We identified autoantibodies (AAb) reacting with a variant IA-2 molecule (IA-2var) that has three amino acid substitutions (Cys 27 , Gly 608 , and Pro 671) within the full-length molecule. We examined IA-2var AAb in first-degree relatives of type 1 diabetes (T1D) probands from the TrialNet Pathway to Prevention Study. The presence of IA-2varspecific AAb in relatives was associated with accelerated progression to T1D in those positive for AAb to GAD65 and/or insulin but negative in the standard test for IA-2 AAb. Furthermore, relatives with single islet AAb (by traditional assays) and carrying both IA-2var AAb and the high-risk HLA-DRB1*04-DQB1*03:02 haplotype progress rapidly to onset of T1D. Molecular modeling of IA-2var predicts that the genomic variation that alters the three amino acids induces changes in the threedimensional structure of the molecule, which may lead to epitope unmasking in the IA-2 extracellular domain. Our observations suggest that the presence of AAb to IA-2var would identify high-risk subjects who would benefit from participation in prevention trials who have one islet antibody by traditional testing and otherwise would be misclassified as "low risk" relatives. Type 1 diabetes (T1D) is an autoimmune disease that results from the targeted destruction of pancreatic b-cells by autoreactive T cells (1,2). The development of T1D is associated with the occurrence of autoantibodies (AAb) to pancreatic islet antigens that can be used as predictive biomarkers of disease progression (3). AAb associated with T1D are mainly directed against proteins that are involved in the secretory pathway of insulin, including insulin, glutamic acid decarboxylase (GAD65), islet tyrosine phosphatase-like protein (IA-2), and zinc transporter 8 SLC30A8 (ZnT8). The presence of AAb to IA-2 is associated with a high risk of T1D development (4-7). Screening for T1D-associated AAb allows for identification of asymptomatic, high-risk individuals (8) and for natural history studies of disease in cadaveric donors (9). The neuroendocrine molecule IA-2 is a transmembrane glycoprotein of the tyrosine phosphatase-like protein family that is localized to the insulin-secretory granules of the pancreatic b-cell (10). IA-2 (PTPRN) encodes a 979-amino acid protein containing three domains: the N-terminal extracellular (or luminal) domain (amino acids 1-556), the transmembrane domain (amino acids 557-600), and the COOH-terminal intracellular (or cytoplasmic) domain (amino acids 601-979) containing a juxtamembrane (JM) domain (amino acids 601-686) and a protein tyrosine phosphatase