{"gene":"TBC1D5","run_date":"2026-06-10T10:51:54","timeline":{"discoveries":[{"year":2009,"finding":"TBC1D5 is a Rab-GAP family protein that interacts with the retromer cargo-selective VPS35/VPS29/VPS26 subcomplex, negatively regulates its recruitment to endosomal membranes, and causes Rab7 to dissociate from the membrane, thereby acting as an inhibitor of retromer membrane association.","method":"Co-immunoprecipitation, membrane fractionation, dominant-negative Rab7 mutant analysis, fluorescence microscopy","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP and functional cell-based assays, foundational paper replicated by multiple subsequent studies","pmids":["19531583"],"is_preprint":false},{"year":2016,"finding":"Crystal structure of the TBC1D5 GAP domain bound to VPS29 shows that a loop from TBC1D5 inserts into a conserved hydrophobic pocket on VPS29 opposite the VPS29-VPS35 interface; a distinct loop of the GAP domain may additionally contact VPS35. Loss of TBC1D5 causes defective retromer-dependent receptor trafficking.","method":"X-ray crystallography, biochemical binding assays, site-directed mutagenesis, cell-based trafficking assays","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with complementary biochemical and mutagenesis validation in same study","pmids":["27827364"],"is_preprint":false},{"year":2014,"finding":"TBC1D5 associates with ATG9, the active ULK1 complex, clathrin, and the AP2 complex during autophagy. Depletion of TBC1D5 causes missorting of ATG9 to late endosomes upon autophagy activation, and inhibition of clathrin-mediated endocytosis or AP2 depletion alters ATG9 trafficking and its association with TBC1D5.","method":"Co-immunoprecipitation, siRNA depletion, fluorescence microscopy, autophagy induction assays","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus multiple functional depletion experiments with defined cargo-sorting readout","pmids":["24603492"],"is_preprint":false},{"year":2017,"finding":"Retromer and its associated GAP TBC1D5 maintain Rab7 activity and localization across multiple compartments (late endosomes, lysosomes, ER, TGN, mitochondria). Loss of TBC1D5 or retromer leads to hyperactivated Rab7 that expands over the entire lysosomal domain, depletes the inactive Rab7 pool on endomembranes, misroutes ATG9a, and impairs autophagosome formation around damaged mitochondria during Parkin-mediated mitophagy.","method":"siRNA depletion, live-cell fluorescence imaging, FRAP, autophagy/mitophagy assays, flow cytometry","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (FRAP, imaging, functional mitophagy assays) across multiple conditions in single study","pmids":["29158324"],"is_preprint":false},{"year":2017,"finding":"During metabolic stress, TBC1D5 is sequestered onto LC3+ autophagic compartments via its LIR motif, relieving its inhibitory interaction with the retromer complex; this enables retromer recruitment to endosomal membranes and GLUT1 plasma membrane translocation. In autophagy-deficient cells, TBC1D5 inhibitory interactions with retromer are maintained, causing GLUT1 missorting to endolysosomes; TBC1D5 depletion in autophagy-deficient cells rescues retromer recruitment and GLUT1 surface recycling.","method":"Autophagy induction/inhibition, TBC1D5 depletion and rescue experiments, cell surface biotinylation, fluorescence microscopy, Co-immunoprecipitation","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods with genetic rescue, reciprocal epistasis experiments, surface biotinylation","pmids":["28602638"],"is_preprint":false},{"year":2018,"finding":"TBC1D5 is a GAP for Rab7b (in addition to Rab7a): it localizes to Rab7b-positive vesicles, physically interacts with Rab7b, and displays GAP activity toward Rab7b in vitro; this GAP activity is further increased by retromer proteins. Loss of TBC1D5 reduces the number of CI-MPR- and sortilin-positive vesicles, similarly to constitutively active Rab7b.","method":"siRNA screen with phenotypic readout, Co-immunoprecipitation, in vitro GAP activity assay, fluorescence microscopy, cell-based trafficking assay","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro GAP assay with biochemical interaction and functional cell-based validation, single lab","pmids":["30111580"],"is_preprint":false},{"year":2018,"finding":"Pharmacological inhibition of TBC1D5 enhances Rab7a activation and leads to a gain-of-function for the retromer complex, improving endosomal sorting.","method":"Chemical inhibition, Rab7a activation assay (RILP pulldown), retromer recruitment imaging","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — functional assays in single lab, limited mechanistic depth in abstract","pmids":["29777037"],"is_preprint":false},{"year":2017,"finding":"The Legionella pneumophila effector RidL competes with TBC1D5 for binding to the Vps29 retromer subunit via a protruding β-hairpin (Ile170 in RidL / Leu152 in Vps29), thereby displacing TBC1D5 from the retromer and from Legionella-containing vacuoles; TBC1D5 displacement promotes intracellular bacterial replication.","method":"Crystal structure of RidL-Vps29 complex, site-directed mutagenesis, Co-immunoprecipitation in eukaryotic cells, in vitro binding assay, intracellular replication assay","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with mutagenesis and cell-based validation, independent structural study confirming TBC1D5-VPS29 interface","pmids":["29146912"],"is_preprint":false},{"year":2020,"finding":"During human papillomavirus entry, binding of retromer to the HPV L2 capsid protein recruits TBC1D5 to the retromer at the endosomal membrane; TBC1D5 then stimulates Rab7-GTP hydrolysis to drive retromer disassembly from HPV and delivery of HPV to the retrograde pathway. HPV trafficking requires cycling between GTP- and GDP-bound Rab7, whereas cellular retromer cargos (CIMPR, DMT1-II) require only GTP-bound Rab7.","method":"Artificial protein selection against TBC1D5 (monobody inhibition), dominant-negative and constitutively active Rab7 mutants, fluorescence microscopy, infection assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional inhibition with dominant mutants and mechanistic trafficking assays, single lab","pmids":["32521275"],"is_preprint":false},{"year":2020,"finding":"The Coxiella burnetii secreted kinase CstK physically interacts with host TBC1D5, co-localizes with it in non-infected cells, and TBC1D5 is recruited to Coxiella-containing vacuoles (CCVs) during infection; TBC1D5 depletion significantly impairs CCV development.","method":"Protein-protein interaction