{"gene":"VPS39","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":1997,"finding":"Vam6p/Vps39p physically interacts with Vam2p/Vps41p and both are components of a large protein complex on vacuolar membranes; loss of either protein results in defective vacuolar protein sorting (CPY, proteinase A, proteinase B, alkaline phosphatase) and accumulation of small vacuole-related structures. Vam6p-GFP localizes to specific regions of vacuolar membranes.","method":"Chemical cross-linking, co-sedimentation in detergent-resistant fractions, GFP tagging/fluorescence microscopy, subcellular fractionation, genetic deletion with vacuolar protein processing assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal biochemical co-fractionation, chemical cross-linking, GFP localization, and functional genetic readouts all in one study","pmids":["9111041"],"is_preprint":false},{"year":2009,"finding":"Yeast Vam6/Vps39 functions as a guanine nucleotide exchange factor (GEF) for the Rag GTPase homolog Gtr1, loading it with GTP to activate the EGO complex (EGOC) and thereby stimulate TORC1 in response to amino acids. Constitutively GTP-bound Gtr1 interacted strongly with TORC1 and conferred partial resistance to leucine deprivation; GDP-bound Gtr1 caused constitutively low TORC1 activity.","method":"Genetic epistasis, dominant active/inactive Gtr1 mutants, co-immunoprecipitation (Gtr1-TORC1 interaction), TORC1 activity assays under amino-acid deprivation","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (Co-IP, dominant mutants, activity assays) in a single rigorous study, and independently corroborated by a concurrent commentary (PMID:19748348)","pmids":["19748353","19748348"],"is_preprint":false},{"year":2010,"finding":"Mammalian Vps39 (mVps39) induces lysosomal clustering but does NOT increase Rab7-GTP levels when overexpressed, and a dominant-negative mVps39 mutant fragments lysosomes and promotes growth-factor independence without decreasing Rab7-GTP. These data indicate mVps39 is NOT a Rab7 GEF in mammalian cells.","method":"Effector pull-down assay (RILP-Rab7 GTP binding), overexpression and dominant-negative mVps39, lysosomal morphology imaging, growth-factor withdrawal survival assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — effector pull-down plus morphological and survival readouts in a single lab study; negative finding robustly supported by multiple assays","pmids":["20363736"],"is_preprint":false},{"year":2012,"finding":"In fission yeast, Vam6 functions upstream of Gtr1-Gtr2 and upstream of TORC1 in the amino-acid-sensing pathway; epistasis analyses placed Vam6 → Gtr1/Gtr2 → TORC1 in a conserved signaling cascade controlling cell growth and sexual differentiation.","method":"Genetic epistasis (deletion mutants combined with constitutively active/inactive Gtr alleles), co-localization of Gtr1/Gtr2 with TORC1 at vacuoles","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis in fission yeast with co-localization support, single lab but consistent with budding yeast data","pmids":["22344254"],"is_preprint":false},{"year":2014,"finding":"Human Vps39 isoform hVps39-2/TRAP1 co-localizes with Rab5 and directly binds Rab5-GTP in vitro, identifying it as a Rab5 effector and suggesting it is the missing Vps3 subunit of a putative human CORVET complex. Neither human Vps39 isoform could complement loss of yeast Vps39.","method":"In vitro pull-down with Rab5-GTP, co-localization by fluorescence microscopy in yeast and HEK293 cells, yeast complementation assay","journal":"Cellular logistics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct in vitro binding and co-localization, single lab, two orthogonal methods","pmids":["25750764"],"is_preprint":false},{"year":2020,"finding":"Yeast Vps39 is required specifically for ethanolamine-stimulated elevation of mitochondrial phosphatidylethanolamine (PE). Deletion of VPS39 prevented mitochondrial PE accumulation without affecting ER PE biosynthesis or transport to other organelles. Vps39 abundance and its recruitment to mitochondria and ER are dependent on local PE levels. This function is independent of the HOPS and vCLAMP complexes, representing a distinct moonlighting role.","method":"Lipid mass spectrometry, genetic deletion of VPS39 vs. HOPS/vCLAMP subunits, subcellular fractionation to assess Vps39 recruitment to mitochondria/ER under varying PE conditions","journal":"Biochimica et biophysica acta. Molecular and cell biology of lipids","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — lipidomics plus fractionation and genetic dissection from HOPS/vCLAMP, single lab","pmids":["32058032"],"is_preprint":false},{"year":2020,"finding":"VPS39 (as a HOPS complex subunit) acts as a negative regulator of ciliogenesis in human renal cells by controlling the localization of IFT20 at the base of cilia through autophagy. This was confirmed in vivo in medaka fish renal tubules.","method":"VPS39 knockdown in human renal cells, IFT20 localization assay, ciliogenesis imaging, autophagy modulation, in vivo medaka fish model","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined cellular and in vivo phenotypic readouts plus autophagy mechanistic link; single lab","pmids":["32077937"],"is_preprint":false},{"year":2021,"finding":"VPS39 deficiency in human myoblasts impairs autophagic flux, alters insulin signaling, disrupts epigenetic enzyme activity and DNA methylation of myogenic regulators, and perturbs myoblast differentiation. Heterozygous Vps39+/- mice show reduced skeletal muscle glucose uptake. These effects mirror changes in myoblasts from individuals with type 2 diabetes.","method":"VPS39 siRNA knockdown in human myoblasts, autophagic flux assays, DNA methylation profiling, gene expression analysis, Vps39+/- mouse muscle glucose uptake assay","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal functional readouts (autophagy, epigenetics, differentiation, glucose uptake in mice), single lab","pmids":["33893273"],"is_preprint":false},{"year":2022,"finding":"SGPL1 upregulation stimulates VPS39 recruitment to mitochondria, enhancing mitochondria-lysosome