Thirteen single-nucleotide polymorphisms in the human osteopontin gene identified by sequencing of the entire gene in Japanese individuals.

Osteopontin (OPN) is one of the major noncollagenous bone matrix proteins produced by osteoblasts and osteoclasts. We systematically surveyed the entire structure of the OPN gene for single-nucleotide polymorphisms (SNPs) by directly sequencing 48 alleles derived from 24 unrelated Japanese individuals. We identified 13 SNPs in the OPN gene. Ten polymorphisms were identified in introns 1, 3, and 5; 2 in the coding region of exons 6 and 7; and 1 in the 3' untranslated region of exon 7. Allele frequencies for some of the polymorphisms were significantly different from those reported in the United States National Center for Biotechnology Information (NCBI) dbSNP database. These polymorphisms will be useful in genetic studies to evaluate the role of OPN proteins in bone metabolism.