{"gene":"VPS33A","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2013,"finding":"Crystal structure of human VPS33A confirmed its identity as a Sec1/Munc18 (SM) family member. VPS16 recruits VPS33A to the HOPS complex via residues 642–736 of VPS16, which are necessary and sufficient for the VPS33A–VPS16 interaction. Mutations at the binding interface disrupt the interaction both in vitro and in cells, preventing VPS33A recruitment to HOPS.","method":"X-ray crystallography (crystal structures of VPS33A alone and in complex with VPS16(642–736)); in vitro binding assays; cell-based interaction assays with interface mutants","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution crystal structures combined with mutagenesis validated in vitro and in cells; replicated functionally in a second study (PMID:25783203)","pmids":["23901104"],"is_preprint":false},{"year":2015,"finding":"Recruitment of VPS33A to HOPS by VPS16 is required for lysosome fusion with endosomes and autophagosomes. VPS16 and VPS33A interface mutants (designed from the crystal structure) that no longer bind each other fail to rescue lysosome–endosome and lysosome–autophagosome fusion in cells depleted of endogenous proteins. VPS33B and VIPAR, paralogs of VPS33A and VPS16 respectively, form a complex distinct from HOPS and are not required for these fusion events.","method":"Crystal-structure-guided mutagenesis; fluorescent dextran delivery to lysosomes assay (endocytic pathway); autophagosome–lysosome fusion assay; immunoprecipitation; siRNA depletion","journal":"Traffic (Copenhagen, Denmark)","confidence":"High","confidence_rationale":"Tier 2 / Strong — structure-guided mutagenesis validated with multiple orthogonal cell-based assays; builds directly on crystal structure paper (PMID:23901104)","pmids":["25783203"],"is_preprint":false},{"year":2009,"finding":"Drosophila VPS33A (carnation/Car) is specifically required for late endosome-to-lysosome fusion and autophagosome–lysosome fusion, but not early endosome function. Car binds dSyntaxin16 (present on lysosomes) in vitro, whereas dVps33B binds the early endosomal Avl Syntaxin, explaining their distinct pathway specificities. dVps33B cannot substitute for Car function.","method":"Null allele generation; eye-specific genetic mosaic analysis; fluorescence microscopy of endocytic receptors and autophagosomes; in vitro Syntaxin-binding assay","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — null mutant with specific phenotypic readouts combined with in vitro binding specificity assay; multiple orthogonal methods","pmids":["19158398"],"is_preprint":false},{"year":2003,"finding":"Mouse buff (bf) mutation maps to Vps33a, identifying VPS33A as the first mammalian defect in the class C vacuole/prevacuole-associated t-SNARE complex. The mutation causes defective biogenesis of melanosomes, lysosomes, and storage granules, phenotypically resembling Hermansky-Pudlak syndrome.","method":"Positional cloning; genetic mapping; sequence analysis of buff mutant","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — positional cloning firmly links gene to phenotype; mechanistic detail (class C complex member) inferred from yeast/Drosophila homology rather than direct biochemical assay in mammals","pmids":["12538872"],"is_preprint":false},{"year":2009,"finding":"VPS33A (buff mouse point mutation D251E) is required for fusion of uroplakin-degrading multivesicular bodies (MVBs) with lysosomes in bladder urothelial umbrella cells. In buff mice, fusiform vesicles are replaced by accumulating Rab27b-negative MVBs, accompanied by increased lysosomal enzyme activities, indicating a block at the MVB–lysosome fusion step.","method":"Histological and ultrastructural analysis of buff mouse urothelium; fluorescence microscopy; lysosomal enzyme activity assays; protein quantification","journal":"Traffic (Copenhagen, Denmark)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo genetic loss-of-function with specific organellar phenotype; single lab, multiple morphological and biochemical readouts","pmids":["19566896"],"is_preprint":false},{"year":2009,"finding":"VPS33A interacts with the cytoplasmic tail of RANKL (identified by pull-down) and mediates transport of RANKL from the Golgi apparatus to secretory lysosomes in osteoblastic cells. Knockdown of VPS33A reduces lysosomal storage of RANKL and causes its accumulation in the Golgi, and disrupts regulated cell-surface expression of RANKL.","method":"Protein pull-down assay; siRNA knockdown; immunofluorescence microscopy; cell-surface expression assay","journal":"Journal