Table 3. Recurrent CNVs associated with NDDs.

CNV locus	Type	Associated phenotypes	Penetrance estimate	Key driver gene(s)
16p11.2	Del/Dup	ASD, ID, schizophrenia, obesity, macro/microcephaly	~25–30%	MVP, MAPK3
22q11.2	Del	Schizophrenia, ID, cardiac defects, palatal anomalies	~25–30%	TBX1, COMT
15q13.3	Del	ASD, ID, epilepsy, schizophrenia	~10–15%	CHRNA7
1q21.1	Del/Dup	ID, macro/microcephaly, ASD, congenital anomalies	~15–20%	GJA5, PRKAB2
NRXN1	Del (exonic 6–24)	ASD, ID, schizophrenia, developmental delay	~32% (3' exons)	NRXN1

This table presents recurrent CNVs that are robustly associated with NDDs. Loci were selected from large-scale cohort studies and meta-analyses. For each CNV, the genomic locus, type (Del or Dup), associated clinical phenotypes, estimated penetrance, and proposed driver gene(s) are provided. Penetrance estimates vary depending on cohort ascertainment and mutation size; values shown represent ranges from published meta-analyses. For NRXN1 deletions, penetrance is highest for deletions involving exons 6–24 (3' region), whereas 5' deletions and intronic deletions confer lower or no risk. ASD, autism spectrum disorder; CNV, copy number variant; Del, deletion; Dup, duplication; ID, intellectual disability; NDD, neurodevelopmental disorder.