Table 1.

Pathologic intronic insertions in humans.

retroelement	length	orientation	position in gene	gene name	abbreviation	Phenotype	mRNA studies	reference
Alu
AluYc1	316bp	antisense	−52bp from the 3′ end of intron 4	glycerol kinase	GK	benign isolated glycerol kinase deficiency	not reported	(Zhang et al., 2000)
AluYb9	~330bp	antisense	−19bp from the 3′ end of intron 18	coagulation factor VIII	F8	hemophilia A	exon 19 skipping	(Ganguly et al., 2003)
AluYa5	331bp	antisense	−50bp from the 3′ end of intron 7	tumor necrosis factor receptor superfamily, member 6	FAS	autoimmune lymphoproliferative syndrome	exon 8 skipping	(Tighe et al., 2002)
AluYa5	368bp	antisense	−19bp from the 3′ end of intron 8	fibroblast growth factor receptor 2	FGFR2	Apert syndrome	ectopic exon 7/8 splicing in lieu of 7/9	(Oldridge et al., 1999)
AluYa5	320bp	antisense	−44bp from the 3′ end of intron 5	neurofibromatosis type 1	NF1	neurofibromatosis type 1	exon 6 skipping	(Wallace et al., 1991)
L1
L1(Ta)	836bp	sense and rearranged	intron 5	cytochrome b-245, beta polypeptide	CYBB	chronic granulomatous disease (CGD)	variable L1 exonization; exon 5 and exon 6 skipping	(Meischl et al., 2000)
L1(Ta)	6kb	antisense	reported as 3′ end of intron 2	hemoglobin, beta	HBB	beta-thalasemia	not reported	(Kimberland et al., 1999)
L1(Ta)	1.2kb	sense	−24bp from the 3′ end of intron 7	fukutin	FKTN	Fukuyama-type congenital muscular dystrophy	variable exon 7, 8, and 9 skipping	(Kondo-Iida et al., 1999)
L1(Ta)	6kb	sense	intron 1	retinitis pigmentosa 2	RP2	X-linked retinitis pigmentosa	no transcript detected by RT-PCR	(Schwahn et al., 1998)
L1(Ta)	2.8kb	antisense and rearranged	−8bp from the 3′ end of intron 3	ribosomal S6 kinase 2 gene	RPS6KA3	Coffin-Lowry syndrome	exon 4 skipping	(Martinez- Garay et al., 2003)
SVA
SVA	2.6kb	sense	intron 1	low density lipoprotein receptor adaptor protein 1	LDLRAP1	autosomal recessive hypercholesterolemia	no expression by Northern blot	(Wilund et al., 2002)