Table 3.

CNVs in cohort in regions of known epilepsy hotspots.

Epilepsy “hotspot”	# cases	Coordinates (hg18)	Epilepsy Phenotype	Neuropsychiatric co- morbidities
1q21.1	1 dup	chr1: 144,984,952–146,317,921	Focal epilepsy with status epilepticus.	DD, learning problems, ADHD
15q11.2	1 dup, 1 del	Duplication: chr15: 20,307,869–20,773,190 Deletion: chr15: 19,121,757–20,851,679	Duplication case - focal seizures Deletion case – neonatal seizures	Duplication case - congenital hydrocephalus, DD, dysmorphic Deletion case – GDD
15q13.3	1 dup, 1 del	chr15: 29,803,656 – 30,298,096 chr15: 28,719,136 – 30,298,096	Duplication case - myoclonic astatic epilepsy Deletion case - primary generalized epilepsy	Duplication case - speech delay Deletion case - GDD, ID, autistic features
15q11-q13 duplication	4 dup	1. chr15: 18,362,555 – 30,232,544 2. chr15: 21,195,208 – 26,214,052 3. chr15: 21,208,377 – 26,208,602 4. chr15: 18,362,555 – 28,160,686 (4 copies) and 28,517,805 – 30686791 (3 copies)	Generalized, focal or mixed epilepsy	All with ID or autism
16p11.2	5 dup, 4 del	Duplications: 1. chr16: 29,572,030 −30,106,852 2. chr16: 29,258,288 – 30,106,808 3. chr16: 28,740,997 – 29,030,068 4. chr16: 21,476,688 – 29,238,851 5. chr16: 29,581,455 – 30,240,082 Deletions: 1. chr16: 2,958,202 – 30,106,252 2. chr16: 29,528,190 – 30,106,852 3. chr16: 28,394,123 – 29,238,851 4. chr16: 30308460 – 30,342,665	Duplication cases – focal, generalized or both with mixture of seizure types including spasms/drop attacks Deletion cases - focal or generalized seizures	Duplication cases– one with polymicrogyria; all with DD/ID; one with autism Deletion cases – all with GDD and/or learning problems; one with macrocephaly
16p13.11	2 dup, 3 del	Duplications: 1. chr16: 15,034,210 – 1619,973 2. chr16: 14,687,636 – 16,199,736 Deletions: 1. chr16: 14,876,356 – 16,174,751 2. chr16: 14,876,356 – 16,199,682 3. chr16: 15,399,028 – 16,199,682	Duplication cases – one with neonatal seizures; one with focal seizures onset at 2 years Deletion cases – generalized or focal epilepsy	Duplication cases – one with normal development; one with cortical dysplasia and DD/ID Deletion cases – all with DD/ID; one with autism spectrum disorder

Because association with epilepsy is most established with deletions, only the deletions were considered in this report as pathogenic CNVs explaining the epilepsy syndromes. ADHD = attention deficit hyperactivity disorder, DD = developmental delay, GDD = global developmental delay, ID = intellectual disability.