{"gene":"VPS16","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":1993,"finding":"Yeast Vps16p associates with a sedimentable particulate protein complex; this association is resistant to detergent and salt extraction but can be disrupted by 6 M urea or alkali buffer, indicating tight integration into a large protein complex. Loss of VPS16 causes severe defects in vacuolar protein sorting and grossly abnormal vacuole morphology.","method":"Subcellular fractionation, gene disruption, biochemical extraction","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — subcellular fractionation and gene disruption with defined phenotypic readouts, single lab, two orthogonal methods","pmids":["8444873"],"is_preprint":false},{"year":1999,"finding":"Yeast Vps16p functions as an inhibitor of the mRNA decapping enzyme Dcp1p; mutations in VPS16 reduce decapping activity in vitro and stabilize mRNAs in vivo. Extracts from vps16 mutant strains inhibit purified Flag-Dcp1p activity, and Vps16p mutations enhance the interaction of Dcp1p with the Hsp70 family member Ssa1p/2p.","method":"In vitro decapping assay, mRNA stability assay in vivo, co-purification with Flag-Dcp1p","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro enzymatic assay plus in vivo mRNA stability measurement, single lab, two orthogonal methods","pmids":["10523645"],"is_preprint":false},{"year":2001,"finding":"Human VPS16 is the homolog of yeast class C VPS16, and like its yeast counterpart is predicted to function in lysosomal protein delivery as part of the class C VPS complex.","method":"Molecular cloning, sequence analysis, expression analysis","journal":"Gene","confidence":"Low","confidence_rationale":"Tier 4 / Weak — sequence/expression characterization only, no functional experiment on the human protein","pmids":["11250079"],"is_preprint":false},{"year":2003,"finding":"Mouse Vps16 (mVps16) interacts with multiple syntaxins and with Vps45p in mammalian cells; the mammalian class C VPS complex localizes to endosomal compartments. Overexpression of mammalian class C VPS proteins does not affect transferrin internalization but inhibits transferrin recycling.","method":"Co-immunoprecipitation, Western blot, transferrin trafficking assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — co-IP for binding partners plus functional transferrin recycling assay, single lab, two methods","pmids":["14623309"],"is_preprint":false},{"year":2013,"finding":"The crystal structure of human VPS33A was determined, confirming it as an SM (Sec1/Munc18) family member. VPS16 residues 642–736 are necessary and sufficient to recruit VPS33A to the HOPS complex; the crystal structure of VPS33A bound to VPS16(642–736) was solved at 2.6 Å. Mutations at the binding interface disrupt the VPS33A–VPS16 interaction both in vitro and in cells, preventing VPS33A recruitment to HOPS.","method":"X-ray crystallography (2.6 Å), in vitro binding assay, interface mutagenesis, cell-based co-immunoprecipitation","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure plus mutagenesis validated both in vitro and in cells, single rigorous study with multiple orthogonal methods","pmids":["23901104"],"is_preprint":false},{"year":2013,"finding":"The crystal structure of yeast Vps33 alone (2.6 Å) and in complex with a C-terminal portion of Vps16 (2.6 Å) was solved, revealing the structural basis for Vps33–Vps16 interaction. Vps33 has the same basic three-domain SM-protein architecture but with domain 1 displaced by 15 Å and rotated 40° relative to other SM families. Binding to Vps16 causes only subtle conformational changes in Vps33.","method":"X-ray crystallography (2.6 Å resolution)","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution crystal structures of both apo and complex forms, replicates and extends structural findings from Graham et al. 2013","pmids":["23840694"],"is_preprint":false},{"year":2015,"finding":"VPS16 is required for fusion of endosomes and autophagosomes with lysosomes in mammalian cells. The crystal structure of the VPS16/VPS33A complex was used to design interface mutants that disrupt VPS33A binding; these mutants fail to rescue lysosome fusion with endosomes or autophagosomes, demonstrating that VPS16-mediated recruitment of VPS33A to HOPS is mechanistically essential for lysosomal fusion. Depletion of VIPAR (VPS16 paralog) or VPS33B had no effect on these fusion events, and immunoprecipitation showed VIPAR and VPS33B form a distinct complex separate from HOPS.","method":"siRNA depletion, fluorescent dextran delivery assay, structure-guided mutagenesis, co-immunoprecipitation","journal":"Traffic (Copenhagen, Denmark)","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — structure-guided mutagenesis combined with functional rescue experiments and Co-IP, multiple