assay (co-immunoprecipitation/pull-down), co-localization by fluorescence microscopy, siRNA depletion with CCV morphology readout","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP and imaging with functional depletion, single study, limited mechanistic depth","pmids":["32303638"],"is_preprint":false},{"year":2024,"finding":"SARS-CoV-2 ORF3a, in complex with Vps39, sequesters TBC1D5 and displaces Rab7 from the TBC1D5-Rab7 complex, thereby disrupting the GTP hydrolysis cycle of Rab7 and causing Rab7 hyperactivation. This impairs CI-M6PR retrieval from late endosomes to TGN, disrupts lysosomal hydrolase biosynthetic transport, and reduces tethering of Rab7- and Arl8b-positive compartments.","method":"Co-immunoprecipitation, dominant-negative Rab7 mutant rescue of viral replication, fluorescence microscopy, ORF3a variant expression studies","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, mutant rescue, and multiple functional readouts in single study","pmids":["38448435"],"is_preprint":false},{"year":2023,"finding":"Under nutrient-replete conditions, MTORC1-mediated autophagy inhibition controls the abundance of retromer+ endosomes. Upon autophagy activation (MTOR inhibition or nutrient withdrawal), phagophores capture retromer-TBC1D5 endosomes for bulk destruction; TBC1D5 and its ability to bind retromer (but not its C-terminal LIR motif or nutrient-regulated dephosphorylation) is required for autophagosomal capture of retromer endosomes, leading to lysosomal turnover of recycling cargoes.","method":"MTOR inhibition, autophagy induction, TBC1D5 mutant analysis (LIR-mutant, retromer-binding mutant), cargo trafficking assays, fluorescence microscopy","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple mutant constructs with defined cargo-sorting and autophagy readouts, single lab","pmids":["37938196"],"is_preprint":false},{"year":2022,"finding":"In Drosophila NMJ, TBC1D5 constrains synaptic growth by regulating Rab7 activity; loss of TBC1D5 increases the protein level of the BMP type II receptor Wishful Thinking (Wit) at the NMJ, upregulating BMP signaling. Disruption of TBC1D5 interactions with Rab7 and retromer phenocopies TBC1D5 loss. TBC1D5 is also functionally linked to Rab6 in regulating synaptic growth.","method":"Drosophila genetics (loss-of-function mutants, transgenic rescue), electron microscopy, immunofluorescence, BMP signaling reporter assays","journal":"Journal of genetics and genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis in Drosophila NMJ with ultrastructural and signaling readouts, consistent with mammalian function","pmids":["36473687"],"is_preprint":false},{"year":2021,"finding":"In ischemic/hypoxic cardiomyocytes, TBC1D5 is reduced, leading to blockade of the Rab7 membrane cycle; this impedes retromer binding to microtubules and motor proteins, impairing retrograde transport and decreasing CI-MPR levels, which disrupts trafficking of lysosomal cathepsins.","method":"Ischemia/hypoxia cell model, Western blot, immunofluorescence, microtubule-binding assay, cathepsin trafficking assay","journal":"Frontiers in cardiovascular medicine","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single study, largely correlative with limited mechanistic depth in abstract","pmids":["35004909"],"is_preprint":false},{"year":2024,"finding":"NHE6-mediated inside-out proton signaling activates Rab7 through potent inactivation of the Rab7 GAP TBC1D5 at decreasing endosomal pH; NHE6 physically interacts with TBC1D5 in a complex with Rab7. Epistatic knockdown of TBC1D5 in NHE6-null neurons rescues Rab7 GTPase cycling and endosome maturation, establishing TBC1D5 as the downstream effector of pH-dependent Rab7 regulation.","method":"Co-immunoprecipitation (NHE6-TBC1D5-Rab7 complex), pH-dependent GAP activity assay, NHE6-null mouse neurons, epistatic siRNA knockdown, endosome maturation assay","journal":"bioRxiv (preprint)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis plus biochemical complex identification, preprint status limits confidence","pmids":["bio_10.1101_2024.12.09.627558"],"is_preprint":true}],"current_model":"TBC1D5 is a Rab7 (and Rab7b) GTPase-activating protein that docks onto the retromer VPS29 subunit via a hydrophobic loop (structurally defined by crystal structure), where it inactivates Rab7 to drive retromer membrane uncoating; its activity is pH-regulated through interaction with the endosomal Na+/H+ exchanger NHE6, and it shuttles between the retromer and LC3+ autophagic compartments to coordinately control retromer-dependent cargo recycling (GLUT1, CI-MPR, ATG9), ATG9 sorting for autophagosome formation, Parkin-dependent mitophagy, and synaptic BMP receptor levels—making TBC1D5 a central regulatory hub linking endosomal maturation, retrograde trafficking, and autophagy."},"narrative":{"mechanistic_narrative":"TBC1D5 is a Rab-GAP that inactivates Rab7 to control the membrane association cycle of the retromer cargo-selective complex, positioning it as a central regulator linking endosomal maturation, retrograde cargo recycling, and autophagy [PMID:19531583, PMID:29158324]. It docks onto the retromer VPS29 subunit through a loop that inserts into a conserved hydrophobic pocket opposite the VPS29–VPS35 interface, and loss of this interaction produces defective retromer-dependent receptor trafficking [PMID:27827364]. By driving Rab7-GTP hydrolysis, TBC1D5 confines active Rab7 in space: its loss causes Rab7 hyperactivation that spreads across the lysosomal domain, depletes the inactive endomembrane Rab7 pool, misroutes ATG9a, and impairs autophagosome formation during Parkin-mediated mitophagy [PMID:29158324]. Beyond Rab7a, TBC1D5 acts as a GAP for Rab7b, an activity stimulated by retromer, and controls CI-MPR- and sortilin-positive vesicle numbers [PMID:30111580]. TBC1D5 toggles between inhibiting retromer and being sequestered onto LC3+ compartments: during metabolic stress it is captured via its LIR motif, relieving retromer inhibition to enable GLUT1 surface recycling, while in autophagy-deficient cells persistent inhibition causes GLUT1 missorting [PMID:28602638]. It additionally associates with ATG9, the ULK1 complex, clathrin and AP2 to direct ATG9 sorting during autophagy [PMID:24603492], and phagophores can capture retromer–TBC1D5 endosomes for bulk lysosomal turnover [PMID:37938196]. This hub is targeted by multiple pathogens — the Legionella effector RidL competitively displaces TBC1D5 from VPS29 to promote bacterial replication [PMID:29146912], and SARS-CoV-2 ORF3a sequesters TBC1D5 to hyperactivate