Allosteric regulation is central to protein function in cellular networks1. However, despite technological advances2,3 most studies of allosteric effects on function are conducted in heterologous environments2,4,5, limiting the discovery of allosteric mechanisms that rely on endogenous binding partners or posttranslational modifications to modulate activity. Here we report an approach that enables probing of new sites of allosteric regulation at residue-level resolution in essential eukaryotic proteins in their native biological context by comprehensive mutational scanning. We apply our approach to the central GTPase Gsp1/Ran. GTPases are highly regulated molecular switches that control signaling, with switching occurring via catalyzed GTP hydrolysis and nucleotide exchange. We find that 28% of 4,315 assayed mutations in Gsp1/Ran are highly deleterious, showing a toxic response identified by our assay as gain-of-function (GOF). Remarkably, a third of all positions enriched for GOF mutations (20/60) are outside the GTPase active site. Kinetic analysis shows that these distal sites are allosterically coupled to the active site, including a novel cluster of sites that alter the nucleotide preference of Gsp1 from GDP to GTP. We describe multiple distinct mechanisms by which allosteric mutations alter Gsp1/Ran cellular function by modulating GTPase switching. Our systematic discovery of new regulatory sites provides a functional map relevant to other GTPases such as Ras that could be exploited for targeting and reprogramming critical biological processes.