orthogonal methods in one study","pmids":["25783203"],"is_preprint":false},{"year":2021,"finding":"Bi-allelic VPS16 variants reduce VPS16 protein levels by ~85% in patient fibroblasts and cause coordinate reduction of other HOPS/CORVET subunits including VPS33A; re-expression of VPS16 restores levels of other subunits. Patient fibroblasts show defective endosomal trafficking of transferrin and accumulation of autophagosomes and lysosomal compartments, all rescued by VPS16 re-expression. Zebrafish with disrupted vps16 show impaired myelination and accumulation of lysosomes/autophagosomes in brain glia.","method":"Patient fibroblast biochemistry (Western blot, protein quantification), VPS16 re-expression rescue, transferrin trafficking assay, zebrafish vps16 knockdown with IHC","journal":"EMBO molecular medicine","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (quantitative Western blot, trafficking assay, rescue experiment, zebrafish model) establishing VPS16 as a scaffold controlling HOPS/CORVET complex levels","pmids":["33938619"],"is_preprint":false},{"year":2024,"finding":"Loss of Vps16 function in zebrafish causes hypomyelination, increased neuronal cell death, systemic defects, and behavioral/cognitive impairment, demonstrating a required role for Vps16 in myelination and neuronal survival in vivo.","method":"Zebrafish vps16 knockout, immunohistochemistry, behavioral assays (visuomotor response, acoustic/tap stimuli, memory test)","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function in vivo with multiple behavioral and histological readouts, single lab","pmids":["39000367"],"is_preprint":false}],"current_model":"VPS16 is a scaffolding subunit of the HOPS (and CORVET) membrane-tethering complex whose C-terminal region (residues 642–736 in humans) directly recruits the SM protein VPS33A via a structurally defined interface; this VPS16–VPS33A interaction is essential for HOPS-mediated fusion of late endosomes and autophagosomes with lysosomes, and VPS16 also controls the steady-state levels of other HOPS/CORVET subunits, with loss of function causing lysosomal storage-like pathology, hypomyelination, and dystonia in humans and model organisms."},"narrative":{"mechanistic_narrative":"VPS16 is a scaffolding subunit of the class C VPS (HOPS/CORVET) membrane-tethering machinery that drives delivery of cargo to the lysosome/vacuole, first established by gene disruption in yeast that produced severe vacuolar protein-sorting defects and grossly abnormal vacuole morphology and showed Vps16p tightly integrated into a large sedimentable protein complex [PMID:8444873, PMID:11250079]. Its defining mechanistic function is the direct recruitment of the SM (Sec1/Munc18) protein VPS33A: residues 642–736 of human VPS16 are necessary and sufficient to bind VPS33A, and a 2.6 Å co-crystal structure defines the interface whose mutation abolishes VPS33A recruitment to HOPS in vitro and in cells [PMID:23901104, PMID:23840694]. This recruitment is mechanistically essential for fusion of late endosomes and autophagosomes with lysosomes, as interface mutants that cannot bind VPS33A fail to rescue these fusion events, whereas the paralogous VIPAR–VPS33B module forms a distinct complex that is dispensable for them [PMID:25783203]. In mammalian cells the complex localizes to endosomal compartments and modulates transferrin recycling, and VPS16 sets the steady-state levels of partner HOPS/CORVET subunits including VPS33A [PMID:14623309, PMID:33938619]. Bi-allelic VPS16 variants that deplete VPS16 protein coordinately reduce other subunits and cause defective endosomal trafficking with accumulation of autophagosomes and lysosomes, while loss of vps16 in zebrafish produces hypomyelination, neuronal cell death, and behavioral impairment, defining VPS16 as the basis of a lysosomal storage-like, hypomyelinating neurological disorder [PMID:33938619, PMID:39000367]. A separately reported yeast activity as an inhibitor of the mRNA decapping enzyme Dcp1p [PMID:10523645] is not connected to the membrane-trafficking role in the available corpus.","teleology":[{"year":1993,"claim":"Established that VPS16 is a constituent of a large, tightly assembled protein complex required for vacuolar protein sorting, answering whether the gene acts in the lysosomal/vacuolar delivery pathway.","evidence":"Subcellular fractionation, gene disruption, and biochemical extraction in yeast","pmids":["8444873"],"confidence":"Medium","gaps":["Complex composition and the identity of partner subunits not resolved","No structural or mechanistic basis for complex assembly"]},{"year":1999,"claim":"Reported a distinct activity in which yeast Vps16p inhibits the mRNA decapping enzyme Dcp1p, raising a possible second function unrelated to membrane trafficking.","evidence":"In