Rab7 and impair CI-M6PR retrieval [PMID:38448435]. In Drosophila, TBC1D5 constrains synaptic growth by limiting BMP receptor levels through Rab7 and retromer [PMID:36473687].","teleology":[{"year":2009,"claim":"Established TBC1D5 as a retromer-associated Rab-GAP, answering whether a TBC-domain protein gates retromer membrane recruitment.","evidence":"Co-IP, membrane fractionation, and dominant-negative Rab7 analysis in cells","pmids":["19531583"],"confidence":"High","gaps":["Did not define the structural basis of the TBC1D5–retromer interaction","Direct GAP activity toward Rab7 not biochemically reconstituted here"]},{"year":2014,"claim":"Linked TBC1D5 to autophagy by showing it associates with ATG9 and the autophagy machinery and is required for correct ATG9 sorting.","evidence":"Co-IP, siRNA depletion, and autophagy-induction imaging with ATG9 cargo readout","pmids":["24603492"],"confidence":"High","gaps":["Mechanism coupling TBC1D5 GAP activity to ATG9 sorting not resolved","Role of clathrin/AP2 in recruiting TBC1D5 incompletely defined"]},{"year":2016,"claim":"Defined the atomic basis of TBC1D5 docking onto retromer, showing a GAP-domain loop inserts into a VPS29 hydrophobic pocket.","evidence":"X-ray crystallography with binding assays, mutagenesis, and cell-based trafficking assays","pmids":["27827364"],"confidence":"High","gaps":["Did not capture the Rab7-bound catalytic state","Regulation of the docked complex on membranes not addressed"]},{"year":2017,"claim":"Showed TBC1D5/retromer spatially restrict Rab7 activity, and that its loss causes Rab7 hyperactivation that disrupts ATG9 routing and mitophagy.","evidence":"siRNA depletion, live imaging, FRAP, and Parkin-mitophagy assays","pmids":["29158324"],"confidence":"High","gaps":["How retromer stimulates TBC1D5 GAP activity in cells not detailed","Compartment-specific recruitment cues unresolved"]},{"year":2017,"claim":"Revealed an autophagy-gated switch in which LIR-dependent sequestration of TBC1D5 relieves retromer inhibition to drive GLUT1 surface recycling.","evidence":"Autophagy induction/inhibition, depletion and rescue, surface biotinylation, and Co-IP","pmids":["28602638"],"confidence":"High","gaps":["Signals controlling LIR-mediated capture beyond metabolic stress not mapped","Quantitative partitioning between retromer and LC3 pools unknown"]},{"year":2018,"claim":"Extended TBC1D5 substrate range to Rab7b and showed retromer stimulates this GAP activity, broadening its trafficking control.","evidence":"siRNA screen, Co-IP, in vitro GAP assay, and cell-based trafficking readouts","pmids":["30111580"],"confidence":"High","gaps":["Relative physiological contribution of Rab7a vs Rab7b not quantified","Structural basis of Rab7b recognition not determined"]},{"year":2018,"claim":"Demonstrated that pharmacological TBC1D5 inhibition is a gain-of-function lever for retromer sorting, linking GAP suppression to enhanced endosomal recycling.","evidence":"Chemical inhibition with Rab7a activation (RILP pulldown) and retromer imaging","pmids":["29777037"],"confidence":"Medium","gaps":["Limited mechanistic depth on inhibitor selectivity","Long-term consequences of sustained inhibition not assessed"]},{"year":2020,"claim":"Showed pathogens hijack the TBC1D5–VPS29 interface: Legionella RidL competitively displaces TBC1D5 to promote bacterial replication.","evidence":"Crystal structure of RidL–Vps29, mutagenesis, Co-IP, and intracellular replication assays","pmids":["29146912"],"confidence":"High","gaps":["Downstream Rab7 consequences of displacement in infected cells not fully traced"]},{"year":2020,"claim":"Implicated TBC1D5-driven Rab7 cycling in viral entry, with HPV uniquely requiring GTP/GDP cycling for retromer disassembly and retrograde delivery.","evidence":"Monobody inhibition of TBC1D5, dominant Rab7 mutants, imaging, and infection assays","pmids":["32521275"],"confidence":"Medium","gaps":["Direct demonstration of TBC1D5 GAP turnover on HPV-containing endosomes limited to inhibition data","Single-lab study"]},{"year":2020,"claim":"Identified TBC1D5 as a target recruited to Coxiella vacuoles via a bacterial kinase, supporting a role in pathogen vacuole development.","evidence":"Co-IP/pull-down, co-localization imaging, and siRNA depletion with CCV morphology readout","pmids":["32303638"],"confidence":"Medium","gaps":["Whether CstK modifies TBC1D5 enzymatically not established","Mechanistic link to Rab7 activity at the CCV unresolved"]},{"year":2021,"claim":"Correlated reduced TBC1D5 in ischemic cardiomyocytes with blocked Rab7 cycling and impaired retrograde transport and cathepsin trafficking.","evidence":"Ischemia/hypoxia cell model with Western blot, microtubule-binding, and cathepsin trafficking assays","pmids":["35004909"],"confidence":"Low","gaps":["Largely correlative with limited mechanistic depth","Causality of TBC1D5 loss not established by rescue"]},{"year":2022,"claim":"Showed in vivo that TBC1D5 constrains synaptic growth by limiting BMP receptor levels through Rab7 and retromer.","evidence":"Drosophila loss-of-function genetics, transgenic rescue, EM, and BMP signaling reporters","pmids":["36473687"],"confidence":"Medium","gaps":["Mechanism by which Rab7/retromer set Wit receptor abundance not detailed","Functional link to Rab6 only partially defined"]},{"year":2023,"claim":"Established that phagophores capture retromer–TBC1D5 endosomes for bulk degradation in an MTORC1/autophagy-controlled, retromer-binding-dependent manner.","evidence":"MTOR inhibition, TBC1D5 LIR- and retromer-binding mutants, and cargo trafficking assays","pmids":["37938196"],"confidence":"Medium","gaps":["Distinguishing retromer-binding requirement from LIR/dephosphorylation incompletely resolved","Single-lab study"]},{"year":2024,"claim":"Showed SARS-CoV-2 ORF3a–Vps39 sequesters TBC1D5 and displaces Rab7, hyperactivating Rab7 and disrupting CI-M6PR retrieval and lysosomal hydrolase transport.","evidence":"Co-IP, dominant-negative Rab7 rescue of viral replication, imaging, and ORF3a variant studies","pmids":["38448435"],"confidence":"Medium","gaps":["Direct effect on TBC1D5 catalytic cycle not biochemically isolated","Single-study mechanism"]},{"year":2024,"claim":"Placed TBC1D5 as the downstream effector of pH-dependent Rab7 regulation, inhibited by NHE6-mediated proton signaling at low endosomal pH.","evidence":"Co-IP of NHE6–TBC1D5–Rab7 complex, pH-dependent GAP assay, and epistatic knockdown in NHE6-null neurons (preprint)","pmids":["bio_10.1101_2024.12.09.627558"],"confidence":"Medium","gaps":["Preprint