membrane contact sites (MCS). VPS39 downregulation compromises mitochondrial network maintenance and basal autophagic flux in MICU1-deficient mammalian cells. In mouse-derived muscles, VPS39 recruitment to mitochondria is a signature of altered OXPHOS.","method":"Transcriptomics and proteomics in C. elegans micu-1 mutants, biochemical fractionation and imaging for VPS39 mitochondrial localization, VPS39 siRNA knockdown with mitochondrial morphology and autophagy flux assays in mammalian cells, mouse muscle tissue analysis","journal":"Molecular metabolism","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cross-species validation with biochemical, imaging, and functional readouts; single lab but multiple orthogonal methods","pmids":["35452878"],"is_preprint":false},{"year":2023,"finding":"ASFV protein CP204L interacts with VPS39, blocking VPS39's association with the lysosomal HOPS complex, which modulates endolysosomal trafficking and promotes lysosome clustering. CP204L and VPS39 are redirected to virus factories. Loss of VPS39 reduces early-phase viral protein synthesis and delays ASFV replication.","method":"Co-immunoprecipitation, co-localization imaging, VPS39 knockdown with viral replication assays, HOPS complex assembly assays","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus functional KD readout and localization, single lab, multiple orthogonal methods","pmids":["36722971"],"is_preprint":false},{"year":2023,"finding":"Vam6/VPS39 in iNKT cells is essential for formation of a Rab7a-Vam6-AMPK complex that recruits AMPK to lysosomes to activate it; AMPK then negatively regulates mTORC1. VDAC1 inhibits this complex formation at mitochondria-lysosome contact sites, and Vam6 relieves this inhibition.","method":"Co-immunoprecipitation (Rab7a-Vam6-AMPK complex), flow cytometry for mTORC1 activity, genetic Vam6 knockout mice, imaging of lysosomal AMPK recruitment, RNA sequencing","journal":"Frontiers in immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP of ternary complex, KO mouse model with functional mTORC1 readouts; single lab","pmids":["36741382"],"is_preprint":false},{"year":2020,"finding":"Crystal structure of the C-terminal proposed zinc-finger domain of VPS39 was solved, but it adopts a non-native fold (anti-parallel β-hairpin incorporated into a homotetrameric β-barrel stabilized by His-tag-coordinated zinc and an intramolecular disulphide), indicating this region does not form the predicted RING zinc finger under the purification conditions used.","method":"Recombinant protein expression, purification, X-ray crystallography","journal":"Wellcome open research","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — crystal structure determined but authors conclude the fold is non-native; single study with explicit caveat","pmids":["32724865"],"is_preprint":false},{"year":2025,"finding":"VPS39 regulates NPC2 trafficking (via CI-MPR/retromer) and BMP biosynthesis to control lysosomal cholesterol egress. SARS-CoV-2 ORF3a binds VPS39, trapping CI-MPR and retromer in endosomes/lysosomes to impair NPC2 delivery and reducing lysosome-mitochondrion MCS, which decreases mitochondrial phosphatidylglycerol transfer needed for BMP synthesis. VPS39 deletion recapitulates both defects.","method":"Co-IP (ORF3a-VPS39 interaction), lipidomics (BMP and PG levels), proteomics, retromer/VPS39 deletion with cholesterol trafficking assays, MCS quantification by imaging","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, lipidomics, proteomics, genetic deletion) in single preprint lab study; not yet peer-reviewed","pmids":["39605369"],"is_preprint":true},{"year":2010,"finding":"VPS39-deficient mice die before embryonic day E6.5, demonstrating that VPS39 is non-redundantly essential for early embryonic development. Heterozygous mice show no overt phenotype.","method":"Genetic knockout mouse generation, embryonic lethality analysis","journal":"Immunobiology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean KO with defined developmental phenotype, single lab, limited mechanistic detail beyond essentiality","pmids":["20961651"],"is_preprint":false}],"current_model":"VPS39/Vam6 is a multifunctional subunit of the HOPS tethering complex that localizes to vacuolar/lysosomal membranes where it physically interacts with Vam2/Vps41 to mediate vacuole fusion and endolysosomal protein sorting; it additionally functions as a GEF for the Rag-family GTPase Gtr1 to activate TORC1 in response to amino acids, acts as part of the vCLAMP membrane contact site to facilitate phosphatidylethanolamine and BMP lipid transfer to mitochondria, scaffolds a Rab7a-AMPK complex at lysosomes to regulate mTORC1 negatively, and controls autophagic flux and ciliogenesis—while in mammalian cells it does not serve as a Rab7 GEF despite its yeast counterpart's role in Ypt7 regulation."},"narrative":{"mechanistic_narrative":"VPS39 is a membrane-tethering and trafficking scaffold that operates at the heart of endolysosomal sorting, organelle contact-site biology, and nutrient-sensing signaling [PMID:9111041, PMID:19748353, PMID:19748348]. It was first defined in yeast as a subunit of a large vacuolar-membrane protein complex, where it physically associates with Vam2/Vps41 and is required for vacuolar protein sorting and vacuole biogenesis [PMID:9111041]. Beyond tethering, yeast Vps39 acts as a guanine nucleotide exchange factor for the Rag-family GTPase Gtr1, loading it with GTP to activate the EGO complex and thereby stimulate TORC1 in response to amino acids, placing Vps39 upstream of Gtr1/Gtr2 → TORC1 in a conserved growth-control cascade [PMID:19748353, PMID:19748348, PMID:22344254]. In mammalian cells VPS39 retains its lysosomal tethering role as a HOPS subunit but does not function as a Rab7 GEF, and a human isoform instead binds Rab5-GTP as a Rab5 effector [PMID:20363736, PMID:25750764]. VPS39 additionally functions at mitochondria-lysosome membrane contact sites, where its recruitment supports phospholipid transfer—mitochondrial phosphatidylethanolamine accumulation in yeast and BMP biosynthesis and lysosomal