Chromosome 3q13.31 deletion syndrome

Summary

Chromosome 3q13.31 deletion syndrome (MONDO:0014185) is a disease with 3 cohort genes.

At a glance

• Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
• Cohort genes: 3
• ClinVar variants: 4
• Phenotypes (HPO): 17

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

Type	Class	Value	Geography	Validation
Cases/families		42	Worldwide	Validated
Point prevalence	<1 / 1 000 000		Worldwide	Validated

Signs & symptoms

Clinical features (HPO)

17 HPO clinical features (Orphanet curated; top 17 by frequency):

HPO ID	Term	Frequency
HP:0000028	Cryptorchidism	Very frequent (80-99%)
HP:0000079	Abnormality of the urinary system	Very frequent (80-99%)
HP:0000235	Abnormality of the fontanelles or cranial sutures	Very frequent (80-99%)
HP:0000256	Macrocephaly	Very frequent (80-99%)
HP:0000286	Epicanthus	Very frequent (80-99%)
HP:0000316	Hypertelorism	Very frequent (80-99%)
HP:0000343	Long philtrum	Very frequent (80-99%)
HP:0000431	Wide nasal bridge	Very frequent (80-99%)
HP:0000463	Anteverted nares	Very frequent (80-99%)
HP:0000470	Short neck	Very frequent (80-99%)
HP:0000774	Narrow chest	Very frequent (80-99%)
HP:0001155	Abnormality of the hand	Very frequent (80-99%)
HP:0001252	Hypotonia	Very frequent (80-99%)
HP:0001274	Agenesis of corpus callosum	Very frequent (80-99%)
HP:0001387	Joint stiffness	Very frequent (80-99%)
HP:0006610	Wide intermamillary distance	Very frequent (80-99%)
HP:0008736	Hypoplasia of penis	Very frequent (80-99%)

Identifiers

Disease identifiers

Field	Value
Canonical name	chromosome 3q13.31 deletion syndrome
Mondo ID	MONDO:0014185
MeSH	C536808
OMIM	615433
Orphanet	1621
DOID	DOID:0060418
SNOMED CT	726705007
UMLS	C3809490
MedGen	815820
GARD	0016573
Is cancer (heuristic)	no

Also known as: 3q13 microdeletion syndrome · chromosome 3q13.31 deletion syndrome · Del(3)(q13) · monosomy 3q13

Data availability: 4 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 3 › partial deletion of the long arm of chromosome 3 › chromosome 3q13.31 deletion syndrome

Related subtypes (4): chromosome 3q29 microdeletion syndrome, blepharophimosis-epicanthus inversus-ptosis due to 3q23 rearrangement syndrome, 3q26q27 microdeletion syndrome, 3q26q28 deletion 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

4 retrieved; paginated sample, class counts are floors:

4 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
1703653	GRCh37/hg19 3q13.12-13.31(chr3:106598767-115704696)	ABHD10	Pathogenic	no assertion criteria provided
2498335	GRCh37/hg19 3q13.13-13.31(chr3:110966195-115843176)x1	ABHD10	Pathogenic	no assertion criteria provided
1077161	GRCh37/hg19 3q13.31(chr3:113623035-114368128)x1	CCDC191	Pathogenic	no assertion criteria provided
2579175	GRCh38/hg38 3q11.1-21.2(chr3:93979547-124774010)x1	OR5K4	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

3 cohort genes, 3 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	3

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
ABHD10	HGNC:25656	ENSG00000144827	Q9NUJ1	Palmitoyl-protein thioesterase ABHD10, mitochondrial	clinvar
CCDC191	HGNC:29272	ENSG00000163617	Q8NCU4	Coiled-coil domain-containing protein 191	clinvar
OR5K4	HGNC:31291	ENSG00000196098	A6NMS3	Olfactory receptor 5K4	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
ABHD10	Palmitoyl-protein thioesterase ABHD10, mitochondrial	Acts as an acyl-protein thioesterase that hydrolyzes fatty acids from acylated residues in proteins.
OR5K4	Olfactory receptor 5K4	Odorant receptor.

Protein-family classification

Druggable: 2 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.67

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
GPCR	1	8.0×	0.345
Enzyme (other)	1	4.0×	0.345
Other/Unknown	1	0.6×	0.914

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
ABHD10	Enzyme (other)	yes	3.1.1.93	AB_hydrolase_1, AB_hydrolase_fold, ABHD10_acyl-thioesterase
CCDC191	Other/Unknown	no		CACF_protein
OR5K4	GPCR	yes		GPCR_Rhodpsn, Olfact_rcpt, GPCR_Rhodpsn_7TM

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)	1
moderate (6-20)	0
broad (>20)	2
unknown	0

Top tissues across cohort

Tissue	Cohort genes
corpus epididymis	1
middle temporal gyrus	1
nephron tubule	1
bronchial epithelial cell	1
bronchus	1
right uterine tube	1
colonic epithelium	1
granulocyte	1
primordial germ cell in gonad	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
ABHD10	289	ubiquitous	marker	nephron tubule, corpus epididymis, middle temporal gyrus
CCDC191	195	ubiquitous	marker	right uterine tube, bronchial epithelial cell, bronchus
OR5K4	4		yes	primordial germ cell in gonad, granulocyte, colonic epithelium

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
ABHD10	1,790
CCDC191	140
OR5K4	78

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
OR5K4	A6NMS3	86.95
ABHD10	Q9NUJ1	86.70
CCDC191	Q8NCU4	72.36

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 5. Enrichment computed across 3 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
Glucuronidation	1	380.7×	0.013	ABHD10
Phase II - Conjugation of compounds	1	139.3×	0.018	ABHD10
Biological oxidations	1	64.9×	0.026	ABHD10
Expression and translocation of olfactory receptors	1	14.1×	0.087	OR5K4
Metabolism	1	5.8×	0.165	ABHD10

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
glucuronate metabolic process	1	8426.0×	4e-04	ABHD10
protein depalmitoylation	1	2808.7×	5e-04	ABHD10
xenobiotic metabolic process	1	149.1×	0.007	ABHD10

Therapeutics

Drug target analysis

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

Druggability breadth: 1 of 3 evidence-associated genes (33%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
ABHD10	0	0
CCDC191	0	0
OR5K4	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

Symbol	Assays	Type breakdown
ABHD10	1	Binding:1

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
ABHD10	3.1.1.93	mycophenolic acid acyl-glucuronide esterase

Pharmacogenomics

Cohort genes with a PharmGKB record: 3; 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	ABHD10, OR5K4
E	Difficult family or no structure, no drug	1	CCDC191

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
ABHD10	1	—
CCDC191	0	—
OR5K4	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.