Chromosome 17q12 deletion syndrome

Summary

Chromosome 17q12 deletion syndrome (MONDO:0013797) is a disease with 5 cohort genes and 1 clinical trial.

At a glance

• Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
• Cohort genes: 5
• ClinVar variants: 13
• Phenotypes (HPO): 21
• Clinical trials: 1

Clinical features

Epidemiology

Prevalence records

3 prevalence record(s), Orphanet:

Type	Class	Value	Geography	Validation
Cases/families		103	Worldwide	Validated
Point prevalence	<1 / 1 000 000		Worldwide	Validated
Point prevalence	1-9 / 1 000 000	0.16	Denmark	Validated

Signs & symptoms

Clinical features (HPO)

21 HPO clinical features (Orphanet curated; top 21 by frequency):

HPO ID	Term	Frequency
HP:0000003	Multicystic kidney dysplasia	Very frequent (80-99%)
HP:0000819	Diabetes mellitus	Frequent (30-79%)
HP:0004322	Short stature	Frequent (30-79%)
HP:0000028	Cryptorchidism	Occasional (5-29%)
HP:0000049	Shawl scrotum	Occasional (5-29%)
HP:0000070	Ureterocele	Occasional (5-29%)
HP:0000083	Renal insufficiency	Occasional (5-29%)
HP:0000239	Large fontanelles	Occasional (5-29%)
HP:0000365	Hearing impairment	Occasional (5-29%)
HP:0000717	Autism	Occasional (5-29%)
HP:0001249	Intellectual disability	Occasional (5-29%)
HP:0001250	Seizure	Occasional (5-29%)
HP:0001263	Global developmental delay	Occasional (5-29%)
HP:0001562	Oligohydramnios	Occasional (5-29%)
HP:0002059	Cerebral atrophy	Occasional (5-29%)
HP:0002463	Language impairment	Occasional (5-29%)
HP:0002910	Elevated circulating hepatic transaminase concentration	Occasional (5-29%)
HP:0008678	Renal hypoplasia/aplasia	Occasional (5-29%)
HP:0011968	Feeding difficulties	Occasional (5-29%)
HP:0012157	Subcortical cerebral atrophy	Occasional (5-29%)
HP:0100801	Pancreatic aplasia	Occasional (5-29%)

Identifiers

Disease identifiers

Field	Value
Canonical name	chromosome 17q12 deletion syndrome
Mondo ID	MONDO:0013797
OMIM	614527
Orphanet	261265
DOID	DOID:0060404
SNOMED CT	733519008
UMLS	C3281138
MedGen	482768
GARD	0013297
Is cancer (heuristic)	no

Also known as: 17q12 deletion syndrome · 17q12 microdeletion syndrome · 17q12 recurrent deletion syndrome · chromosome 17q12 deletion syndrome · Del(17)(q12) · monosomy 17q12

Data availability: 13 ClinVar variants.

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 17q12 deletion syndrome

Related subtypes (5): chromosome 17q23.1-q23.2 deletion syndrome, chromosome 17q11.2 deletion syndrome, 1.4Mb, 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

13 retrieved; paginated sample, class counts are floors:

12 pathogenic, 1 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
3252081	NC_000017.10:g.(?34,822,466)(36,410,720_?)del		Pathogenic	criteria provided, single submitter
1703619	GRCh37/hg19 17q12(chr17:34463923-36410559)	AATF	Pathogenic	no assertion criteria provided
1703620	GRCh37/hg19 17q12(chr17:34822465-36410559)	AATF	Pathogenic	no assertion criteria provided
2579204	GRCh38/hg38 17q12(chr17:36486532-37745203)x1	AATF	Pathogenic	criteria provided, single submitter
3775095	Single allele	AATF	Pathogenic	criteria provided, single submitter
4081873	NC_000017.11:g.36486690_38189436del	AATF	Pathogenic	no assertion criteria provided
4819204	Single allele	AATF	Pathogenic	criteria provided, single submitter
625689	GRCh37/hg19 17q12(chr17:34819191-36194230)	AATF	Pathogenic	criteria provided, single submitter
2574697	GRCh37/hg19 17q11.2-12(chr17:30572862-35843988)	C17orf50	Pathogenic	no assertion criteria provided
209211	NC_000017.10:g.(34360227_34437475)_(36214026_36473024)del	CCL3L1	Pathogenic	criteria provided, single submitter
375218	GRCh37/hg19 17q12(chr17:34815072-36192492)x1	DDX52	Pathogenic	no assertion criteria provided
2580315	GRCh37/hg19 17q12(chr17:34752221-36105007)x3	DHRS11	Pathogenic	criteria provided, single submitter
1330160	GRCh37/hg19 17q12(chr17:34807069-36284994)x1	AATF	Likely pathogenic	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

