Sequence variations of the CST2 gene related to the polymorphism of salivary cystatin SA

The CST2 locus has two polymorphic alleles, CST2*1 and CST2*2, which produce cystatin proteins SAI and SA2, respectively (Shintani et al., 1994). The purpose of this study was to define nucleotide sequence variations of the protein-coding region of the two alleles. The variations were investigated by direct sequencing of amplified DNA from individuals with different CST2 phenotypes. The sequence of three exons obtained from DNA of the CST2 1 phenotype was found to be identical to the published sequence of the CST2 gene (Saitoh et al., 1987), whereas two-point mutations were found in the sequence obtained from DNA of the CST2 2 phenotype. One of the mutations was a G --> A transition in exon 2, resulting in loss of a commonly occurring AciI restriction site. This mutation resulted in a Gly59 --> Asp59 substitution in the protein. The other mutation was an A --> T transversion in exon 3, resulting in the generation of a SfaNI restriction site. This mutation also produced a Glu120 --> Asp120 substitution in the protein. PCR-RFLP assay with AciI and SfaNI restriction enzymes revealed that the two-point mutations were always correlated with cystatin SA polymorphism. The difference in the electrophoretic positions of the two proteins, SA1 and SA2, in a basic gel and in an isoelectric focusing gel agreed with the expected mobilities of the proteins with the SA2 variant at a more anodal position. The CST2*2 allele is a unique allele, which shows amino acid substitution in one of the most conserved regions responsible for cysteine proteinase inhibitory activity.