A cDNA encoding a possible novel human 116-kDa polypeptide subunit of the osteoclastic proton pump (OC-116KDa) has been identified by differential screening of a human osteoclastoma cDNA library. The predicted sequence of OC-116kDa consists of 822 amino acids and is 46.9% and 47.2% identical at the amino acid level to the 116-KDa polypeptide of the vacuolar proton pump of rat and bovine brain respectively. OC-116KDa mRNA was found at high levels in osteoclastomas by Northern analysis but was not detected in tumor stromal cells or in other tissues including kidney, liver, skeletal muscle and brain. OC-116KDa mRNA was localized to multinucleated giant cells within the osteoclastoma tumor by in situ hybridization.