Analysis of CYP2D6 Allele Frequencies and Identification of Novel SNPs and Sequence Variations in Sardinians

Table 4

List of novel SNPs and new haplotypes found in Sardinian DNA samples by Sequencing Analysis. SNPs are shown in bold characters. Novel SNPs are between horizontal lines. “Sardinian haplotype 1” (SH1) and “Sardinian haplotype 3” (SH3) were found in both homozygous and heterozygous statuses in 37 and 5 samples, respectively. “Sardinian haplotype 2” (SH2) was found in only two samples, one associated to CYP2D6*35A and one to “SH1.” “Sardinian haplotype 4” (SH4) was found in only one sample and associated to CYP2D6*1A. Due to the presence of –1584C>G SNP, it was possible to confirm haplotype phase for all new haplotypes by Single Allele Analysis. –1237_–1236insAA was not investigated.

SNP	CYP2D6* 2M	CYP2D6* 41	SH1; (CYP2D6*2M–*41 hybrid)	SH2; (CYP2D6*2M–*41 hybrid)	SH3; (modification of CYP2D6*2M)	SH4; (modification of CYP2D6*2M)	Position	Variation
–1584C>G	C	C	C	C	G	G	5′-UTR
–1237_–1236insAA	AA	–	Not investigated	Not investigated	Not investigated	Not investigated	5′-UTR
–1235A>G	G	G	G	G	G	G	5′-UTR
–948C>A	C	C	C	A	C	C	5′-UTR
–750_–749delGA	del	GA	GA	GA	GA	GA	5′-UTR
–740C>T	T	T	T	T	T	T	5′-UTR
–678G>A	A	A	A	A	A	A	5′-UTR
CYP2D7P gene; conversion in Intron 1	Conversion	Conversion	Conversion	Conversion	Conversion	Conversion	Intron 1
310G>T	T	G	T	T	T	T	Intron 1
746C>G	G	C	G	G	G	G	Intron 1
843T>G	G	T	G	G	G	G	Intron 1
1661G>C	C	C	C	C	C	C	Exon 3
2850C>T	T	T	T	T	T	T	Exon 6	R296C
2988G>A	G	A	A	A	G	G	Intron 6	splicing defect
3176C>T	C	C	C	T	C	C	Exon 7
3384A>C	C	A	C	C	C	C	Intron 7
3584G>A	A	G	A	A	A	A	Intron 7
3790C>T	T	C	T	T	T	T	Intron 7
3948T>G	T	T	T	T	T	G	Intron 8
4180G>C	C	C	C	C	C	C	Exon 9	S486T
4481G>A	A	G	A	A	A	A	3′-UTR