status limits confidence","Structural basis of pH-dependent TBC1D5 inhibition not defined"]},{"year":null,"claim":"How the multiple inputs converging on TBC1D5 — retromer docking, LIR-mediated autophagic capture, pH signaling, and phosphoregulation — are integrated to set Rab7 activity at distinct compartments remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model of how competing recruitment cues are prioritized","Catalytic state of TBC1D5 on Rab7 not captured structurally","In vivo mammalian phenotypes of TBC1D5 loss largely uncharacterized in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,3,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,3,6]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,4]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,3,4]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[3,10]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[4,5]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1,5]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[2,3,4,11]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[4,10,13]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[7,8,9,10]}],"complexes":["retromer (VPS35/VPS29/VPS26)"],"partners":["VPS29","VPS35","RAB7A","RAB7B","ATG9","NHE6","ULK1","AP2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q92609","full_name":"TBC1 domain family member 5","aliases":[],"length_aa":795,"mass_kda":89.0,"function":"May act as a GTPase-activating protein (GAP) for Rab family protein(s). May act as a GAP for RAB7A. Can displace RAB7A and retromer CSC subcomplex from the endosomal membrane to the cytosol; at least retromer displacement seems to require its catalytic activity (PubMed:19531583, PubMed:20923837). Required for retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN); the function seems to require its catalytic activity. Involved in regulation of autophagy (PubMed:22354992). May act as a molecular switch between endosomal and autophagosomal transport and is involved in reprogramming vesicle trafficking upon autophagy induction. Involved in the trafficking of ATG9A upon activation of autophagy. May regulate the recruitment of ATG9A-AP2-containing vesicles to autophagic membranes (PubMed:24603492)","subcellular_location":"Endosome membrane; Cytoplasmic vesicle, autophagosome","url":"https://www.uniprot.org/uniprotkb/Q92609/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TBC1D5","classification":"Not Classified","n_dependent_lines":44,"n_total_lines":1208,"dependency_fraction":0.03642384105960265},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"VPS35","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TBC1D5","total_profiled":1310},"omim":[{"mim_id":"615740","title":"TBC1 DOMAIN FAMILY, MEMBER 5; TBC1D5","url":"https://www.omim.org/entry/615740"},{"mim_id":"606932","title":"VPS29 RETROMER COMPLEX COMPONENT; VPS29","url":"https://www.omim.org/entry/606932"},{"mim_id":"605506","title":"VPS26 RETROMER COMPLEX COMPONENT A; VPS26A","url":"https://www.omim.org/entry/605506"},{"mim_id":"602298","title":"RAS-ASSOCIATED PROTEIN RAB7A; RAB7A","url":"https://www.omim.org/entry/602298"},{"mim_id":"601501","title":"VPS35 RETROMER COMPLEX COMPONENT; VPS35","url":"https://www.omim.org/entry/601501"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Vesicles","reliability":"Supported"},{"location":"Golgi apparatus","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TBC1D5"},"hgnc":{"alias_symbol":["KIAA0210"],"prev_symbol":[]},"alphafold":{"accession":"Q92609","domains":[{"cath_id":"-","chopping":"46-263","consensus_level":"high","plddt":89.169,"start":46,"end":263},{"cath_id":"1.10.472.80","chopping":"294-427","consensus_level":"high","plddt":91.7658,"start":294,"end":427},{"cath_id":"1.10.287","chopping":"598-660","consensus_level":"high","plddt":80.7981,"start":598,"end":660}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q92609","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q92609-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q92609-F1-predicted_aligned_error_v6.png","plddt_mean":64.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TBC1D5","jax_strain_url":"https://www.jax.org/strain/search?query=TBC1D5"},"sequence":{"accession":"Q92609","fasta_url":"https://rest.uniprot.org/uniprotkb/Q92609.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q92609/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q92609"}},"corpus_meta":[{"pmid":"19531583","id":"PMC_19531583","title":"Membrane recruitment of the cargo-selective retromer subcomplex is catalysed by the small GTPase Rab7 and inhibited by the Rab-GAP TBC1D5.","date":"2009","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/19531583","citation_count":306,"is_preprint":false},{"pmid":"29158324","id":"PMC_29158324","title":"Control of RAB7 activity and localization through the retromer-TBC1D5 complex enables RAB7-dependent mitophagy.","date":"2017","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/29158324","citation_count":163,"is_preprint":false},{"pmid":"24603492","id":"PMC_24603492","title":"TBC1D5 and the AP2 complex regulate ATG9 trafficking and initiation of autophagy.","date":"2014","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/24603492","citation_count":147,"is_preprint":false},{"pmid":"28602638","id":"PMC_28602638","title":"Autophagy-Dependent Shuttling of TBC1D5 Controls Plasma Membrane Translocation of GLUT1 and Glucose Uptake.","date":"2017","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/28602638","citation_count":121,"is_preprint":false},{"pmid":"27827364","id":"PMC_27827364","title":"Structural and mechanistic insights into regulation of the retromer coat by TBC1d5.","date":"2016","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/27827364","citation_count":92,"is_preprint":false},{"pmid":"29777037","id":"PMC_29777037","title":"Inhibition of TBC1D5 activates Rab7a and can enhance the function of the retromer cargo-selective complex.","date":"2018","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/29777037","citation_count":64,"is_preprint":false},{"pmid":"29146912","id":"PMC_29146912","title":"Structural insights into Legionella RidL-Vps29 retromer subunit interaction reveal displacement of the regulator TBC1D5.","date":"2017","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29146912","citation_count":42,"is_preprint":false},{"pmid":"38448435","id":"PMC_38448435","title":"SARS-CoV-2 virulence factor ORF3a blocks lysosome function by modulating TBC1D5-dependent Rab7 GTPase cycle.