Chromosome 1q41-q42 deletion syndrome

disease

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Also known as 1q41-q42 deletion syndrome1q41q42 microdeletion syndromechromosome 1q41-q42 deletion syndrome, isolated casesDel(1)(q41q42)deletion 1q41-q42monosomy 1q41-q42monosomy 1q41q42

Summary

Chromosome 1q41-q42 deletion syndrome (MONDO:0012927) is a disease with 1 cohort gene.

At a glance

Prevalence: Unknown (Worldwide)
Cohort genes: 1
ClinVar variants: 1
Phenotypes (HPO): 32

Clinical features

Signs & symptoms

Clinical features (HPO)

32 HPO clinical features (Orphanet curated; top 32 by frequency):

HPO ID	Term	Frequency
HP:0000271	Abnormality of the face	Very frequent (80-99%)
HP:0001249	Intellectual disability	Very frequent (80-99%)
HP:0001250	Seizure	Very frequent (80-99%)
HP:0001263	Global developmental delay	Very frequent (80-99%)
HP:0001319	Neonatal hypotonia	Very frequent (80-99%)
HP:0001510	Growth delay	Very frequent (80-99%)
HP:0004322	Short stature	Very frequent (80-99%)
HP:0002007	Frontal bossing	Very frequent (80-99%)
HP:0011344	Severe global developmental delay	Very frequent (80-99%)
HP:0000430	Underdeveloped nasal alae	Frequent (30-79%)
HP:0000455	Broad nasal tip	Frequent (30-79%)
HP:0000490	Deeply set eye	Frequent (30-79%)
HP:0000582	Upslanted palpebral fissure	Frequent (30-79%)
HP:0000708	Atypical behavior	Frequent (30-79%)
HP:0001762	Talipes equinovarus	Frequent (30-79%)
HP:0001792	Small nail	Frequent (30-79%)
HP:0002011	Morphological central nervous system abnormality	Frequent (30-79%)
HP:0005280	Depressed nasal bridge	Frequent (30-79%)
HP:0012471	Thick vermilion border	Frequent (30-79%)
HP:0000028	Cryptorchidism	Occasional (5-29%)
HP:0000078	Abnormality of the genital system	Occasional (5-29%)
HP:0000175	Cleft palate	Occasional (5-29%)
HP:0000176	Submucous cleft hard palate	Occasional (5-29%)
HP:0000280	Coarse facial features	Occasional (5-29%)
HP:0000486	Strabismus	Occasional (5-29%)
HP:0000525	Abnormality iris morphology	Occasional (5-29%)
HP:0000601	Hypotelorism	Occasional (5-29%)
HP:0000776	Congenital diaphragmatic hernia	Occasional (5-29%)
HP:0000815	Hypergonadotropic hypogonadism	Occasional (5-29%)
HP:0001360	Holoprosencephaly	Occasional (5-29%)
HP:0002089	Pulmonary hypoplasia	Occasional (5-29%)
HP:0011447	Hyposegmentation of neutrophil nuclei	Occasional (5-29%)

Identifiers

Disease identifiers

Field	Value
Canonical name	chromosome 1q41-q42 deletion syndrome
Mondo ID	MONDO:0012927
OMIM	612530
Orphanet	250999
DOID	DOID:0060412
SNOMED CT	716515000
UMLS	C2675857
MedGen	382704
GARD	0003738
Is cancer (heuristic)	no

Also known as: 1q41-q42 deletion syndrome · 1q41q42 microdeletion syndrome · chromosome 1q41-q42 deletion syndrome · chromosome 1q41-q42 deletion syndrome, isolated cases · Del(1)(q41q42) · deletion 1q41-q42 · monosomy 1q41-q42 · monosomy 1q41q42

Data availability: 1 ClinVar variant.

Disease family

Classification path: disease › human disease › disease by body system or component › syndromic disease › holoprosencephaly › chromosome 1q41-q42 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

1 retrieved; paginated sample, class counts are floors:

1 pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
1703636	GRCh37/hg19 1q42.11-42.12(chr1:224432682-225142704)	CNIH3	Pathogenic	no assertion criteria 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
CNIH3	HGNC:26802	ENSG00000143786	Q8TBE1	Protein cornichon homolog 3	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
CNIH3	Protein cornichon homolog 3	Regulates the trafficking and gating properties of AMPA-selective glutamate receptors (AMPARs).

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 1 · 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	1	1.8×	0.558

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
CNIH3	Other/Unknown	no		Cornichon, Cornichon_conserved

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
cortical plate	1
endothelial cell	1
primordial germ cell in gonad	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
CNIH3	204	ubiquitous	marker	primordial germ cell in gonad, cortical plate, endothelial cell

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
CNIH3	1,072

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
CNIH3	Q8TBE1	85.15

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 2. 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
Cargo concentration in the ER	1	335.9×	0.006	CNIH3
COPII-mediated vesicle transport	1	163.1×	0.006	CNIH3

GO biological processes by enrichment

GO term	Cohort genes	Fold	FDR	Sample cohort genes
regulation of AMPA receptor activity	1	1685.2×	0.003	CNIH3
neurotransmitter receptor localization to postsynaptic specialization membrane	1	802.5×	0.003	CNIH3
synaptic transmission, glutamatergic	1	358.6×	0.005	CNIH3
regulation of membrane potential	1	230.8×	0.005	CNIH3
vesicle-mediated transport	1	96.3×	0.010	CNIH3

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
CNIH3	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	CNIH3

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)
CNIH3	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.

Cohort genes: CNIH3