vitro decapping assay, in vivo mRNA stability, and co-purification with Flag-Dcp1p in yeast","pmids":["10523645"],"confidence":"Medium","gaps":["Not connected mechanistically to the trafficking complex role","No evidence this activity is conserved in the human protein"]},{"year":2001,"claim":"Identified human VPS16 as the homolog of yeast class C VPS16, predicting conservation of the lysosomal delivery role in mammals.","evidence":"Molecular cloning, sequence and expression analysis","pmids":["11250079"],"confidence":"Low","gaps":["Sequence/expression only — no functional experiment on the human protein","No partner or localization data"]},{"year":2003,"claim":"Demonstrated that mammalian Vps16 engages syntaxins and Vps45 at endosomes and influences cargo recycling, placing the complex in endosomal trafficking.","evidence":"Co-immunoprecipitation, Western blot, and transferrin trafficking assays in mammalian cells","pmids":["14623309"],"confidence":"Medium","gaps":["Direct versus indirect nature of syntaxin interactions not resolved","Mechanism by which recycling is inhibited not defined"]},{"year":2013,"claim":"Defined the atomic basis of VPS16-mediated SM-protein recruitment, showing that a discrete VPS16 C-terminal segment binds and incorporates VPS33A into HOPS.","evidence":"X-ray crystallography of VPS33A alone and bound to VPS16(642–736), interface mutagenesis, and cell-based co-IP (human and yeast structures)","pmids":["23901104","23840694"],"confidence":"High","gaps":["Structure of the full HOPS holocomplex not determined","How VPS33A engages SNAREs within the assembled complex not shown"]},{"year":2015,"claim":"Established that VPS16-dependent recruitment of VPS33A is mechanistically essential for endosome- and autophagosome-lysosome fusion, distinguishing it from the separate VIPAR–VPS33B module.","evidence":"siRNA depletion, fluorescent dextran delivery, structure-guided interface mutagenesis with rescue, and co-IP in mammalian cells","pmids":["25783203"],"confidence":"High","gaps":["Step in the fusion reaction directly catalyzed by the VPS16–VPS33A interface not pinpointed","Distinct cargo/compartment roles of HOPS versus CORVET not delineated"]},{"year":2021,"claim":"Showed VPS16 acts as a stability scaffold setting the levels of HOPS/CORVET subunits, and that its loss causes a human trafficking disease with lysosome/autophagosome accumulation.","evidence":"Patient fibroblast biochemistry, VPS16 re-expression rescue, transferrin trafficking, and zebrafish knockdown with IHC","pmids":["33938619"],"confidence":"High","gaps":["Whether destabilization reflects failed complex assembly versus enhanced degradation not resolved","Tissue-specific basis of myelination defects not defined"]},{"year":2024,"claim":"Confirmed in vivo that VPS16 is required for myelination and neuronal survival, linking the trafficking defect to a neurological phenotype.","evidence":"Zebrafish vps16 knockout with immunohistochemistry and behavioral assays","pmids":["39000367"],"confidence":"Medium","gaps":["Cell-autonomous versus non-autonomous origin of hypomyelination not established","Molecular link between lysosomal fusion failure and neuronal death not defined"]},{"year":null,"claim":"How VPS16 coordinates HOPS versus CORVET assembly and whether the reported decapping-inhibitor activity has any role in human cells remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structure of the full holocomplex or of CORVET-specific assembly","Human relevance of the Dcp1p-inhibitor activity untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[4,5,6]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,7]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[3]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[6,7]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[3,6,7]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[6,7]}],"complexes":["HOPS","CORVET","class C VPS complex"],"partners":["VPS33A","VPS45","SYNTAXINS"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H269","full_name":"Vacuolar protein sorting-associated protein 16 homolog","aliases":[],"length_aa":839,"mass_kda":94.7,"function":"Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act as a core component of the putative HOPS and CORVET endosomal tethering complexes which are 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. The CORVET complex is proposed to function as a Rab5 effector to mediate early endosome fusion probably in specific endosome subpopulations (PubMed:11382755, PubMed:23351085, PubMed:24554770, PubMed:25266290, PubMed:25783203). Required for recruitment of VPS33A to the HOPS complex (PubMed:23901104). Required for fusion of endosomes and autophagosomes with lysosomes; the function is dependent on its association with VPS33A