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38448435","citation_count":38,"is_preprint":false},{"pmid":"30111580","id":"PMC_30111580","title":"TBC1D5 controls the GTPase cycle of Rab7b.","date":"2018","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/30111580","citation_count":38,"is_preprint":false},{"pmid":"32521275","id":"PMC_32521275","title":"TBC1D5-Catalyzed Cycling of Rab7 Is Required for Retromer-Mediated Human Papillomavirus Trafficking during Virus Entry.","date":"2020","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/32521275","citation_count":34,"is_preprint":false},{"pmid":"32303638","id":"PMC_32303638","title":"The secreted protein kinase CstK from Coxiella burnetii influences vacuole development and interacts with the GTPase-activating host protein TBC1D5.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32303638","citation_count":13,"is_preprint":false},{"pmid":"37938196","id":"PMC_37938196","title":"Autophagy captures the retromer-TBC1D5 complex to inhibit receptor recycling.","date":"2023","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/37938196","citation_count":10,"is_preprint":false},{"pmid":"38848175","id":"PMC_38848175","title":"Enhancing Rab7 Activity by Inhibiting TBC1D5 Expression Improves Mitophagy in Alzheimer's Disease Models.","date":"2024","source":"Journal of Alzheimer's disease : JAD","url":"https://pubmed.ncbi.nlm.nih.gov/38848175","citation_count":10,"is_preprint":false},{"pmid":"38419050","id":"PMC_38419050","title":"TBC1D5 reverses the capability of HIF-2α in tumor progression and lipid metabolism in clear cell renal cell carcinoma by regulating the autophagy.","date":"2024","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38419050","citation_count":7,"is_preprint":false},{"pmid":"22623674","id":"PMC_22623674","title":"Integration of H-2Z1, a somatosensory cortex-expressed transgene, interferes with the expression of the Satb1 and Tbc1d5 flanking genes and affects the differentiation of a subset of cortical interneurons.","date":"2012","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/22623674","citation_count":7,"is_preprint":false},{"pmid":"31904427","id":"PMC_31904427","title":"miR-10 involved in salinity-induced stress responses and targets TBC1D5 in the sea cucumber, Apostichopus japonicas.","date":"2020","source":"Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/31904427","citation_count":7,"is_preprint":false},{"pmid":"36473687","id":"PMC_36473687","title":"GTPase-activating protein TBC1D5 coordinates with retromer to constrain synaptic growth by inhibiting BMP signaling.","date":"2022","source":"Journal of genetics and genomics = Yi chuan xue bao","url":"https://pubmed.ncbi.nlm.nih.gov/36473687","citation_count":6,"is_preprint":false},{"pmid":"35004909","id":"PMC_35004909","title":"Impaired Retrograde Transport Due to Lack of TBC1D5 Contributes to the Trafficking Defect of Lysosomal Cathepsins in Ischemic/Hypoxic Cardiomyocytes.","date":"2021","source":"Frontiers in cardiovascular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35004909","citation_count":0,"is_preprint":false},{"pmid":"32364436","id":"PMC_32364436","title":"Gender-Discordant Monochorionic-Diamniotic Twins Both With 45,X/46,X, Idic(Y) Mosaicism and a Novel Deletion Within the TBC1D5 Gene.","date":"2020","source":"Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society","url":"https://pubmed.ncbi.nlm.nih.gov/32364436","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.12.09.627558","title":"Endosome maturation is orchestrated by inside-out proton signaling through a Na+/H+ exchanger and pH-dependent Rab GTPase cycling","date":"2024-12-12","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.09.627558","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12100,"output_tokens":4039,"usd":0.048442,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11760,"output_tokens":4692,"usd":0.08805,"stage2_stop_reason":"end_turn"},"total_usd":0.136492,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2009,\n      \"finding\": \"TBC1D5 is a Rab-GAP family protein that interacts with the retromer cargo-selective VPS35/VPS29/VPS26 subcomplex, negatively regulates its recruitment to endosomal membranes, and causes Rab7 to dissociate from the membrane, thereby acting as an inhibitor of retromer membrane association.\",\n      \"method\": \"Co-immunoprecipitation, membrane fractionation, dominant-negative Rab7 mutant analysis, fluorescence microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP and functional cell-based assays, foundational paper replicated by multiple subsequent studies\",\n      \"pmids\": [\"19531583\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Crystal structure of the TBC1D5 GAP domain bound to VPS29 shows that a loop from TBC1D5 inserts into a conserved hydrophobic pocket on VPS29 opposite the VPS29-VPS35 interface; a distinct loop of the GAP domain may additionally contact VPS35. Loss of TBC1D5 causes defective retromer-dependent receptor trafficking.\",\n      \"method\": \"X-ray crystallography, biochemical binding assays, site-directed mutagenesis, cell-based trafficking assays\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with complementary biochemical and mutagenesis validation in same study\",\n      \"pmids\": [\"27827364\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TBC1D5 associates with ATG9, the active ULK1 complex, clathrin, and the AP2 complex during autophagy. Depletion of TBC1D5 causes missorting of ATG9 to late endosomes upon autophagy activation, and inhibition of clathrin-mediated endocytosis or AP2 depletion alters ATG9 trafficking and its association with TBC1D5.\",\n      \"method\": \"Co-immunoprecipitation, siRNA depletion, fluorescence microscopy, autophagy induction assays\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus multiple functional depletion experiments with defined cargo-sorting readout\",\n      \"pmids\": [\"24603492\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Retromer and its associated GAP TBC1D5 maintain Rab7 activity and localization across multiple compartments (late endosomes, lysosomes, ER, TGN, mitochondria). Loss of TBC1D5 or retromer leads to hyperactivated Rab7 that expands over the entire lysosomal domain, depletes the inactive Rab7 pool on endomembranes, misroutes ATG9a, and impairs autophagosome formation around damaged mitochondria during Parkin-mediated mitophagy.