It is controversial whether mutation in the melancortin-3 receptor (MC3R) gene is a cause for monogenic obesity in humans. Three novel mutations in the MC3R, A293T, I335S, and X361S, were identified from morbidly obese subjects. We investigated whether these mutations caused loss-of-function and the molecular defects if any. Ligand binding, signaling, and cell surface expression of the mutant MC3Rs were studied. I335S resulted in a complete loss of ligand binding and signaling due to intracellular retention. A293T and X361S MC3Rs had normal ligand binding and signaling as wild type MC3R. Co-expression studies showed that the mutants did not affect wild type MC3R signaling. Hence the I335S variant previously identified from obese patients is not expressed at the cell surface when expressed in vitro, suggesting that it might contribute to obesity in carriers of this variant. Whether A293T and X361S cause obesity remains to be investigated. Additional mutations at I335 showed that I335, part of the highly conserved N/DPxxY motif, was critical for multiple aspects of the MC3R function, including cell surface expression, ligand binding, and signaling.