but not VPS33B (PubMed:25783203). The function in autophagosome-lysosome fusion implicates STX17 but not UVRAG (PubMed:24554770)","subcellular_location":"Late endosome membrane; Lysosome membrane; Early endosome; Cytoplasmic vesicle, clathrin-coated vesicle; Cytoplasmic vesicle, autophagosome","url":"https://www.uniprot.org/uniprotkb/Q9H269/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/VPS16","classification":"Not Classified","n_dependent_lines":407,"n_total_lines":1208,"dependency_fraction":0.33692052980132453},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000215305","cell_line_id":"CID001857","localizations":[{"compartment":"vesicles","grade":3},{"compartment":"cytoplasmic","grade":2}],"interactors":[{"gene":"VPS41","stoichiometry":10.0},{"gene":"VPS33A","stoichiometry":10.0},{"gene":"VPS18","stoichiometry":10.0},{"gene":"TGFBRAP1","stoichiometry":0.2},{"gene":"VPS11","stoichiometry":0.2},{"gene":"VPS8","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001857","total_profiled":1310},"omim":[{"mim_id":"619389","title":"SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 29; SCAR29","url":"https://www.omim.org/entry/619389"},{"mim_id":"619291","title":"DYSTONIA 30; DYT30","url":"https://www.omim.org/entry/619291"},{"mim_id":"618366","title":"VPS8 CORVET COMPLEX SUBUNIT; VPS8","url":"https://www.omim.org/entry/618366"},{"mim_id":"610034","title":"VPS33A CORE SUBUNIT OF CORVET AND HOPS COMPLEXES; VPS33A","url":"https://www.omim.org/entry/610034"},{"mim_id":"608552","title":"VPS33B LATE ENDOSOME AND LYSOSOME ASSOCIATED; VPS33B","url":"https://www.omim.org/entry/608552"}],"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/VPS16"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q9H269","domains":[{"cath_id":"2.40.128","chopping":"1-18_211-330","consensus_level":"medium","plddt":91.9364,"start":1,"end":330},{"cath_id":"1.25.40","chopping":"518-601","consensus_level":"medium","plddt":92.1106,"start":518,"end":601}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H269","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H269-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H269-F1-predicted_aligned_error_v6.png","plddt_mean":91.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=VPS16","jax_strain_url":"https://www.jax.org/strain/search?query=VPS16"},"sequence":{"accession":"Q9H269","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H269.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H269/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H269"}},"corpus_meta":[{"pmid":"25783203","id":"PMC_25783203","title":"Recruitment of VPS33A to HOPS by VPS16 Is Required for Lysosome Fusion with Endosomes and Autophagosomes.","date":"2015","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/25783203","citation_count":127,"is_preprint":false},{"pmid":"8444873","id":"PMC_8444873","title":"The VPS16 gene product associates with a sedimentable protein complex and is essential for vacuolar protein sorting in yeast.","date":"1993","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8444873","citation_count":103,"is_preprint":false},{"pmid":"32808683","id":"PMC_32808683","title":"Loss-of-Function Variants in HOPS Complex Genes VPS16 and VPS41 Cause Early Onset Dystonia Associated with Lysosomal Abnormalities.","date":"2020","source":"Annals of neurology","url":"https://pubmed.ncbi.nlm.nih.gov/32808683","citation_count":94,"is_preprint":false},{"pmid":"23901104","id":"PMC_23901104","title":"Structural basis of Vps33A recruitment to the human HOPS complex by Vps16.","date":"2013","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/23901104","citation_count":82,"is_preprint":false},{"pmid":"11250079","id":"PMC_11250079","title":"Molecular cloning and characterization of human VPS18, VPS 11, VPS16, and VPS33.","date":"2001","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/11250079","citation_count":59,"is_preprint":false},{"pmid":"23840694","id":"PMC_23840694","title":"Crystal Structures of the Sec1/Munc18 (SM) Protein Vps33, Alone and Bound to the Homotypic Fusion and Vacuolar Protein Sorting (HOPS) Subunit Vps16*.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23840694","citation_count":51,"is_preprint":false},{"pmid":"27174565","id":"PMC_27174565","title":"Homozygous mutation of VPS16 gene is responsible for an autosomal recessive adolescent-onset primary dystonia.