The disclosure provides nucleic acid molecules, including cDNA, comprising an alteration that encodes a truncated human Single Immunoglobulin Interleukin-1 Receptor Related (SIGIRR) protein. The disclosure also provides isolated and recombinant human SIGIRR protein variants that comprise a truncation at a position corresponding to position 215. The truncation, and the nucleic acid molecules encoding this change, associate with early-onset inflammatory bowel disease (EO-IBD). The disclosure also provides methods for determining whether a subject has or has a risk of developing EO-IBD, based on the identification of such alterations in the nucleic acid molecules encoding SIGIRR.