cholesterol egress in mammalian cells—and maintains mitochondrial network integrity and basal autophagic flux [PMID:32058032, PMID:35452878, PMID:39605369]. Through control of autophagy it negatively regulates ciliogenesis by governing IFT20 localization, and in iNKT cells it nucleates a Rab7a-Vam6-AMPK complex that recruits AMPK to lysosomes to negatively regulate mTORC1 [PMID:32077937, PMID:36741382]. VPS39 loss impairs autophagic flux, alters insulin signaling and myoblast differentiation, and reduces skeletal muscle glucose uptake, and the gene is non-redundantly essential for early mouse embryonic development [PMID:33893273, PMID:20961651]. Viral proteins from ASFV and SARS-CoV-2 hijack VPS39 to disrupt HOPS association and endolysosomal trafficking [PMID:36722971, PMID:39605369].","teleology":[{"year":1997,"claim":"Established VPS39 as a physical component of a vacuolar-membrane tethering complex, answering whether it acts at vacuoles and with which partner.","evidence":"Chemical cross-linking, co-sedimentation, GFP localization, and vacuolar protein-sorting assays in yeast","pmids":["9111041"],"confidence":"High","gaps":["Stoichiometry and architecture of the complex not resolved","Did not address signaling or non-tethering roles"]},{"year":2009,"claim":"Revealed an unexpected enzymatic function beyond tethering—VPS39/Vam6 as a GEF for Gtr1 that activates TORC1 in response to amino acids.","evidence":"Genetic epistasis, dominant Gtr1 mutants, Co-IP, and TORC1 activity assays under amino-acid deprivation in budding yeast","pmids":["19748353","19748348"],"confidence":"High","gaps":["Whether the GEF role is conserved in mammals not tested here","Structural basis of Gtr1 nucleotide exchange unresolved"]},{"year":2010,"claim":"Showed mammalian VPS39 diverges from its yeast counterpart by not acting as a Rab7 GEF, redefining its mammalian role at lysosomes.","evidence":"RILP-Rab7 effector pull-down, overexpression and dominant-negative VPS39, lysosomal morphology and growth-factor withdrawal assays","pmids":["20363736"],"confidence":"Medium","gaps":["Mechanism of lysosomal clustering not defined","Identity of the relevant mammalian GTPase regulator left open"]},{"year":2010,"claim":"Demonstrated VPS39 is non-redundantly required for early mammalian development.","evidence":"Genetic knockout mouse with embryonic lethality analysis","pmids":["20961651"],"confidence":"Medium","gaps":["Cellular cause of E6.5 lethality not determined","No conditional/tissue-specific dissection of essential function"]},{"year":2012,"claim":"Confirmed the Vam6 → Gtr1/Gtr2 → TORC1 cascade is conserved across yeasts, supporting a deeply conserved nutrient-sensing role.","evidence":"Genetic epistasis and Gtr1/Gtr2-TORC1 co-localization in fission yeast","pmids":["22344254"],"confidence":"Medium","gaps":["Direct biochemical GEF activity not re-demonstrated in this system","Mammalian conservation still untested"]},{"year":2014,"claim":"Identified a human VPS39 isoform as a Rab5 effector, proposing it as a CORVET subunit and showing functional divergence from yeast.","evidence":"In vitro Rab5-GTP pull-down, co-localization in yeast and HEK293, and failed yeast complementation","pmids":["25750764"],"confidence":"Medium","gaps":["Composition of a human CORVET complex not biochemically reconstituted","Functional consequence of Rab5 binding in cells not defined"]},{"year":2020,"claim":"Uncovered a HOPS/vCLAMP-independent moonlighting role for VPS39 in mitochondrial phosphatidylethanolamine accumulation, linking it to interorganelle lipid transfer.","evidence":"Lipid mass spectrometry, VPS39 vs HOPS/vCLAMP deletions, and PE-dependent fractionation in yeast","pmids":["32058032"],"confidence":"Medium","gaps":["Molecular mechanism of PE transfer not resolved","Whether VPS39 carries lipid directly or recruits transfer machinery unknown"]},{"year":2020,"claim":"Connected VPS39 to negative control of ciliogenesis through autophagy-dependent regulation of IFT20.","evidence":"VPS39 knockdown in human renal cells, IFT20 localization and ciliogenesis imaging, and in vivo medaka model","pmids":["32077937"],"confidence":"Medium","gaps":["Direct link between HOPS tethering and IFT20 turnover not established","Whether effect is cell-type specific unclear"]},{"year":2020,"claim":"Tested the predicted VPS39 C-terminal RING zinc finger, finding it does not adopt the expected fold under the conditions used.","evidence":"Recombinant expression, purification, and X-ray crystallography","pmids":["32724865"],"confidence":"Medium","gaps":["Non-native fold attributed to His-tag and disulphide; native structure unresolved","Functional role of this domain unknown"]},{"year":2021,"claim":"Linked VPS39 deficiency to impaired autophagy, altered insulin signaling, epigenetic dysregulation, and reduced muscle glucose uptake, implicating it in metabolic disease.","evidence":"VPS39 siRNA in human myoblasts, autophagic flux and DNA methylation assays, and Vps39+/- mouse muscle glucose uptake","pmids":["33893273"],"confidence":"Medium","gaps":["Causal chain from autophagy defect to epigenetic change not dissected","Direct VPS39 effector for insulin signaling not identified"]},{"year":2022,"claim":"Established VPS39 recruitment to mitochondria as a regulator of mitochondria-lysosome contact sites controlling mitochondrial network and autophagic flux.","evidence":"Cross-species transcriptomics/proteomics, fractionation and imaging of mitochondrial VPS39, and siRNA knockdown with morphology/flux assays","pmids":["35452878"],"confidence":"Medium","gaps":["Trigger for SGPL1-driven recruitment mechanism incompletely defined","Direct tethering partners at the contact site not mapped"]},{"year":2023,"claim":"Showed ASFV CP204L sequesters VPS39 away from HOPS to reprogram endolysosomal trafficking for viral replication.","evidence":"Co-IP, co-localization, and VPS39 knockdown viral replication assays","pmids":["36722971"],"confidence":"Medium","gaps":["Binding interface on VPS39 not mapped","Reciprocal validation of HOPS displacement limited"]},{"year":2023,"claim":"Defined a