A 4.7 kb cDNA of tyrosine phosphatase-like protein, phogrin, was isolated from a human islet cDNA library. Sequencing of the resulting clone identified a 3,045 residue open-reading frame encoding a 1,015 amino acid polypeptide with predicted molecular mass of 111,303 daltons. Phogrin's amino acid sequence has a single transmembrane region and one putative tyrosine phosphatase catalytic domain. Phogrin is 74% identical to the ICA512/IA-2 autoantigen of type 1 diabetes in the cytoplasmic domain, but only 29% in the luminal domain. It showed > 90% identity to rat phogrin and mouse IA-2 beta. Autoantibody radioassays utilizing full-length and the cytoplasmic domain of phogrin were compared. With positivity defined above the 99th percentile of 105 normal control subjects, 37 (48%) and 47 (61%) of sera from 77 new-onset patients with type 1 diabetes were positive for autoantibodies to full-length and the cytoplasmic domain of phogrin, respectively. The assay utilizing cytoplasmic human phogrin gave higher sensitivity with identical specificity to the assay utilizing the full-length molecule primarily due to lower "background" binding. Phogrin is an additional major autoantigen for type 1 diabetes and the isolation of the cDNA of this molecule from human islets will aid in studies of the pathogenesis of type 1 diabetes.