Integrin-linked kinase (ILK), a central component of the intracellular ILK–pinch–parvin complex, localizes together with paxillin to focal adhesions and regulates integrin-mediated cell functions. ILK was initially misclassified as a kinase based on phenotypical characterization of cells expressing ILK mutated in the “kinase” domain, such as the E359K and K220M mutants and a V386G/T387G mutation in the paxillin-binding site (PBS). ILK is now known to be a pseudokinase, and mechanisms of action of these mutants are not clear. We selectively induced expression of only the E359K, PBS, and K220M ILK mutations in the developing kidney collecting system and kidney collecting duct (CD) cells and analyzed their impact on structural integrity using molecular dynamics (MD) simulations. Mice or CD cells carrying the E359K mutation had a severe phenotype that is indistinguishable from ILK-null mice or ILK-null CD cells. The K220M mutant mice developed normally, and K220M-CD cells had a mild adhesion, migration, and tubulogenesis defect. The PBS mutant mice had a subtle developmental defect, and PBS-CD cells had moderate functional abnormalities. Consistent with these observed phenotypes, MD studies suggest that the E359K mutant produces the most structurally perturbed, and K220M the most WT-like ILK molecules. Although all three mutations disrupted ILK binding to parvin and paxillin in vitro, only the E359K mutation decreased ILK binding to pinch suggesting that it increases ILK misfolding. Thus, point mutations in the ILK pseudokinase domain cause functional abnormalities by altering the ILK structure, leading to increased turnover and destabilization of ILK–parvin and (sometimes) ILK–pinch interactions. The integrin-linked kinase (ILK)–pinch–parvin (IPP) complex is a critical component of focal adhesions that binds to the cytoplasmic tail of the integrin β subunits. Integrins, composed of an α and a β subunit, are the principal receptors that mediate cell–extracellular matrix interactions and regulate many cell functions, including adhesion, spreading, migration, polarization, and tubulogenesis. ILK is a 450 amino acid multidomain.