Rab7a-Vam6-AMPK complex through which VPS39 recruits AMPK to lysosomes to negatively regulate mTORC1, with VDAC1 as an antagonist.","evidence":"Co-IP of the ternary complex, Vam6 knockout mice, flow cytometry for mTORC1 activity, and lysosomal AMPK imaging in iNKT cells","pmids":["36741382"],"confidence":"Medium","gaps":["Direct binding topology within the ternary complex not resolved","Generality beyond iNKT cells untested"]},{"year":2025,"claim":"Connected VPS39 to lysosomal cholesterol egress via NPC2/retromer trafficking and BMP biosynthesis, and identified SARS-CoV-2 ORF3a as a hijacker of this function.","evidence":"Co-IP, lipidomics, proteomics, and retromer/VPS39 deletion with cholesterol trafficking and MCS imaging (preprint)","pmids":["39605369"],"confidence":"Medium","gaps":["Not yet peer-reviewed","Direct vs indirect role in NPC2 sorting not fully separated"]},{"year":null,"claim":"Whether mammalian VPS39 possesses any GEF/effector enzymatic activity analogous to its yeast Gtr1 role, and how a single scaffold coordinates HOPS tethering, contact-site lipid transfer, and nutrient signaling, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No demonstrated mammalian GEF substrate","Structural basis for partitioning between distinct complexes unknown","How the same protein switches between vacuolar/lysosomal, mitochondrial, and signaling roles undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,3]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,10]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[0,2,10]},{"term_id":"GO:0005773","term_label":"vacuole","supporting_discovery_ids":[0]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[5,8]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[4,12]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,9]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[6,7,8]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1,10]}],"complexes":["HOPS complex","EGO complex (EGOC)","Rab7a-Vam6-AMPK complex","vCLAMP"],"partners":["VPS41","GTR1","RAB5","RAB7A","AMPK","VDAC1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96JC1","full_name":"Vam6/Vps39-like protein","aliases":["TRAP1-like protein","hVam6p"],"length_aa":886,"mass_kda":101.8,"function":"Regulator of TGF-beta/activin signaling, inhibiting SMAD3- and activating SMAD2-dependent transcription. Acts by interfering with SMAD3/SMAD4 complex formation, this would lead to inhibition of SMAD3-dependent transcription and relieve SMAD3 inhibition of SMAD2-dependent promoters, thus increasing SMAD2-dependent transcription. Does not affect TGF-beta-induced SMAD2 or SMAD3 phosphorylation, nor SMAD2/SMAD4 complex formation Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Acts as a component of the HOPS endosomal tethering complex. This complex is proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE-mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes (PubMed:23351085). Involved in homotypic vesicle fusions between late endosomes and in heterotypic fusions between late endosomes and lysosomes (PubMed:11448994, PubMed:23167963, PubMed:23351085). Required for fusion of endosomes and autophagosomes with lysosomes (PubMed:25783203, PubMed:37821429)","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q96JC1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/VPS39","classification":"Not Classified","n_dependent_lines":200,"n_total_lines":1208,"dependency_fraction":0.16556291390728478},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000166887","cell_line_id":"CID001861","localizations":[{"compartment":"vesicles","grade":3},{"compartment":"cytoplasmic","grade":2}],"interactors":[{"gene":"RBM25","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001861","total_profiled":1310},"omim":[{"mim_id":"612188","title":"VPS39 SUBUNIT OF HOPS COMPLEX; VPS39","url":"https://www.omim.org/entry/612188"},{"mim_id":"610034","title":"VPS33A CORE SUBUNIT OF CORVET AND HOPS COMPLEXES; VPS33A","url":"https://www.omim.org/entry/610034"},{"mim_id":"608549","title":"VPS11 CORE SUBUNIT OF CORVET AND HOPS COMPLEXES; VPS11","url":"https://www.omim.org/entry/608549"},{"mim_id":"607623","title":"NPC INTRACELLULAR CHOLESTEROL TRANSPORTER 1; NPC1","url":"https://www.omim.org/entry/607623"},{"mim_id":"605419","title":"SCHIZOPHRENIA 10; SCZD10","url":"https://www.omim.org/entry/605419"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/VPS39"},"hgnc":{"alias_symbol":["KIAA0770","VAM6"],"prev_symbol":[]},"alphafold":{"accession":"Q96JC1","domains":[{"cath_id":"-","chopping":"2-46_257-311","consensus_level":"medium","plddt":90.9327,"start":2,"end":311}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JC1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JC1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96JC1-F1-predicted_aligned_error_v6.png","plddt_mean":88.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=VPS39","jax_strain_url":"https://www.jax.org/strain/search?query=VPS39"},"sequence":{"accession":"Q96JC1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96JC1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96JC1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96JC1"}},"corpus_meta":[{"pmid":"19748353","id":"PMC_19748353","title":"The Vam6 GEF controls TORC1 by activating the EGO complex.","date":"2009","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/19748353","citation_count":361,"is_preprint":false},{"pmid":"9111041","id":"PMC_9111041","title":"Vam2/Vps41p and Vam6/Vps39p are components of a protein complex on the vacuolar membranes and involved in the vacuolar assembly in the yeast Saccharomyces cerevisiae.","date":"1997","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9111041","citation_count":144,"is_preprint":false},{"pmid":"20363736","id":"PMC_20363736","title":"Differential effects of TBC1D15 and mammalian Vps39 on Rab7 activation state, lysosomal morphology, and growth factor dependence.