Chromosome 17q23.1-q23.2 deletion syndrome

Summary

Chromosome 17q23.1-q23.2 deletion syndrome (MONDO:0013238) is a disease with 1 cohort gene.

At a glance

• Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
• Cohort genes: 1
• ClinVar variants: 1
• Phenotypes (HPO): 46

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

Type	Class	Value	Geography	Validation
Cases/families		7	Worldwide	Validated
Point prevalence	<1 / 1 000 000		Worldwide	Validated

Signs & symptoms

Clinical features (HPO)

46 HPO clinical features (Orphanet curated; top 46 by frequency):

HPO ID	Term	Frequency
HP:0000750	Delayed speech and language development	Very frequent (80-99%)
HP:0010511	Long toe	Very frequent (80-99%)
HP:0011342	Mild global developmental delay	Very frequent (80-99%)
HP:0011343	Moderate global developmental delay	Very frequent (80-99%)
HP:0100807	Long fingers	Very frequent (80-99%)
HP:0000252	Microcephaly	Frequent (30-79%)
HP:0001511	Intrauterine growth retardation	Frequent (30-79%)
HP:0001643	Patent ductus arteriosus	Frequent (30-79%)
HP:0002007	Frontal bossing	Frequent (30-79%)
HP:0002092	Pulmonary arterial hypertension	Frequent (30-79%)
HP:0004322	Short stature	Frequent (30-79%)
HP:0000049	Shawl scrotum	Occasional (5-29%)
HP:0000160	Narrow mouth	Occasional (5-29%)
HP:0000272	Malar flattening	Occasional (5-29%)
HP:0000286	Epicanthus	Occasional (5-29%)
HP:0000316	Hypertelorism	Occasional (5-29%)
HP:0000365	Hearing impairment	Occasional (5-29%)
HP:0000389	Chronic otitis media	Occasional (5-29%)
HP:0000411	Protruding ear	Occasional (5-29%)
HP:0000414	Bulbous nose	Occasional (5-29%)
HP:0000486	Strabismus	Occasional (5-29%)
HP:0000498	Blepharitis	Occasional (5-29%)
HP:0000527	Long eyelashes	Occasional (5-29%)
HP:0000687	Widely spaced teeth	Occasional (5-29%)
HP:0000708	Atypical behavior	Occasional (5-29%)
HP:0000960	Sacral dimple	Occasional (5-29%)
HP:0001252	Hypotonia	Occasional (5-29%)
HP:0001347	Hyperreflexia	Occasional (5-29%)
HP:0001376	Limitation of joint mobility	Occasional (5-29%)
HP:0001508	Failure to thrive	Occasional (5-29%)
HP:0001631	Atrial septal defect	Occasional (5-29%)
HP:0001763	Pes planus	Occasional (5-29%)
HP:0001852	Sandal gap	Occasional (5-29%)
HP:0002020	Gastroesophageal reflux	Occasional (5-29%)
HP:0002094	Dyspnea	Occasional (5-29%)
HP:0002553	Highly arched eyebrow	Occasional (5-29%)
HP:0002650	Scoliosis	Occasional (5-29%)
HP:0002803	Congenital contracture	Occasional (5-29%)
HP:0003065	Patellar hypoplasia	Occasional (5-29%)
HP:0003182	Shallow acetabular fossae	Occasional (5-29%)
HP:0003279	Coxa magna	Occasional (5-29%)
HP:0004209	Clinodactyly of the 5th finger	Occasional (5-29%)
HP:0005280	Depressed nasal bridge	Occasional (5-29%)
HP:0005930	Abnormality of epiphysis morphology	Occasional (5-29%)
HP:0007598	Bilateral single transverse palmar creases	Occasional (5-29%)
HP:0011803	Bifid nose	Occasional (5-29%)

Identifiers

Disease identifiers

Field	Value
Canonical name	chromosome 17q23.1-q23.2 deletion syndrome
Mondo ID	MONDO:0013238
OMIM	613355
Orphanet	261279
DOID	DOID:0060405
SNOMED CT	719584008
UMLS	C3150607
MedGen	461957
GARD	0010936
Is cancer (heuristic)	no

Also known as: 17q23.1q23.2 microdeletion syndrome · chromosome 17q23.1-q23.2 deletion syndrome · chromosome 17q23.1-q23.2 deletion syndrome, isolated cases · Del(17)(q23.1q23.2) · monosomy 17q23.1-q23.2 · monosomy 17q23.1q23.2

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 deletion › partial deletion of chromosome 17 › partial deletion of the long arm of chromosome 17 › chromosome 17q23.1-q23.2 deletion syndrome

Related subtypes (5): chromosome 17q11.2 deletion syndrome, 1.4Mb, chromosome 17q12 deletion syndrome, distal monosomy 17q, Koolen-de Vries syndrome due to 17q21.31 microdeletion syndrome, 17q24.2 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