\",\n      \"method\": \"siRNA depletion, live-cell fluorescence imaging, FRAP, autophagy/mitophagy assays, flow cytometry\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (FRAP, imaging, functional mitophagy assays) across multiple conditions in single study\",\n      \"pmids\": [\"29158324\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"During metabolic stress, TBC1D5 is sequestered onto LC3+ autophagic compartments via its LIR motif, relieving its inhibitory interaction with the retromer complex; this enables retromer recruitment to endosomal membranes and GLUT1 plasma membrane translocation. In autophagy-deficient cells, TBC1D5 inhibitory interactions with retromer are maintained, causing GLUT1 missorting to endolysosomes; TBC1D5 depletion in autophagy-deficient cells rescues retromer recruitment and GLUT1 surface recycling.\",\n      \"method\": \"Autophagy induction/inhibition, TBC1D5 depletion and rescue experiments, cell surface biotinylation, fluorescence microscopy, Co-immunoprecipitation\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods with genetic rescue, reciprocal epistasis experiments, surface biotinylation\",\n      \"pmids\": [\"28602638\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TBC1D5 is a GAP for Rab7b (in addition to Rab7a): it localizes to Rab7b-positive vesicles, physically interacts with Rab7b, and displays GAP activity toward Rab7b in vitro; this GAP activity is further increased by retromer proteins. Loss of TBC1D5 reduces the number of CI-MPR- and sortilin-positive vesicles, similarly to constitutively active Rab7b.\",\n      \"method\": \"siRNA screen with phenotypic readout, Co-immunoprecipitation, in vitro GAP activity assay, fluorescence microscopy, cell-based trafficking assay\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro GAP assay with biochemical interaction and functional cell-based validation, single lab\",\n      \"pmids\": [\"30111580\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Pharmacological inhibition of TBC1D5 enhances Rab7a activation and leads to a gain-of-function for the retromer complex, improving endosomal sorting.\",\n      \"method\": \"Chemical inhibition, Rab7a activation assay (RILP pulldown), retromer recruitment imaging\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — functional assays in single lab, limited mechanistic depth in abstract\",\n      \"pmids\": [\"29777037\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The Legionella pneumophila effector RidL competes with TBC1D5 for binding to the Vps29 retromer subunit via a protruding β-hairpin (Ile170 in RidL / Leu152 in Vps29), thereby displacing TBC1D5 from the retromer and from Legionella-containing vacuoles; TBC1D5 displacement promotes intracellular bacterial replication.\",\n      \"method\": \"Crystal structure of RidL-Vps29 complex, site-directed mutagenesis, Co-immunoprecipitation in eukaryotic cells, in vitro binding assay, intracellular replication assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with mutagenesis and cell-based validation, independent structural study confirming TBC1D5-VPS29 interface\",\n      \"pmids\": [\"29146912\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"During human papillomavirus entry, binding of retromer to the HPV L2 capsid protein recruits TBC1D5 to the retromer at the endosomal membrane; TBC1D5 then stimulates Rab7-GTP hydrolysis to drive retromer disassembly from HPV and delivery of HPV to the retrograde pathway. HPV trafficking requires cycling between GTP- and GDP-bound Rab7, whereas cellular retromer cargos (CIMPR, DMT1-II) require only GTP-bound Rab7.\",\n      \"method\": \"Artificial protein selection against TBC1D5 (monobody inhibition), dominant-negative and constitutively active Rab7 mutants, fluorescence microscopy, infection assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional inhibition with dominant mutants and mechanistic trafficking assays, single lab\",\n      \"pmids\": [\"32521275\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The Coxiella burnetii secreted kinase CstK physically interacts with host TBC1D5, co-localizes with it in non-infected cells, and TBC1D5 is recruited to Coxiella-containing vacuoles (CCVs) during infection; TBC1D5 depletion significantly impairs CCV development.\",\n      \"method\": \"Protein-protein interaction assay (co-immunoprecipitation/pull-down), co-localization by fluorescence microscopy, siRNA depletion with CCV morphology readout\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP and imaging with functional depletion, single study, limited mechanistic depth\",\n      \"pmids\": [\"32303638\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SARS-CoV-2 ORF3a, in complex with Vps39, sequesters TBC1D5 and displaces Rab7 from the TBC1D5-Rab7 complex, thereby disrupting the GTP hydrolysis cycle of Rab7 and causing Rab7 hyperactivation. This impairs CI-M6PR retrieval from late endosomes to TGN, disrupts lysosomal hydrolase biosynthetic transport, and reduces tethering of Rab7- and Arl8b-positive compartments.\",\n      \"method\": \"Co-immunoprecipitation, dominant-negative Rab7 mutant rescue of viral replication, fluorescence microscopy, ORF3a variant expression studies\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, mutant rescue, and multiple functional readouts in single study\",\n      \"pmids\": [\"38448435\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Under nutrient-replete conditions, MTORC1-mediated autophagy inhibition controls the abundance of retromer+ endosomes. Upon autophagy activation (MTOR inhibition or nutrient withdrawal), phagophores capture retromer-TBC1D5 endosomes for bulk destruction; TBC1D5 and its ability to bind retromer (but not its C-terminal LIR motif or nutrient-regulated dephosphorylation) is required for autophagosomal capture of retromer endosomes, leading to lysosomal turnover of recycling cargoes.\",\n      \"method\": \"MTOR inhibition, autophagy induction, TBC1D5 mutant analysis (LIR-mutant, retromer-binding mutant), cargo trafficking assays, fluorescence microscopy\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple mutant constructs with defined cargo-sorting and autophagy readouts, single lab\",\n      \"pmids\": [\"37938196\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In Drosophila NMJ, TBC1D5 constrains synaptic growth by regulating Rab7 activity; loss of TBC1D5 increases the protein level of the BMP type II receptor Wishful Thinking (Wit) at the NMJ, upregulating BMP signaling. Disruption of TBC1D5 interactions with Rab7 and retromer phenocopies TBC1D5 loss. TBC1D5 is also functionally linked to Rab6 in regulating synaptic growth.