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/27174565","citation_count":48,"is_preprint":false},{"pmid":"10523645","id":"PMC_10523645","title":"Mutations in VPS16 and MRT1 stabilize mRNAs by activating an inhibitor of the decapping enzyme.","date":"1999","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10523645","citation_count":29,"is_preprint":false},{"pmid":"33938619","id":"PMC_33938619","title":"Bi-allelic VPS16 variants limit HOPS/CORVET levels and cause a mucopolysaccharidosis-like disease.","date":"2021","source":"EMBO molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/33938619","citation_count":27,"is_preprint":false},{"pmid":"34013567","id":"PMC_34013567","title":"Homozygous missense VPS16 variant is associated with a novel disease, resembling mucopolysaccharidosis-plus syndrome in two siblings.","date":"2021","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34013567","citation_count":21,"is_preprint":false},{"pmid":"34901436","id":"PMC_34901436","title":"Transcript-Specific Loss-of-Function Variants in VPS16 Are Enriched in Patients With Dystonia.","date":"2021","source":"Neurology. Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34901436","citation_count":16,"is_preprint":false},{"pmid":"33482438","id":"PMC_33482438","title":"Mutation screening of VPS16 gene in patients with isolated dystonia.","date":"2021","source":"Parkinsonism & related disorders","url":"https://pubmed.ncbi.nlm.nih.gov/33482438","citation_count":15,"is_preprint":false},{"pmid":"14623309","id":"PMC_14623309","title":"Identification of mouse Vps16 and biochemical characterization of mammalian class C Vps complex.","date":"2003","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/14623309","citation_count":15,"is_preprint":false},{"pmid":"38291845","id":"PMC_38291845","title":"Dominant VPS16 Pathogenic Variants: Not Only Isolated Dystonia.","date":"2023","source":"Movement disorders clinical practice","url":"https://pubmed.ncbi.nlm.nih.gov/38291845","citation_count":11,"is_preprint":false},{"pmid":"39000367","id":"PMC_39000367","title":"Hypomyelinated vps16 Mutant Zebrafish Exhibit Systemic and Neurodevelopmental Pathologies.","date":"2024","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/39000367","citation_count":6,"is_preprint":false},{"pmid":"35367832","id":"PMC_35367832","title":"Overexpression of VPS16 correlates with tumor progression and chemoresistance in colorectal cancer.","date":"2022","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/35367832","citation_count":6,"is_preprint":false},{"pmid":"41200738","id":"PMC_41200738","title":"Expanding the Genetic and Phenotypic Spectrum of DYT-VPS16: The Importance of Splice-Site Variants.","date":"2025","source":"Movement disorders : official journal of the Movement Disorder Society","url":"https://pubmed.ncbi.nlm.nih.gov/41200738","citation_count":2,"is_preprint":false},{"pmid":"40970427","id":"PMC_40970427","title":"VPS16-Related Dystonia: Expanding the Clinical Spectrum and Therapeutic Insights.","date":"2025","source":"Movement disorders clinical practice","url":"https://pubmed.ncbi.nlm.nih.gov/40970427","citation_count":2,"is_preprint":false},{"pmid":"39055541","id":"PMC_39055541","title":"Familial Mediterranean fever gene variations could trigger VPS16-associated early-onset dystonia and diabetes mellitus: clinical identification of a family with MEFV and VPS16 genetic variation association.","date":"2024","source":"Rheumatology advances in practice","url":"https://pubmed.ncbi.nlm.nih.gov/39055541","citation_count":2,"is_preprint":false},{"pmid":"40626728","id":"PMC_40626728","title":"The Plasmodium falciparum homolog of Vps16 interacts with the core members of the Vps-C tethering complex.","date":"2025","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/40626728","citation_count":0,"is_preprint":false},{"pmid":"42233462","id":"PMC_42233462","title":"[Case report: VPS16 - a new cause of generalized dystonia].","date":"2026","source":"Ideggyogyaszati szemle","url":"https://pubmed.ncbi.nlm.nih.gov/42233462","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.07.617026","title":"Characterization of the  <i>Plasmodium falciparum</i>  homologue of Vps16, a member of the Vps-C tethering complex","date":"2024-10-07","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.07.617026","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.12.02.24316741","title":"Genetic Diversity and Expanded Phenotypes in Dystonia: Insights from Large-Scale Exome Sequencing","date":"2024-12-05","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.02.24316741","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.07.10.25330831","title":"Rare but Relevant: Assessing Variants in Dystonia-linked Genes in Parkinson’s Disease","date":"2025-07-11","source":"bioRxiv","url":"https://doi.org/10.1101/2025.07.10.25330831","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.07.17.603885","title":"A powdery mildew core effector protein targets host endosome tethering complexes HOPS and CORVET","date":"2024-07-22","source":"bioRxiv","url":"https://doi.org/10.1101/2024.07.17.603885","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14190,"output_tokens":2357,"usd":0.038962,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9487,"output_tokens":2939,"usd":0.060455,"stage2_stop_reason":"end_turn"},"total_usd":0.099417,"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\": 1993,\n      \"finding\": \"Yeast Vps16p associates with a sedimentable particulate protein complex; this association is resistant to detergent and salt extraction but can be disrupted by 6 M urea or alkali buffer, indicating tight integration into a large protein complex. Loss of VPS16 causes severe defects in vacuolar protein sorting and grossly abnormal vacuole morphology.