	1	18.7×	0.055	CHL1
signal transduction	1	8.0×	0.121	CHL1

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 2

Druggability breadth: 0 of 2 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
CHL1	0	0
DDX11	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
DDX11	3.6.4.12, 3.6.4.13	DNA helicase, RNA helicase

Pharmacogenomics

Cohort genes with a PharmGKB record: 2; 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	2	CHL1, DDX11
E	Difficult family or no structure, no drug	0

Undrugged target profiles

2 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
CHL1	0	—
DDX11	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.