A new spontaneous mutation, abnormal hair appearance in the rat, has been identified as a non-functional Tuft1 (tuftelin 1) gene. The pleiotropic effects of this mutation regulate glucose and lipid metabolism. Analysis of the liver proteome revealed possible molecular mechanisms for the metabolic effects of the Tuft1 gene. Recently, we identified a recessive mutation, an abnormal coat appearance, in BXH6 strain, a member of the HXB/BXH set of recombinant inbred strains derived from the SHR (spontaneously hypertensive rat) and BN-Lx (Brown Norway rat) progenitors. Whole genome sequencing of the mutant rats identified the 195875980 G/A mutation in the Tuft1 (tuftelin 1) gene on chromosome 2, which resulted in a premature stop codon. Compared to wild-type BXH6 rats, BXH6-Tuft1 mutant rats exhibited lower body weight due to reduced visceral fat and ectopic fat accumulation in the liver and heart. Reduced adiposity was associated with decreased serum glucose and insulin, and increased insulin-stimulated glycogenesis in skeletal muscle. In addition, mutant rats had lower serum MCP-1 and leptin levels, indicative of reduced inflammation. Analysis of the liver proteome identified differentially expressed proteins from fatty acid metabolism and beta oxidation, peroxisomes, carbohydrate metabolism, inflammation, and proteasome pathways. These results provide evidence for an important role of Tuft1 gene in the regulation of lipid and glucose metabolism and suggest underlying molecular mechanisms.