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The decreased cost of human exome and genome sequencing provides new opportunities for diagnosing genetic disorders. In order to utilize this information, we need better and more robust methods for interpreting sequencing results, including determining whether specific missense variants are likely to be pathogenic. Using the protein PTEN (phosphatase and tensin homolog) as an example, we show how recent developments in both experiments and computational modeling can be used to determine whether a missense variant is likely to be pathogenic. Missense variants in PTEN can cause both autism spectrum disorder and increased risk of different forms of cancer, yet distinguishing such disease-associated variants from more harmless genetic variation is difficult. One approach relies on multiplexed experiments that enable determination of the effect of all possible missense variants in a cellular assay. Another approach is to use computational methods to predict variant effects. We compared two different multiplexed experiments and two computational methods to classify variant effects in PTEN. We distinguished between methods that focus on effects on protein stability and protein-specific methods that are more directly related to enzyme activity. Our results on PTEN suggest that ∼60% of pathogenic variants cause loss of function because they destabilize the folded protein, which is subsequently degraded. Methods that quantify a broader range of effects on PTEN activity perform better at predicting variant effects. Either experimental method performs better than the corresponding computational predictions, so that, for example, experiments that probe cellular abundance perform better at identifying pathogenic variants than predictions of thermodynamic stability. Our results suggest that loss of stability of PTEN is a key driver for disease, and we hypothesize that experiments and prediction methods that probe protein stability can be used to find variants with similar mechanisms in other genes.

In order to be functional, most proteins must fold into a well-defined and stable three-dimensional structure. Evolution, however, selects for function and not directly for stability, and consequently, the native, biologically active state is often only marginally stable under physiological conditions. Accordingly, as a result of mutations or stress conditions, proteins are prone to become structurally destabilized or locked in misfolded conformations. Since such protein species can be toxic and form various aggregates, all cells have evolved a protein quality control (PQC) system that constantly scans the intracellular space for nonnative proteins. Upon encountering such proteins, molecular chaperones and proteases of the PQC system ensure their rapid elimination from the cell, via either refolding or degradation. A number of studies have linked the PQC system with disease. For instance, a defective PQC system may lead to accumulation of toxic protein species that can cause disease, including numerous neurodegenerative disorders. Conversely, in cases where a disease-linked mutation causes a structural destabilization of the germline-encoded protein, an overmeticulous PQC system can lead to hereditary diseases, including cystic fibrosis, diabetes, phenylketonuria, and Lynch syndrome. Here, we briefly summarize the molecular mechanisms of the PQC system and its importance for various genetic disorders.

The cellular proteome performs highly varied functions to sustain life. Since most of these functions require proteins to fold properly, they can be impaired by mutations that affect protein structure, leading to diseases such as Alzheimer's disease, cystic fibrosis, and Lynch syndrome. The cell has evolved an intricate protein quality control (PQC) system that includes degradation pathways and a multitude of molecular chaperones and co-chaperones, all working together to catalyze the refolding or removal of aberrant proteins. Thus, the PQC system limits the harmful consequences of dysfunctional proteins, including those arising from disease-causing mutations. This complex system is still not fully understood. In particular the structural and sequence motifs that, when exposed, trigger degradation of misfolded proteins are currently under investigation. Moreover, several attempts are being made to activate or inhibit parts of the PQC system as a treatment for diseases. Here, we briefly review the present knowledge on the PQC system and list current strategies that are employed to exploit the system in disease treatment.