\",\n      \"method\": \"Subcellular fractionation, gene disruption, biochemical extraction\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — subcellular fractionation and gene disruption with defined phenotypic readouts, single lab, two orthogonal methods\",\n      \"pmids\": [\"8444873\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Yeast Vps16p functions as an inhibitor of the mRNA decapping enzyme Dcp1p; mutations in VPS16 reduce decapping activity in vitro and stabilize mRNAs in vivo. Extracts from vps16 mutant strains inhibit purified Flag-Dcp1p activity, and Vps16p mutations enhance the interaction of Dcp1p with the Hsp70 family member Ssa1p/2p.\",\n      \"method\": \"In vitro decapping assay, mRNA stability assay in vivo, co-purification with Flag-Dcp1p\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro enzymatic assay plus in vivo mRNA stability measurement, single lab, two orthogonal methods\",\n      \"pmids\": [\"10523645\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Human VPS16 is the homolog of yeast class C VPS16, and like its yeast counterpart is predicted to function in lysosomal protein delivery as part of the class C VPS complex.\",\n      \"method\": \"Molecular cloning, sequence analysis, expression analysis\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — sequence/expression characterization only, no functional experiment on the human protein\",\n      \"pmids\": [\"11250079\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Mouse Vps16 (mVps16) interacts with multiple syntaxins and with Vps45p in mammalian cells; the mammalian class C VPS complex localizes to endosomal compartments. Overexpression of mammalian class C VPS proteins does not affect transferrin internalization but inhibits transferrin recycling.\",\n      \"method\": \"Co-immunoprecipitation, Western blot, transferrin trafficking assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — co-IP for binding partners plus functional transferrin recycling assay, single lab, two methods\",\n      \"pmids\": [\"14623309\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The crystal structure of human VPS33A was determined, confirming it as an SM (Sec1/Munc18) family member. VPS16 residues 642–736 are necessary and sufficient to recruit VPS33A to the HOPS complex; the crystal structure of VPS33A bound to VPS16(642–736) was solved at 2.6 Å. Mutations at the binding interface disrupt the VPS33A–VPS16 interaction both in vitro and in cells, preventing VPS33A recruitment to HOPS.\",\n      \"method\": \"X-ray crystallography (2.6 Å), in vitro binding assay, interface mutagenesis, cell-based co-immunoprecipitation\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure plus mutagenesis validated both in vitro and in cells, single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"23901104\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The crystal structure of yeast Vps33 alone (2.6 Å) and in complex with a C-terminal portion of Vps16 (2.6 Å) was solved, revealing the structural basis for Vps33–Vps16 interaction. Vps33 has the same basic three-domain SM-protein architecture but with domain 1 displaced by 15 Å and rotated 40° relative to other SM families. Binding to Vps16 causes only subtle conformational changes in Vps33.\",\n      \"method\": \"X-ray crystallography (2.6 Å resolution)\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution crystal structures of both apo and complex forms, replicates and extends structural findings from Graham et al. 2013\",\n      \"pmids\": [\"23840694\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"VPS16 is required for fusion of endosomes and autophagosomes with lysosomes in mammalian cells. The crystal structure of the VPS16/VPS33A complex was used to design interface mutants that disrupt VPS33A binding; these mutants fail to rescue lysosome fusion with endosomes or autophagosomes, demonstrating that VPS16-mediated recruitment of VPS33A to HOPS is mechanistically essential for lysosomal fusion. Depletion of VIPAR (VPS16 paralog) or VPS33B had no effect on these fusion events, and immunoprecipitation showed VIPAR and VPS33B form a distinct complex separate from HOPS.