\",\n      \"method\": \"Drosophila genetics (loss-of-function mutants, transgenic rescue), electron microscopy, immunofluorescence, BMP signaling reporter assays\",\n      \"journal\": \"Journal of genetics and genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis in Drosophila NMJ with ultrastructural and signaling readouts, consistent with mammalian function\",\n      \"pmids\": [\"36473687\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In ischemic/hypoxic cardiomyocytes, TBC1D5 is reduced, leading to blockade of the Rab7 membrane cycle; this impedes retromer binding to microtubules and motor proteins, impairing retrograde transport and decreasing CI-MPR levels, which disrupts trafficking of lysosomal cathepsins.\",\n      \"method\": \"Ischemia/hypoxia cell model, Western blot, immunofluorescence, microtubule-binding assay, cathepsin trafficking assay\",\n      \"journal\": \"Frontiers in cardiovascular medicine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single study, largely correlative with limited mechanistic depth in abstract\",\n      \"pmids\": [\"35004909\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NHE6-mediated inside-out proton signaling activates Rab7 through potent inactivation of the Rab7 GAP TBC1D5 at decreasing endosomal pH; NHE6 physically interacts with TBC1D5 in a complex with Rab7. Epistatic knockdown of TBC1D5 in NHE6-null neurons rescues Rab7 GTPase cycling and endosome maturation, establishing TBC1D5 as the downstream effector of pH-dependent Rab7 regulation.\",\n      \"method\": \"Co-immunoprecipitation (NHE6-TBC1D5-Rab7 complex), pH-dependent GAP activity assay, NHE6-null mouse neurons, epistatic siRNA knockdown, endosome maturation assay\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis plus biochemical complex identification, preprint status limits confidence\",\n      \"pmids\": [\"bio_10.1101_2024.12.09.627558\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"TBC1D5 is a Rab7 (and Rab7b) GTPase-activating protein that docks onto the retromer VPS29 subunit via a hydrophobic loop (structurally defined by crystal structure), where it inactivates Rab7 to drive retromer membrane uncoating; its activity is pH-regulated through interaction with the endosomal Na+/H+ exchanger NHE6, and it shuttles between the retromer and LC3+ autophagic compartments to coordinately control retromer-dependent cargo recycling (GLUT1, CI-MPR, ATG9), ATG9 sorting for autophagosome formation, Parkin-dependent mitophagy, and synaptic BMP receptor levels—making TBC1D5 a central regulatory hub linking endosomal maturation, retrograde trafficking, and autophagy.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TBC1D5 is a Rab-GAP that inactivates Rab7 to control the membrane association cycle of the retromer cargo-selective complex, positioning it as a central regulator linking endosomal maturation, retrograde cargo recycling, and autophagy [#0, #3]. It docks onto the retromer VPS29 subunit through a loop that inserts into a conserved hydrophobic pocket opposite the VPS29–VPS35 interface, and loss of this interaction produces defective retromer-dependent receptor trafficking [#1]. By driving Rab7-GTP hydrolysis, TBC1D5 confines active Rab7 in space: its loss causes Rab7 hyperactivation that spreads across the lysosomal domain, depletes the inactive endomembrane Rab7 pool, misroutes ATG9a, and impairs autophagosome formation during Parkin-mediated mitophagy [#3]. Beyond Rab7a, TBC1D5 acts as a GAP for Rab7b, an activity stimulated by retromer, and controls CI-MPR- and sortilin-positive vesicle numbers [#5]. TBC1D5 toggles between inhibiting retromer and being sequestered onto LC3+ compartments: during metabolic stress it is captured via its LIR motif, relieving retromer inhibition to enable GLUT1 surface recycling, while in autophagy-deficient cells persistent inhibition causes GLUT1 missorting [#4]. It additionally associates with ATG9, the ULK1 complex, clathrin and AP2 to direct ATG9 sorting during autophagy [#2], and phagophores can capture retromer–TBC1D5 endosomes for bulk lysosomal turnover [#11]. This hub is targeted by multiple pathogens — the Legionella effector RidL competitively displaces TBC1D5 from VPS29 to promote bacterial replication [#7], and SARS-CoV-2 ORF3a sequesters TBC1D5 to hyperactivate Rab7 and impair CI-M6PR retrieval [#10]. In Drosophila, TBC1D5 constrains synaptic growth by limiting BMP receptor levels through Rab7 and retromer [#12].\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Established TBC1D5 as a retromer-associated Rab-GAP, answering whether a TBC-domain protein gates retromer membrane recruitment.\",\n      \"evidence\": \"Co-IP, membrane fractionation, and dominant-negative Rab7 analysis in cells\",\n      \"pmids\": [\"19531583\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the structural basis of the TBC1D5–retromer interaction\", \"Direct GAP activity toward Rab7 not biochemically reconstituted here\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Linked TBC1D5 to autophagy by showing it associates with ATG9 and the autophagy machinery and is required for correct ATG9 sorting.\",\n      \"evidence\": \"Co-IP, siRNA depletion, and autophagy-induction imaging with ATG9 cargo readout\",\n      \"pmids\": [\"24603492\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism coupling TBC1D5 GAP activity to ATG9 sorting not resolved\", \"Role of clathrin/AP2 in recruiting TBC1D5 incompletely defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defined the atomic basis of TBC1D5 docking onto retromer, showing a GAP-domain loop inserts into a VPS29 hydrophobic pocket.\",\n      \"evidence\": \"X-ray crystallography with binding assays, mutagenesis, and cell-based trafficking assays\",\n      \"pmids\": [\"27827364\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not capture the Rab7-bound catalytic state\", \"Regulation of the docked complex on membranes not addressed\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Showed TBC1D5/retromer spatially restrict Rab7 activity, and that its loss causes Rab7 hyperactivation that disrupts ATG9 routing and mitophagy.\",\n      \"evidence\": \"siRNA depletion, live imaging, FRAP, and Parkin-mitophagy assays\",\n      \"pmids\": [\"29158324\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How retromer stimulates TBC1D5 GAP activity in cells not detailed\", \"Compartment-specific recruitment cues unresolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Revealed an autophagy-gated switch in which LIR-dependent sequestration of TBC1D5 relieves retromer inhibition to drive GLUT1 surface recycling.