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20363736","citation_count":102,"is_preprint":false},{"pmid":"22344254","id":"PMC_22344254","title":"The Vam6 and Gtr1-Gtr2 pathway activates TORC1 in response to amino acids in fission yeast.","date":"2012","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/22344254","citation_count":54,"is_preprint":false},{"pmid":"18077594","id":"PMC_18077594","title":"The zebrafish mutant lbk/vam6 resembles human multisystemic disorders caused by aberrant trafficking of endosomal vesicles.","date":"2007","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/18077594","citation_count":47,"is_preprint":false},{"pmid":"33893273","id":"PMC_33893273","title":"VPS39-deficiency observed in type 2 diabetes impairs muscle stem cell differentiation via altered autophagy and epigenetics.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33893273","citation_count":33,"is_preprint":false},{"pmid":"20961651","id":"PMC_20961651","title":"The TGF-β signaling modulators TRAP1/TGFBRAP1 and VPS39/Vam6/TLP are essential for early embryonic development.","date":"2010","source":"Immunobiology","url":"https://pubmed.ncbi.nlm.nih.gov/20961651","citation_count":32,"is_preprint":false},{"pmid":"25750764","id":"PMC_25750764","title":"The Vps39-like TRAP1 is an effector of Rab5 and likely the missing Vps3 subunit of human CORVET.","date":"2014","source":"Cellular logistics","url":"https://pubmed.ncbi.nlm.nih.gov/25750764","citation_count":25,"is_preprint":false},{"pmid":"32077937","id":"PMC_32077937","title":"The HOPS complex subunit VPS39 controls ciliogenesis through autophagy.","date":"2020","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32077937","citation_count":20,"is_preprint":false},{"pmid":"36722971","id":"PMC_36722971","title":"CP204L Is a Multifunctional Protein of African Swine Fever Virus That Interacts with the VPS39 Subunit of the Homotypic Fusion and Vacuole Protein Sorting Complex and Promotes Lysosome Clustering.","date":"2023","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/36722971","citation_count":16,"is_preprint":false},{"pmid":"32058032","id":"PMC_32058032","title":"Vps39 is required for ethanolamine-stimulated elevation in mitochondrial phosphatidylethanolamine.","date":"2020","source":"Biochimica et biophysica acta. 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Vacuole and Mitochondria Patch (vCLAMP) Protein Vam6 Is Involved in Maintenance of Mitochondrial and Vacuolar Functions Under Oxidative Stress in Candida albicans. Antioxidants 2021, 10, 136.","date":"2026","source":"Antioxidants (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/41897552","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13454,"output_tokens":3798,"usd":0.048666,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11465,"output_tokens":4422,"usd":0.083937,"stage2_stop_reason":"end_turn"},"total_usd":0.132603,"stage1_batch_id":"msgbatch_01UT1AahFPCAyn2uVweS7A9z","stage2_batch_id":"msgbatch_01HuKWtKNT4Pqj1bc8eEP5RV","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1997,\n      \"finding\": \"Vam6p/Vps39p physically interacts with Vam2p/Vps41p and both are components of a large protein complex on vacuolar membranes; loss of either protein results in defective vacuolar protein sorting (CPY, proteinase A, proteinase B, alkaline phosphatase) and accumulation of small vacuole-related structures. Vam6p-GFP localizes to specific regions of vacuolar membranes.\",\n      \"method\": \"Chemical cross-linking, co-sedimentation in detergent-resistant fractions, GFP tagging/fluorescence microscopy, subcellular fractionation, genetic deletion with vacuolar protein processing assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal biochemical co-fractionation, chemical cross-linking, GFP localization, and functional genetic readouts all in one study\",\n      \"pmids\": [\"9111041\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Yeast Vam6/Vps39 functions as a guanine nucleotide exchange factor (GEF) for the Rag GTPase homolog Gtr1, loading it with GTP to activate the EGO complex (EGOC) and thereby stimulate TORC1 in response to amino acids. Constitutively GTP-bound Gtr1 interacted strongly with TORC1 and conferred partial resistance to leucine deprivation; GDP-bound Gtr1 caused constitutively low TORC1 activity.\",\n      \"method\": \"Genetic epistasis, dominant active/inactive Gtr1 mutants, co-immunoprecipitation (Gtr1-TORC1 interaction), TORC1 activity assays under amino-acid deprivation\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (Co-IP, dominant mutants, activity assays) in a single rigorous study, and independently corroborated by a concurrent commentary (PMID:19748348)\",\n      \"pmids\": [\"19748353\", \"19748348\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Mammalian Vps39 (mVps39) induces lysosomal clustering but does NOT increase Rab7-GTP levels when overexpressed, and a dominant-negative mVps39 mutant fragments lysosomes and promotes growth-factor independence without decreasing Rab7-GTP. These data indicate mVps39 is NOT a Rab7 GEF in mammalian cells.\",\n      \"method\": \"Effector pull-down assay (RILP-Rab7 GTP binding), overexpression and dominant-negative mVps39, lysosomal morphology imaging, growth-factor withdrawal survival assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — effector pull-down plus morphological and survival readouts in a single lab study; negative finding robustly supported by multiple assays\",\n      \"pmids\": [\"20363736\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"In fission yeast, Vam6 functions upstream of Gtr1-Gtr2 and upstream of TORC1 in the amino-acid-sensing pathway; epistasis analyses placed Vam6 → Gtr1/Gtr2 → TORC1 in a conserved signaling cascade controlling cell growth and sexual differentiation.\",\n      \"method\": \"Genetic epistasis (deletion mutants combined with constitutively active/inactive Gtr alleles), co-localization of Gtr1/Gtr2 with TORC1 at vacuoles\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis in fission yeast with co-localization support, single lab but consistent with budding yeast data\",\n      \"pmids\": [\"22344254\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Human Vps39 isoform hVps39-2/TRAP1 co-localizes with Rab5 and directly binds Rab5-GTP in vitro, identifying it as a Rab5 effector and suggesting it is the missing Vps3 subunit of a putative human CORVET complex. Neither human Vps39 isoform could complement loss of yeast Vps39.