\",\n      \"method\": \"siRNA depletion, fluorescent dextran delivery assay, structure-guided mutagenesis, co-immunoprecipitation\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — structure-guided mutagenesis combined with functional rescue experiments and Co-IP, multiple orthogonal methods in one study\",\n      \"pmids\": [\"25783203\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Bi-allelic VPS16 variants reduce VPS16 protein levels by ~85% in patient fibroblasts and cause coordinate reduction of other HOPS/CORVET subunits including VPS33A; re-expression of VPS16 restores levels of other subunits. Patient fibroblasts show defective endosomal trafficking of transferrin and accumulation of autophagosomes and lysosomal compartments, all rescued by VPS16 re-expression. Zebrafish with disrupted vps16 show impaired myelination and accumulation of lysosomes/autophagosomes in brain glia.\",\n      \"method\": \"Patient fibroblast biochemistry (Western blot, protein quantification), VPS16 re-expression rescue, transferrin trafficking assay, zebrafish vps16 knockdown with IHC\",\n      \"journal\": \"EMBO molecular medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (quantitative Western blot, trafficking assay, rescue experiment, zebrafish model) establishing VPS16 as a scaffold controlling HOPS/CORVET complex levels\",\n      \"pmids\": [\"33938619\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Loss of Vps16 function in zebrafish causes hypomyelination, increased neuronal cell death, systemic defects, and behavioral/cognitive impairment, demonstrating a required role for Vps16 in myelination and neuronal survival in vivo.\",\n      \"method\": \"Zebrafish vps16 knockout, immunohistochemistry, behavioral assays (visuomotor response, acoustic/tap stimuli, memory test)\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function in vivo with multiple behavioral and histological readouts, single lab\",\n      \"pmids\": [\"39000367\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"VPS16 is a scaffolding subunit of the HOPS (and CORVET) membrane-tethering complex whose C-terminal region (residues 642–736 in humans) directly recruits the SM protein VPS33A via a structurally defined interface; this VPS16–VPS33A interaction is essential for HOPS-mediated fusion of late endosomes and autophagosomes with lysosomes, and VPS16 also controls the steady-state levels of other HOPS/CORVET subunits, with loss of function causing lysosomal storage-like pathology, hypomyelination, and dystonia in humans and model organisms.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"VPS16 is a scaffolding subunit of the class C VPS (HOPS/CORVET) membrane-tethering machinery that drives delivery of cargo to the lysosome/vacuole, first established by gene disruption in yeast that produced severe vacuolar protein-sorting defects and grossly abnormal vacuole morphology and showed Vps16p tightly integrated into a large sedimentable protein complex [#0, #2]. Its defining mechanistic function is the direct recruitment of the SM (Sec1/Munc18) protein VPS33A: residues 642\\u2013736 of human VPS16 are necessary and sufficient to bind VPS33A, and a 2.6 \\u00c5 co-crystal structure defines the interface whose mutation abolishes VPS33A recruitment to HOPS in vitro and in cells [#4, #5]. This recruitment is mechanistically essential for fusion of late endosomes and autophagosomes with lysosomes, as interface mutants that cannot bind VPS33A fail to rescue these fusion events, whereas the paralogous VIPAR\\u2013VPS33B module forms a distinct complex that is dispensable for them [#6]. In mammalian cells the complex localizes to endosomal compartments and modulates transferrin recycling, and VPS16 sets the steady-state levels of partner HOPS/CORVET subunits including VPS33A [#3, #7]. Bi-allelic VPS16 variants that deplete VPS16 protein coordinately reduce other subunits and cause defective endosomal trafficking with accumulation of autophagosomes and lysosomes, while loss of vps16 in zebrafish produces hypomyelination, neuronal cell death, and behavioral impairment, defining VPS16 as the basis of a lysosomal storage-like, hypomyelinating neurological disorder [#7, #8]. A separately reported yeast activity as an inhibitor of the mRNA decapping enzyme Dcp1p [#1] is not connected to the membrane-trafficking role in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 1993,\n      \"claim\": \"Established that VPS16 is a constituent of a large, tightly assembled protein complex required for vacuolar protein sorting, answering whether the gene acts in the lysosomal/vacuolar delivery pathway.