In this thesis, the effects of amino acid substitutions in selected proteins were investigated. The first study focuses on aspartoacylase (ASPA), an enzyme that catalyzes the hydrolysis N-acetyl-aspartate into acetate and aspartate within oligodendrocytes of the brain. Loss of ASPA activity leads to the recessive, degenerative leukodystrophy, known as Canavan ́s disease. Currently more than 150 different ASPA gene variants have been reported, many of which are so-called variants of unknown significance (VUS), where their involvement in Canavan’s disease is unknown. Using deep mutational scanning, the cellular abundance was determined for 6152 out of the 6260 possible (~98%) single- site missense and nonsense ASPA variants. The abundance data correlate with computational analyses on ASPA structural stability and evolutionary conservation, and show that loss of abundance is a major driver for pathogenicity of disease-linked ASPA variants. Systematic mapping of degradation signals (degrons) revealed several protein quality control (PQC) degrons embedded within the ASPA protein sequence. In structurally destabilized ASPA variants, these degrons may target the proteins for ubiquitin-dependent proteasomal degradation. Finally, additional screening and sequencing of the library of ASPA variants showed that prolonged expression of certain low- abundance ASPA variants was toxic, revealing an intimate link between loss of structural stability, degradation and toxicity. In the second study, bioinformatics analyses were applied to demonstrate, that although lysine is a common amino acid in the human proteome, hundreds of human proteins contain long stretches completely devoid of lysine. Importantly, many of these so-called lysine deserts are phylogenetically conserved and enriched for intrinsically disordered regions and within proteins associated with the ubiquitin-proteasome system (UPS). In selected UPS-associated lysine desert proteins, including RAD23A, UBQLN1 and BAG6, substituting arginines with lysines resulted in an increased ubiquitylation. For UBQLN1 and BAG6, the lysine variants also showed increased proteasomal degradation. However, for RAD23A the cellular stability was unaffected, but caused a partial loss of function phenotype when expressed in fission yeast. In conclusion, these data indicate that lysine- depletion is a common and evolutionarily conserved mechanism for avoiding unwarranted ubiquitylation and degradation of UPS components.