ClinVar germline variants

1 retrieved; paginated sample, class counts are floors:

1 pathogenic/likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
16118	NM_006516.4(SLC2A1):c.376C>T (p.Arg126Cys)	SLC2A1	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 7 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
SLC2A1	Orphanet:168577	Hereditary cryohydrocytosis with reduced stomatin
SLC2A1	Orphanet:1942	Epilepsy with myoclonic-atonic seizures
SLC2A1	Orphanet:2131	Alternating hemiplegia of childhood
SLC2A1	Orphanet:53583	Paroxysmal dystonic choreathetosis with episodic ataxia and spasticity
SLC2A1	Orphanet:71277	Classic glucose transporter type 1 deficiency syndrome
SLC2A1	Orphanet:86911	Epilepsy with myoclonic absences
SLC2A1	Orphanet:98811	Paroxysmal exertion-induced dyskinesia

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
SLC2A1	HGNC:11005	ENSG00000117394	P11166	Solute carrier family 2, facilitated glucose transporter member 1	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
SLC2A1	Solute carrier family 2, facilitated glucose transporter member 1	Facilitative glucose transporter, which is responsible for constitutive or basal glucose uptake.

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
Transporter	1	77.8×	0.013

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
SLC2A1	Transporter	yes		Glu_transpt_1, Sugar/inositol_transpt, MFS_sugar_transport-like

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
skin of abdomen	1
sural nerve	1
tibial nerve	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
SLC2A1	250	ubiquitous	marker	tibial nerve, sural nerve, skin of abdomen

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
SLC2A1	5,711

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
SLC2A1	P11166	5

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 5. 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
Defective SLC2A1 causes GLUT1 deficiency syndrome 1 (GLUT1DS1)	1	11420.0×	4e-04	SLC2A1
Lactose synthesis	1	3806.7×	7e-04	SLC2A1
Vitamin C (ascorbate) metabolism	1	1427.5×	0.001	SLC2A1
Cellular hexose transport	1	543.8×	0.002	SLC2A1
Regulation of insulin secretion	1	219.6×	0.005	SLC2A1

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
response to Thyroglobulin triiodothyronine	1	5617.3×	0.002	SLC2A1
long-chain fatty acid import across plasma membrane	1	4213.0×	0.002	SLC2A1
GDP-L-fucose salvage	1	4213.0×	0.002	SLC2A1
D-glucose import across plasma membrane	1	2808.7×	0.002	SLC2A1
L-ascorbic acid metabolic process	1	1532.0×	0.002	SLC2A1
dehydroascorbic acid transport	1	1203.7×	0.002	SLC2A1
cellular hyperosmotic response	1	1203.7×	0.002	SLC2A1
D-glucose transmembrane transport	1	936.2×	0.003	SLC2A1
obsolete D-glucose import	1	842.6×	0.003	SLC2A1
photoreceptor cell maintenance	1	358.6×	0.005	SLC2A1
cellular response to glucose starvation	1	337.0×	0.005	SLC2A1
response to insulin	1	230.8×	0.006	SLC2A1
cellular response to mechanical stimulus	1	216.1×	0.006	SLC2A1
female pregnancy	1	210.7×	0.006	SLC2A1
cerebral cortex development	1	205.5×	0.006	SLC2A1
transport across blood-brain barrier	1	179.3×	0.007	SLC2A1
central nervous system development	1	115.4×	0.009	SLC2A1
protein-containing complex assembly	1	113.9×	0.009	SLC2A1
response to hypoxia	1	95.8×	0.010	SLC2A1

Therapeutics

Drug target analysis

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

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

Symbol	Example approved molecule
SLC2A1	EMETINE

Top cohort targets by molecule count

Symbol	Molecules	Max phase
SLC2A1	7	4

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
EMETINE	4	SLC2A1
GOSSYPOL	3	SLC2A1
CYCLOHEXIMIDE	2	SLC2A1
GENISTEIN	2	SLC2A1
COLFORSIN	2	SLC2A1
KAEMPFEROL	1	SLC2A1
PD-0166285	1	SLC2A1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

Symbol	Assays	Type breakdown
SLC2A1	158	Binding:130, ADMET:24, Functional:4

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

Symbol	ChEMBL assays
SLC2A1	158

Pharmacogenomics

Cohort genes with a PharmGKB record: 0; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

7 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.

Compound	Max phase	Cohort target (bioactivity)
EMETINE	4	SLC2A1
GOSSYPOL	3	SLC2A1
CYCLOHEXIMIDE	2	SLC2A1
GENISTEIN	2	SLC2A1
COLFORSIN	2	SLC2A1
KAEMPFEROL	1	SLC2A1
PD-0166285	1	SLC2A1

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	1	SLC2A1
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	0

Undrugged target profiles

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

Clinical trials & evidence

Clinical trials

Clinical trials: 0.