\",\n      \"evidence\": \"Subcellular fractionation, gene disruption, and biochemical extraction in yeast\",\n      \"pmids\": [\"8444873\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Complex composition and the identity of partner subunits not resolved\", \"No structural or mechanistic basis for complex assembly\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Reported a distinct activity in which yeast Vps16p inhibits the mRNA decapping enzyme Dcp1p, raising a possible second function unrelated to membrane trafficking.\",\n      \"evidence\": \"In vitro decapping assay, in vivo mRNA stability, and co-purification with Flag-Dcp1p in yeast\",\n      \"pmids\": [\"10523645\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Not connected mechanistically to the trafficking complex role\", \"No evidence this activity is conserved in the human protein\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Identified human VPS16 as the homolog of yeast class C VPS16, predicting conservation of the lysosomal delivery role in mammals.\",\n      \"evidence\": \"Molecular cloning, sequence and expression analysis\",\n      \"pmids\": [\"11250079\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Sequence/expression only \\u2014 no functional experiment on the human protein\", \"No partner or localization data\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Demonstrated that mammalian Vps16 engages syntaxins and Vps45 at endosomes and influences cargo recycling, placing the complex in endosomal trafficking.\",\n      \"evidence\": \"Co-immunoprecipitation, Western blot, and transferrin trafficking assays in mammalian cells\",\n      \"pmids\": [\"14623309\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus indirect nature of syntaxin interactions not resolved\", \"Mechanism by which recycling is inhibited not defined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Defined the atomic basis of VPS16-mediated SM-protein recruitment, showing that a discrete VPS16 C-terminal segment binds and incorporates VPS33A into HOPS.\",\n      \"evidence\": \"X-ray crystallography of VPS33A alone and bound to VPS16(642\\u2013736), interface mutagenesis, and cell-based co-IP (human and yeast structures)\",\n      \"pmids\": [\"23901104\", \"23840694\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure of the full HOPS holocomplex not determined\", \"How VPS33A engages SNAREs within the assembled complex not shown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Established that VPS16-dependent recruitment of VPS33A is mechanistically essential for endosome- and autophagosome-lysosome fusion, distinguishing it from the separate VIPAR\\u2013VPS33B module.\",\n      \"evidence\": \"siRNA depletion, fluorescent dextran delivery, structure-guided interface mutagenesis with rescue, and co-IP in mammalian cells\",\n      \"pmids\": [\"25783203\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Step in the fusion reaction directly catalyzed by the VPS16\\u2013VPS33A interface not pinpointed\", \"Distinct cargo/compartment roles of HOPS versus CORVET not delineated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed VPS16 acts as a stability scaffold setting the levels of HOPS/CORVET subunits, and that its loss causes a human trafficking disease with lysosome/autophagosome accumulation.\",\n      \"evidence\": \"Patient fibroblast biochemistry, VPS16 re-expression rescue, transferrin trafficking, and zebrafish knockdown with IHC\",\n      \"pmids\": [\"33938619\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether destabilization reflects failed complex assembly versus enhanced degradation not resolved\", \"Tissue-specific basis of myelination defects not defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Confirmed in vivo that VPS16 is required for myelination and neuronal survival, linking the trafficking defect to a neurological phenotype.\",\n      \"evidence\": \"Zebrafish vps16 knockout with immunohistochemistry and behavioral assays\",\n      \"pmids\": [\"39000367\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cell-autonomous versus non-autonomous origin of hypomyelination not established\", \"Molecular link between lysosomal fusion failure and neuronal death not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How VPS16 coordinates HOPS versus CORVET assembly and whether the reported decapping-inhibitor activity has any role in human cells remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structure of the full holocomplex or of CORVET-specific assembly\", \"Human relevance of the Dcp1p-inhibitor activity untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [4, 5, 6]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [3, 6, 7]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"complexes\": [\"HOPS\", \"CORVET\", \"class C VPS complex\"],\n    \"partners\": [\"VPS33A\", \"VPS45\", \"syntaxins\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}