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

Cohort genes → proteins

5 cohort genes, 5 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	5

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
CCL3L1	HGNC:10628	ENSG00000277768	P16619	C-C motif chemokine 3-like 1	clinvar
AATF	HGNC:19235	ENSG00000275700	Q9NY61	Protein AATF	clinvar
DDX52	HGNC:20038	ENSG00000278053	Q9Y2R4	Probable ATP-dependent RNA helicase DDX52	clinvar
DHRS11	HGNC:28639	ENSG00000278535	Q6UWP2	Dehydrogenase/reductase SDR family member 11	clinvar
C17orf50	HGNC:29581	ENSG00000270806	Q8WW18	Uncharacterized protein C17orf50	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
CCL3L1	C-C motif chemokine 3-like 1	Chemotactic for lymphocytes and monocytes.
AATF	Protein AATF	Part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit.
DDX52	Probable ATP-dependent RNA helicase DDX52	Required for efficient ribosome biogenesis.
DHRS11	Dehydrogenase/reductase SDR family member 11	Catalyzes the conversion of the 17-keto group of estrone, 4- and 5-androstenes and 5-alpha-androstanes into their 17-beta-hydroxyl metabolites and the conversion of the 3-keto group of 3-, 3,17- and 3,20- diketosteroids into their 3beta-hy…

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 5 · 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	5	1.8×	0.054

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
CCL3L1	Other/Unknown	no		Chemokine_CC_CS, Chemokine_IL8-like_dom, Interleukin_8-like_sf
AATF	Other/Unknown	no		AATF_C, AATF, AATF/Bfr2
DDX52	Other/Unknown	no		Helicase_C-like, DEAD/DEAH_box_helicase_dom, Helicase_ATP-bd
DHRS11	Other/Unknown	no		SDR_fam, Sc_DH/Rdtase_CS, NAD(P)-bd_dom_sf
C17orf50	Other/Unknown	no		DUF4637

Expression context

Cohort genes with no expression data: 0.

4 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)	4
unknown	1

Top tissues across cohort

Tissue	Cohort genes
granulocyte	1
leukocyte	1
monocyte	1
endometrium	1
male germ line stem cell (sensu Vertebrata) in testis	1
sural nerve	1
duodenum	1
mucosa of transverse colon	1
rectum	1
left testis	1
right testis	1
sperm	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
CCL3L1		broad	marker
AATF	134	ubiquitous	marker	monocyte, leukocyte, granulocyte
DDX52	134	ubiquitous	marker	sural nerve, endometrium, male germ line stem cell (sensu Vertebrata) in testis
DHRS11	134	ubiquitous	marker	duodenum, mucosa of transverse colon, rectum
C17orf50	118	tissue_specific	yes	left testis, right testis, sperm

Protein interactions among cohort

Intra-cohort edges: 1.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
DHRS11	3,492
AATF	3,194
DDX52	2,336
CCL3L1	1,606
C17orf50	178

Intra-cohort edges

A	B	Sources
AATF	DDX52	biogrid_interaction, string_interaction

Structural data

PDB: 3 · AlphaFold-only: 2 · No structure: 0

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
AATF	Q9NY61	3
DDX52	Q9Y2R4	1
DHRS11	Q6UWP2	1

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
CCL3L1	P16619	90.15
C17orf50	Q8WW18	58.44

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 9. Enrichment computed across 5 evidence-associated genes (3 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 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Interleukin-10 signaling	1	77.7×	0.024	CCL3L1
Cell death signalling via NRAGE, NRIF and NADE	1	73.2×	0.024	AATF
p75 NTR receptor-mediated signalling	1	62.4×	0.024	AATF
Chemokine receptors bind chemokines	1	62.4×	0.024	CCL3L1
rRNA modification in the nucleus and cytosol	1	62.4×	0.024	DDX52
NRAGE signals death through JNK	1	61.4×	0.024	AATF
Death Receptor Signaling	1	46.4×	0.027	AATF
Major pathway of rRNA processing in the nucleolus and cytosol	1	20.6×	0.054	DDX52
Signal Transduction	1	3.4×	0.267	AATF

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
negative regulation of amyloid precursor protein biosynthetic process	1	526.6×	0.013	AATF
embryonic cleavage	1	421.3×	0.013	AATF
estrogen biosynthetic process	1	383.0×	0.013	DHRS11
maturation of SSU-rRNA	1	191.5×	0.018	DDX52
steroid biosynthetic process	1	150.5×	0.018	DHRS11
negative regulation of apoptotic signaling pathway	1	140.4×	0.018	AATF
chemokine-mediated signaling pathway	1	81.0×	0.026	CCL3L1
regulation of mitotic cell cycle	1	60.2×	0.029	AATF
ribosomal small subunit biogenesis	1	56.9×	0.029	AATF
cell chemotaxis	1	46.3×	0.032	CCL3L1
antimicrobial humoral immune response mediated by antimicrobial peptide	1	40.5×	0.033	CCL3L1
positive regulation of cell migration	1	15.4×	0.079	CCL3L1
negative regulation of cell population proliferation	1	10.5×	0.103	CCL3L1
inflammatory response	1	9.4×	0.103	CCL3L1
cell adhesion	1	9.4×	0.103	AATF

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 5

Druggability breadth: 0 of 5 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
CCL3L1	0	0
AATF	0	0
DDX52	0	0
DHRS11	0	0
C17orf50	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 5; 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	5	CCL3L1, AATF, DDX52, DHRS11, C17orf50

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
CCL3L1	0	—
AATF	0	—
DDX52	0	—
DHRS11	0	—
C17orf50	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 1.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT01238250	Not specified	RECRUITING	Online Study of People Who Have Genetic Changes and Features of Autism: Simons Searchlight