Altered cellular lipid composition activates the endoplasmic reticulum unfolded protein response (UPR) and UPR signaling effects important changes in lipid metabolism. Secondary effects on protein folding homeostasis likely contribute to UPR activation, but deletion of the unfolded protein stress-sensing luminal domain of the UPR transducers PERK and IRE1α does not abolish their responsiveness to lipid perturbation. This finding suggests that PERK and IRE1α also directly recognize the membrane aberrancy wrought by lipid perturbation. However, beyond the need for a transmembrane domain (TMD), little is known about the features involved. Regulation of the UPR transducers entails changes in their oligomeric state and is easily corrupted by over-expression. Therefore CRISPR/Cas9-mediated gene editing of the Ern1 locus, was used to study the role of the TMD in the ability of the endogenous IRE1α protein to recognize membrane aberrancy in mammalian cells. Conducted in the background of a point mutation that isolated the response to membrane aberrancy induced by palmitate from unfolded protein stress, our analysis shows that generic membrane spanning features of the TMD are sufficient for IRE1α’s responsiveness to membrane aberrancy. Our data suggests that IRE1α’s conserved TMD may have been selected for features imparting a relatively muted response to acyl-chain saturation.