Identifying pathogenic variants and underlying functional alterations is challenging. To this end, we introduce MutPred2, a tool that improves the prioritization of pathogenic amino acid substitutions over existing methods, generates molecular mechanisms potentially causative of disease, and returns interpretable pathogenicity score distributions on individual genomes. Whilst its prioritization performance is state-of-the-art, a distinguishing feature of MutPred2 is the probabilistic modeling of variant impact on specific aspects of protein structure and function that can serve to guide experimental studies of phenotype-altering variants. We demonstrate the utility of MutPred2 in the identification of the structural and functional mutational signatures relevant to Mendelian disorders and the prioritization of de novo mutations associated with complex neurodevelopmental disorders. We then experimentally validate the functional impact of several variants identified in patients with such disorders. We argue that mechanism-driven studies of human inherited disease have the potential to significantly accelerate the discovery of clinically actionable variants.

Mild inhibition of mitochondrial respiration extends the lifespan of many species. In Caenorhabditis elegans, reactive oxygen species (ROS) promote longevity by activating hypoxia-inducible factor 1 (HIF-1) in response to reduced mitochondrial respiration. However, the physiological role and mechanism of ROS-induced longevity are poorly understood. Here, we show that a modest increase in ROS increases the immunity and lifespan of C. elegans through feedback regulation by HIF-1 and AMP-activated protein kinase (AMPK). We found that activation of AMPK as well as HIF-1 mediates the longevity response to ROS. We further showed that AMPK reduces internal levels of ROS, whereas HIF-1 amplifies the levels of internal ROS under conditions that increase ROS. Moreover, mitochondrial ROS increase resistance to various pathogenic bacteria, suggesting a possible association between immunity and long lifespan. Thus, AMPK and HIF-1 may control immunity and longevity tightly by acting as feedback regulators of ROS.aging | mitochondria | immunity | reactive oxygen species | C. elegans M itochondria are essential for various physiological processes, including energy production, apoptosis, metabolism, and signaling (1). Thus, it is not surprising that defects in mitochondrial function are linked to many diseases. Interestingly, however, mild inhibition of mitochondrial respiration increases the lifespans of many organisms (2, 3). In particular, genetic inhibition of components of the mitochondrial electron transport chain (ETC) increases longevity of the roundworm Caenorhabditis elegans. For example, mutations in clk-1 (a ubiquinone hydroxylase) and isp-1 (iron-sulfur protein 1 in the mitochondrial complex III) extend the lifespans of worms (4, 5). Longevity resulting from mitochondrial ETC inhibition also has been observed in Drosophila (6, 7) and mice (8, 9). Thus, the mechanisms responsible for longevity may be evolutionarily conserved.Key genetic factors that mediate longevity caused by reduced mitochondrial respiration in C. elegans have been identified recently (10-17). However, the mechanisms are not completely understood. Hypoxia-inducible factor 1 (HIF-1), the master transcriptional regulator of cellular responses to hypoxia, is one of the mediators of longevity caused by inhibition of mitochondrial respiration in C. elegans (12). The physiological importance of HIF-1α in humans is underscored by the fact that mutations in VHL, the von HippelLindau tumor suppressor gene, which encodes an E3-ubiquitin ligase component required for the degradation of HIF-1, lead to an inherited form of cancer (18,19). HIF-1 regulates adaptation to low oxygen and various other biological processes, including axon guidance, immunity, iron homeostasis, and aging (20-29). Increased levels of HIF-1 by vhl-1 mutations or by overexpression of HIF-1 lengthen the lifespan of C. elegans (27, 28). In addition, we previously showed that inhibition of mitochondrial respiration promotes longevity by elevating reactive oxygen species (ROS) levels and incr...

MotivationLoss-of-function genetic variants are frequently associated with severe clinical phenotypes, yet many are present in the genomes of healthy individuals. The available methods to assess the impact of these variants rely primarily upon evolutionary conservation with little to no consideration of the structural and functional implications for the protein. They further do not provide information to the user regarding specific molecular alterations potentially causative of disease.ResultsTo address this, we investigate protein features underlying loss-of-function genetic variation and develop a machine learning method, MutPred-LOF, for the discrimination of pathogenic and tolerated variants that can also generate hypotheses on specific molecular events disrupted by the variant. We investigate a large set of human variants derived from the Human Gene Mutation Database, ClinVar and the Exome Aggregation Consortium. Our prediction method shows an area under the Receiver Operating Characteristic curve of 0.85 for all loss-of-function variants and 0.75 for proteins in which both pathogenic and neutral variants have been observed. We applied MutPred-LOF to a set of 1142 de novo vari3ants from neurodevelopmental disorders and find enrichment of pathogenic variants in affected individuals. Overall, our results highlight the potential of computational tools to elucidate causal mechanisms underlying loss of protein function in loss-of-function variants.Availability and Implementation http://mutpred.mutdb.org

An improved understanding of protein conformational changes has broad implications for elucidating the mechanisms of various biological processes and for the design of protein engineering experiments. Understanding rearrangements of residue interactions is a key component in the challenge of describing structural transitions. Evolutionary properties of protein sequences and structures are extensively studied; however, evolution of protein motions, especially with respect to interaction rearrangements, has yet to be explored. Here, we investigated the relationship between sequence evolution and protein conformational changes and discovered that structural transitions are encoded in amino acid sequences as coevolving residue pairs. Furthermore, we found that highly coevolving residues are clustered in the flexible regions of proteins and facilitate structural transitions by forming and disrupting their interactions cooperatively. Our results provide insight into the evolution of protein conformational changes and help to identify residues important for structural transitions.

MON-2, which mediates Golgi-endosome trafficking, mediates mitochondrial inhibition–induced longevity by enhancing autophagy.