Table 3.

High copy repeats detected at the breakpoints of CNVs associated with clinical phenotypes

Phenotype	Critical genes	Type of variant	Locus	Repetitive elements involved	Ref.
Peutz-Jeghers syndrome	STK11	Del	19p13.3	Several AluY/AluY pairs	[23]
Spastic paraplegia 4	SPAST, SLC30A6	Dup/Del	2p22.3	Several Alu pairs	[25]
OTC deficiency	OTC	Del	Xp11.4	AluSx/AluSq pair	[27, 56]
Miller-Dieker syndrome and 17p13.3 duplication syndrome	LIS1	Del	17p13.3	Several Alu pairs	[6, 24]
Breast cancer	BRCA1	Del	17q21.31	AluSx/AluSc pair	[29, 57]
Autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)	LMNB1	Dup/Trip	5q23.2	LIPA3 LINE repeats	[26]
				AluYA/AluYB pair
Azoospermia	AZFa	Del	Yq11	HERV15 A/B proviruses	[34, 58]
Mental retardation, X-linked 60 (MRX60)	OPHN1	Del	Xq12	AluY/AluY pair	[35]
Pelizaeus-Merzbacher disease	PLP1	Del	Xq22	AluSq/AluSx pair	[3, 6, 59]
DiGeorge syndrome/velo-cardio facial syndrome	COMT, TBX1	Del	22q11.2	Unclassified Alu/Alu pair	[6, 17, 40]
Charcot-Marie-Tooth type 1A	PMP22	Dup	17p12	AluY/AluY pair	[39]
				AluSg/AluSg pair
Williams-Beuren syndrome	28 dosage-sensitive genes	Dup/Del	7q11.23	AluS subfamily elements	[36]
Parkinson’s disease	SNCA	Dup/Trip	4q21	Several Alu pairs	[32]