\",\n      \"method\": \"In vitro pull-down with Rab5-GTP, co-localization by fluorescence microscopy in yeast and HEK293 cells, yeast complementation assay\",\n      \"journal\": \"Cellular logistics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct in vitro binding and co-localization, single lab, two orthogonal methods\",\n      \"pmids\": [\"25750764\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Yeast Vps39 is required specifically for ethanolamine-stimulated elevation of mitochondrial phosphatidylethanolamine (PE). Deletion of VPS39 prevented mitochondrial PE accumulation without affecting ER PE biosynthesis or transport to other organelles. Vps39 abundance and its recruitment to mitochondria and ER are dependent on local PE levels. This function is independent of the HOPS and vCLAMP complexes, representing a distinct moonlighting role.\",\n      \"method\": \"Lipid mass spectrometry, genetic deletion of VPS39 vs. HOPS/vCLAMP subunits, subcellular fractionation to assess Vps39 recruitment to mitochondria/ER under varying PE conditions\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular and cell biology of lipids\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — lipidomics plus fractionation and genetic dissection from HOPS/vCLAMP, single lab\",\n      \"pmids\": [\"32058032\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"VPS39 (as a HOPS complex subunit) acts as a negative regulator of ciliogenesis in human renal cells by controlling the localization of IFT20 at the base of cilia through autophagy. This was confirmed in vivo in medaka fish renal tubules.\",\n      \"method\": \"VPS39 knockdown in human renal cells, IFT20 localization assay, ciliogenesis imaging, autophagy modulation, in vivo medaka fish model\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined cellular and in vivo phenotypic readouts plus autophagy mechanistic link; single lab\",\n      \"pmids\": [\"32077937\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"VPS39 deficiency in human myoblasts impairs autophagic flux, alters insulin signaling, disrupts epigenetic enzyme activity and DNA methylation of myogenic regulators, and perturbs myoblast differentiation. Heterozygous Vps39+/- mice show reduced skeletal muscle glucose uptake. These effects mirror changes in myoblasts from individuals with type 2 diabetes.\",\n      \"method\": \"VPS39 siRNA knockdown in human myoblasts, autophagic flux assays, DNA methylation profiling, gene expression analysis, Vps39+/- mouse muscle glucose uptake assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal functional readouts (autophagy, epigenetics, differentiation, glucose uptake in mice), single lab\",\n      \"pmids\": [\"33893273\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SGPL1 upregulation stimulates VPS39 recruitment to mitochondria, enhancing mitochondria-lysosome membrane contact sites (MCS). VPS39 downregulation compromises mitochondrial network maintenance and basal autophagic flux in MICU1-deficient mammalian cells. In mouse-derived muscles, VPS39 recruitment to mitochondria is a signature of altered OXPHOS.\",\n      \"method\": \"Transcriptomics and proteomics in C. elegans micu-1 mutants, biochemical fractionation and imaging for VPS39 mitochondrial localization, VPS39 siRNA knockdown with mitochondrial morphology and autophagy flux assays in mammalian cells, mouse muscle tissue analysis\",\n      \"journal\": \"Molecular metabolism\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cross-species validation with biochemical, imaging, and functional readouts; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"35452878\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ASFV protein CP204L interacts with VPS39, blocking VPS39's association with the lysosomal HOPS complex, which modulates endolysosomal trafficking and promotes lysosome clustering. CP204L and VPS39 are redirected to virus factories. Loss of VPS39 reduces early-phase viral protein synthesis and delays ASFV replication.\",\n      \"method\": \"Co-immunoprecipitation, co-localization imaging, VPS39 knockdown with viral replication assays, HOPS complex assembly assays\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus functional KD readout and localization, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"36722971\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Vam6/VPS39 in iNKT cells is essential for formation of a Rab7a-Vam6-AMPK complex that recruits AMPK to lysosomes to activate it; AMPK then negatively regulates mTORC1. VDAC1 inhibits this complex formation at mitochondria-lysosome contact sites, and Vam6 relieves this inhibition.\",\n      \"method\": \"Co-immunoprecipitation (Rab7a-Vam6-AMPK complex), flow cytometry for mTORC1 activity, genetic Vam6 knockout mice, imaging of lysosomal AMPK recruitment, RNA sequencing\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP of ternary complex, KO mouse model with functional mTORC1 readouts; single lab\",\n      \"pmids\": [\"36741382\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Crystal structure of the C-terminal proposed zinc-finger domain of VPS39 was solved, but it adopts a non-native fold (anti-parallel β-hairpin incorporated into a homotetrameric β-barrel stabilized by His-tag-coordinated zinc and an intramolecular disulphide), indicating this region does not form the predicted RING zinc finger under the purification conditions used.\",\n      \"method\": \"Recombinant protein expression, purification, X-ray crystallography\",\n      \"journal\": \"Wellcome open research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — crystal structure determined but authors conclude the fold is non-native; single study with explicit caveat\",\n      \"pmids\": [\"32724865\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"VPS39 regulates NPC2 trafficking (via CI-MPR/retromer) and BMP biosynthesis to control lysosomal cholesterol egress. SARS-CoV-2 ORF3a binds VPS39, trapping CI-MPR and retromer in endosomes/lysosomes to impair NPC2 delivery and reducing lysosome-mitochondrion MCS, which decreases mitochondrial phosphatidylglycerol transfer needed for BMP synthesis. VPS39 deletion recapitulates both defects.