\",\n      \"evidence\": \"Autophagy induction/inhibition, depletion and rescue, surface biotinylation, and Co-IP\",\n      \"pmids\": [\"28602638\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signals controlling LIR-mediated capture beyond metabolic stress not mapped\", \"Quantitative partitioning between retromer and LC3 pools unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended TBC1D5 substrate range to Rab7b and showed retromer stimulates this GAP activity, broadening its trafficking control.\",\n      \"evidence\": \"siRNA screen, Co-IP, in vitro GAP assay, and cell-based trafficking readouts\",\n      \"pmids\": [\"30111580\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative physiological contribution of Rab7a vs Rab7b not quantified\", \"Structural basis of Rab7b recognition not determined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrated that pharmacological TBC1D5 inhibition is a gain-of-function lever for retromer sorting, linking GAP suppression to enhanced endosomal recycling.\",\n      \"evidence\": \"Chemical inhibition with Rab7a activation (RILP pulldown) and retromer imaging\",\n      \"pmids\": [\"29777037\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Limited mechanistic depth on inhibitor selectivity\", \"Long-term consequences of sustained inhibition not assessed\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed pathogens hijack the TBC1D5–VPS29 interface: Legionella RidL competitively displaces TBC1D5 to promote bacterial replication.\",\n      \"evidence\": \"Crystal structure of RidL–Vps29, mutagenesis, Co-IP, and intracellular replication assays\",\n      \"pmids\": [\"29146912\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream Rab7 consequences of displacement in infected cells not fully traced\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Implicated TBC1D5-driven Rab7 cycling in viral entry, with HPV uniquely requiring GTP/GDP cycling for retromer disassembly and retrograde delivery.\",\n      \"evidence\": \"Monobody inhibition of TBC1D5, dominant Rab7 mutants, imaging, and infection assays\",\n      \"pmids\": [\"32521275\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct demonstration of TBC1D5 GAP turnover on HPV-containing endosomes limited to inhibition data\", \"Single-lab study\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified TBC1D5 as a target recruited to Coxiella vacuoles via a bacterial kinase, supporting a role in pathogen vacuole development.\",\n      \"evidence\": \"Co-IP/pull-down, co-localization imaging, and siRNA depletion with CCV morphology readout\",\n      \"pmids\": [\"32303638\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether CstK modifies TBC1D5 enzymatically not established\", \"Mechanistic link to Rab7 activity at the CCV unresolved\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Correlated reduced TBC1D5 in ischemic cardiomyocytes with blocked Rab7 cycling and impaired retrograde transport and cathepsin trafficking.\",\n      \"evidence\": \"Ischemia/hypoxia cell model with Western blot, microtubule-binding, and cathepsin trafficking assays\",\n      \"pmids\": [\"35004909\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Largely correlative with limited mechanistic depth\", \"Causality of TBC1D5 loss not established by rescue\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showed in vivo that TBC1D5 constrains synaptic growth by limiting BMP receptor levels through Rab7 and retromer.\",\n      \"evidence\": \"Drosophila loss-of-function genetics, transgenic rescue, EM, and BMP signaling reporters\",\n      \"pmids\": [\"36473687\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which Rab7/retromer set Wit receptor abundance not detailed\", \"Functional link to Rab6 only partially defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Established that phagophores capture retromer–TBC1D5 endosomes for bulk degradation in an MTORC1/autophagy-controlled, retromer-binding-dependent manner.\",\n      \"evidence\": \"MTOR inhibition, TBC1D5 LIR- and retromer-binding mutants, and cargo trafficking assays\",\n      \"pmids\": [\"37938196\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Distinguishing retromer-binding requirement from LIR/dephosphorylation incompletely resolved\", \"Single-lab study\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed SARS-CoV-2 ORF3a–Vps39 sequesters TBC1D5 and displaces Rab7, hyperactivating Rab7 and disrupting CI-M6PR retrieval and lysosomal hydrolase transport.\",\n      \"evidence\": \"Co-IP, dominant-negative Rab7 rescue of viral replication, imaging, and ORF3a variant studies\",\n      \"pmids\": [\"38448435\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct effect on TBC1D5 catalytic cycle not biochemically isolated\", \"Single-study mechanism\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed TBC1D5 as the downstream effector of pH-dependent Rab7 regulation, inhibited by NHE6-mediated proton signaling at low endosomal pH.\",\n      \"evidence\": \"Co-IP of NHE6–TBC1D5–Rab7 complex, pH-dependent GAP assay, and epistatic knockdown in NHE6-null neurons (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.12.09.627558\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint status limits confidence\", \"Structural basis of pH-dependent TBC1D5 inhibition not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the multiple inputs converging on TBC1D5 — retromer docking, LIR-mediated autophagic capture, pH signaling, and phosphoregulation — are integrated to set Rab7 activity at distinct compartments remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model of how competing recruitment cues are prioritized\", \"Catalytic state of TBC1D5 on Rab7 not captured structurally\", \"In vivo mammalian phenotypes of TBC1D5 loss largely uncharacterized in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 3, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 3, 6]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 3, 4]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [3, 10]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1, 5]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [2, 3, 4, 11]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [4, 10, 13]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [7, 8, 9, 10]}\n    ],\n    \"complexes\": [\"retromer (VPS35/VPS29/VPS26)\"],\n    \"partners\": [\"VPS29\", \"VPS35\", \"RAB7A\", \"RAB7B\", \"ATG9\", \"NHE6\", \"ULK1\", \"AP2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}