\",\n      \"method\": \"Co-IP (ORF3a-VPS39 interaction), lipidomics (BMP and PG levels), proteomics, retromer/VPS39 deletion with cholesterol trafficking assays, MCS quantification by imaging\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, lipidomics, proteomics, genetic deletion) in single preprint lab study; not yet peer-reviewed\",\n      \"pmids\": [\"39605369\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"VPS39-deficient mice die before embryonic day E6.5, demonstrating that VPS39 is non-redundantly essential for early embryonic development. Heterozygous mice show no overt phenotype.\",\n      \"method\": \"Genetic knockout mouse generation, embryonic lethality analysis\",\n      \"journal\": \"Immunobiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean KO with defined developmental phenotype, single lab, limited mechanistic detail beyond essentiality\",\n      \"pmids\": [\"20961651\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"VPS39/Vam6 is a multifunctional subunit of the HOPS tethering complex that localizes to vacuolar/lysosomal membranes where it physically interacts with Vam2/Vps41 to mediate vacuole fusion and endolysosomal protein sorting; it additionally functions as a GEF for the Rag-family GTPase Gtr1 to activate TORC1 in response to amino acids, acts as part of the vCLAMP membrane contact site to facilitate phosphatidylethanolamine and BMP lipid transfer to mitochondria, scaffolds a Rab7a-AMPK complex at lysosomes to regulate mTORC1 negatively, and controls autophagic flux and ciliogenesis—while in mammalian cells it does not serve as a Rab7 GEF despite its yeast counterpart's role in Ypt7 regulation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"VPS39 is a membrane-tethering and trafficking scaffold that operates at the heart of endolysosomal sorting, organelle contact-site biology, and nutrient-sensing signaling [#0, #1]. It was first defined in yeast as a subunit of a large vacuolar-membrane protein complex, where it physically associates with Vam2/Vps41 and is required for vacuolar protein sorting and vacuole biogenesis [#0]. Beyond tethering, yeast Vps39 acts as a guanine nucleotide exchange factor for the Rag-family GTPase Gtr1, loading it with GTP to activate the EGO complex and thereby stimulate TORC1 in response to amino acids, placing Vps39 upstream of Gtr1/Gtr2 \\u2192 TORC1 in a conserved growth-control cascade [#1, #3]. In mammalian cells VPS39 retains its lysosomal tethering role as a HOPS subunit but does not function as a Rab7 GEF, and a human isoform instead binds Rab5-GTP as a Rab5 effector [#2, #4]. VPS39 additionally functions at mitochondria-lysosome membrane contact sites, where its recruitment supports phospholipid transfer\\u2014mitochondrial phosphatidylethanolamine accumulation in yeast and BMP biosynthesis and lysosomal cholesterol egress in mammalian cells\\u2014and maintains mitochondrial network integrity and basal autophagic flux [#5, #8, #12]. Through control of autophagy it negatively regulates ciliogenesis by governing IFT20 localization, and in iNKT cells it nucleates a Rab7a-Vam6-AMPK complex that recruits AMPK to lysosomes to negatively regulate mTORC1 [#6, #10]. VPS39 loss impairs autophagic flux, alters insulin signaling and myoblast differentiation, and reduces skeletal muscle glucose uptake, and the gene is non-redundantly essential for early mouse embryonic development [#7, #13]. Viral proteins from ASFV and SARS-CoV-2 hijack VPS39 to disrupt HOPS association and endolysosomal trafficking [#9, #12].\",\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Established VPS39 as a physical component of a vacuolar-membrane tethering complex, answering whether it acts at vacuoles and with which partner.\",\n      \"evidence\": \"Chemical cross-linking, co-sedimentation, GFP localization, and vacuolar protein-sorting assays in yeast\",\n      \"pmids\": [\"9111041\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and architecture of the complex not resolved\", \"Did not address signaling or non-tethering roles\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Revealed an unexpected enzymatic function beyond tethering\\u2014VPS39/Vam6 as a GEF for Gtr1 that activates TORC1 in response to amino acids.\",\n      \"evidence\": \"Genetic epistasis, dominant Gtr1 mutants, Co-IP, and TORC1 activity assays under amino-acid deprivation in budding yeast\",\n      \"pmids\": [\"19748353\", \"19748348\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the GEF role is conserved in mammals not tested here\", \"Structural basis of Gtr1 nucleotide exchange unresolved\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Showed mammalian VPS39 diverges from its yeast counterpart by not acting as a Rab7 GEF, redefining its mammalian role at lysosomes.\",\n      \"evidence\": \"RILP-Rab7 effector pull-down, overexpression and dominant-negative VPS39, lysosomal morphology and growth-factor withdrawal assays\",\n      \"pmids\": [\"20363736\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of lysosomal clustering not defined\", \"Identity of the relevant mammalian GTPase regulator left open\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Demonstrated VPS39 is non-redundantly required for early mammalian development.\",\n      \"evidence\": \"Genetic knockout mouse with embryonic lethality analysis\",\n      \"pmids\": [\"20961651\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cellular cause of E6.5 lethality not determined\", \"No conditional/tissue-specific dissection of essential function\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Confirmed the Vam6 \\u2192 Gtr1/Gtr2 \\u2192 TORC1 cascade is conserved across yeasts, supporting a deeply conserved nutrient-sensing role.\",\n      \"evidence\": \"Genetic epistasis and Gtr1/Gtr2-TORC1 co-localization in fission yeast\",\n      \"pmids\": [\"22344254\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical GEF activity not re-demonstrated in this system\", \"Mammalian conservation still untested\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Identified a human VPS39 isoform as a Rab5 effector, proposing it as a CORVET subunit and showing functional divergence from yeast.\",\n      \"evidence\": \"In vitro Rab5-GTP pull-down, co-localization in yeast and HEK293, and failed yeast complementation\",\n      \"pmids\": [\"25750764\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Composition of a human CORVET complex not biochemically reconstituted\", \"Functional consequence of Rab5 binding in cells not defined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Uncovered a HOPS/vCLAMP-independent moonlighting role for VPS39 in mitochondrial phosphatidylethanolamine accumulation, linking it to interorganelle lipid transfer.\",\n      \"evidence\": \"Lipid mass spectrometry, VPS39 vs HOPS/vCLAMP deletions, and PE-dependent fractionation in yeast\",\n      \"pmids\": [\"32058032\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism of PE transfer not resolved\", \"Whether VPS39 carries lipid directly or recruits transfer machinery unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Connected VPS39 to negative control of ciliogenesis through autophagy-dependent regulation of IFT20.\",\n      \"evidence\": \"VPS39 knockdown in human renal cells, IFT20 localization and ciliogenesis imaging, and in vivo medaka model\",\n      \"pmids\": [\"32077937\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct link between HOPS tethering and IFT20 turnover not established\", \"Whether effect is cell-type specific unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Tested the predicted VPS39 C-terminal RING zinc finger, finding it does not adopt the expected fold under the conditions used.\",\n      \"evidence\": \"Recombinant expression, purification, and X-ray crystallography\",\n      \"pmids\": [\"32724865\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Non-native fold attributed to His-tag and disulphide; native structure unresolved\", \"Functional role of this domain unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linked VPS39 deficiency to impaired autophagy, altered insulin signaling, epigenetic dysregulation, and reduced muscle glucose uptake, implicating it in metabolic disease.\",\n      \"evidence\": \"VPS39 siRNA in human myoblasts, autophagic flux and DNA methylation assays, and Vps39+/- mouse muscle glucose uptake\",\n      \"pmids\": [\"33893273\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal chain from autophagy defect to epigenetic change not dissected\", \"Direct VPS39 effector for insulin signaling not identified\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Established VPS39 recruitment to mitochondria as a regulator of mitochondria-lysosome contact sites controlling mitochondrial network and autophagic flux.\",\n      \"evidence\": \"Cross-species transcriptomics/proteomics, fractionation and imaging of mitochondrial VPS39, and siRNA knockdown with morphology/flux assays\",\n      \"pmids\": [\"35452878\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Trigger for SGPL1-driven recruitment mechanism incompletely defined\", \"Direct tethering partners at the contact site not mapped\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed ASFV CP204L sequesters VPS39 away from HOPS to reprogram endolysosomal trafficking for viral replication.\",\n      \"evidence\": \"Co-IP, co-localization, and VPS39 knockdown viral replication assays\",\n      \"pmids\": [\"36722971\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding interface on VPS39 not mapped\", \"Reciprocal validation of HOPS displacement limited\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined a Rab7a-Vam6-AMPK complex through which VPS39 recruits AMPK to lysosomes to negatively regulate mTORC1, with VDAC1 as an antagonist.\",\n      \"evidence\": \"Co-IP of the ternary complex, Vam6 knockout mice, flow cytometry for mTORC1 activity, and lysosomal AMPK imaging in iNKT cells\",\n      \"pmids\": [\"36741382\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding topology within the ternary complex not resolved\", \"Generality beyond iNKT cells untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected VPS39 to lysosomal cholesterol egress via NPC2/retromer trafficking and BMP biosynthesis, and identified SARS-CoV-2 ORF3a as a hijacker of this function.\",\n      \"evidence\": \"Co-IP, lipidomics, proteomics, and retromer/VPS39 deletion with cholesterol trafficking and MCS imaging (preprint)\",\n      \"pmids\": [\"39605369\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Not yet peer-reviewed\", \"Direct vs indirect role in NPC2 sorting not fully separated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether mammalian VPS39 possesses any GEF/effector enzymatic activity analogous to its yeast Gtr1 role, and how a single scaffold coordinates HOPS tethering, contact-site lipid transfer, and nutrient signaling, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No demonstrated mammalian GEF substrate\", \"Structural basis for partitioning between distinct complexes unknown\", \"How the same protein switches between vacuolar/lysosomal, mitochondrial, and signaling roles undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [0, 2, 10]},\n      {\"term_id\": \"GO:0005773\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [5, 8]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [4, 12]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 9]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [6, 7, 8]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 10]}\n    ],\n    \"complexes\": [\"HOPS complex\", \"EGO complex (EGOC)\", \"Rab7a-Vam6-AMPK complex\", \"vCLAMP\"],\n    \"partners\": [\"VPS41\", \"GTR1\", \"RAB5\", \"RAB7A\", \"AMPK\", \"VDAC1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}