of bone and mineral research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — pull-down plus KD with defined trafficking phenotype; single lab, two orthogonal approaches","pmids":["19419298"],"is_preprint":false},{"year":2015,"finding":"The VPS33A(D251E) mutation in buff mice selectively impairs autophagosome–lysosome fusion without compromising the endocytic pathway. Mechanistically, VPS33A(D251E) shows enhanced association with the autophagic SNARE complex (STX17–VAMP8–SNAP29) and enhanced interactions with HOPS subunits VPS41, VPS39, VPS18, and VPS11 (but not VPS16). Reduction of VPS33A–HOPS subunit interactions (via VPS33A(Y440D)) also reduces STX17 association, indicating that HOPS assembly controls autophagosomal SNARE engagement. These defects cause Purkinje cell loss.","method":"Co-immunoprecipitation; autophagy flux assays; endocytic pathway assays; histological analysis of buff mouse brain; behavioral testing","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with multiple HOPS subunits plus functional pathway dissection; single lab, multiple orthogonal methods","pmids":["26259518"],"is_preprint":false},{"year":2019,"finding":"The Arg498Trp missense mutation in VPS33A destabilizes protein folding (predicted by 3D crystal structure), reducing abundance of full-length VPS33A and other HOPS/CORVET components. Proteasome inhibitor treatment rescues the mutant protein from degradation. Patient fibroblasts show vacuolation, disordered endosomal/lysosomal compartments, abnormal lactosylceramide trafficking, and elevated β-D-galactosylsphingosine despite normal cognate lysosomal hydrolase activities.","method":"Crystal structure analysis; immunoblotting; proteasome inhibitor treatment; confocal microscopy; lipidomic screening; glycosaminoglycan urinary analysis","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — structural prediction plus biochemical rescue experiment; single lab, multiple orthogonal methods","pmids":["31070736"],"is_preprint":false},{"year":2017,"finding":"A homozygous VPS33A Arg498Trp mutation causes lysosomal over-acidification and heparan sulphate accumulation (plasma HS ~60× normal) in patient-derived and VPS33A-depleted cells, without affecting endocytic or autophagic pathways, revealing a novel role for VPS33A in controlling lysosomal pH homeostasis and glycosaminoglycan catabolism.","method":"Whole exome/Sanger sequencing; lysosomal pH measurement; GAG quantification; RNAi knockdown in cells; endocytic and autophagic pathway assays","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — patient genetics corroborated by siRNA knockdown with specific functional readouts; single lab, multiple methods","pmids":["28013294"],"is_preprint":false},{"year":2019,"finding":"VPS33A interacts with syntaxin 17 (Stx17) via a VPS33A-binding motif in the Stx17 N-peptide to regulate autophagosome–lysosome fusion. FLIM-FRET in live HeLa cells revealed that Stx17 heterotrimerizes with SNAP29 and VAMP7 (not VAMP8) at the autophagosome. A phosphoserine in the Stx17 N-peptide acts as a master-switch controlling fusion competency, providing a late regulatory checkpoint for autophagy completion.","method":"FLIM-FRET in live HeLa cells; Stx17 N-peptide binding assays; phosphomimetic/phospho-null mutant analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — high-resolution in-situ FRET assay with mutagenesis in cells; single lab, novel method with multiple mutants tested","pmids":["30655294"],"is_preprint":false},{"year":2018,"finding":"BioID proximity biotinylation revealed that VPS33A co-localizes with components of both CORVET and HOPS complexes and with class III PI3-kinase (PI3KC3) complex subunits (PIK3C3, PIK3R4, NRBF2, UVRAG, RUBICON), while VPS33B does not associate with CORVET/HOPS subunits and instead interacts with CCDC22 (a CCC complex member). The VPS33B–VIPAR complex is considerably smaller than CORVET/HOPS.","method":"BioID proximity biotinylation–mass spectrometry; gel filtration fractionation; reciprocal interaction validation","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proximity proteomics with gel filtration validation; single lab, two orthogonal approaches","pmids":["29778605"],"is_preprint":false},{"year":2025,"finding":"VPS33A (as part of the HOPS complex) is required for renin granule (RG) biogenesis in juxtaglomerular cells. The buff mouse VPS33A(D251E) mutation produces smaller RGs and reduced active renin. VPS33A interacts with Stx11 (SNARE), and this interaction is enhanced by the D251E mutation, impairing the SNARE complex (Snap23–Stx11–Vamp8) required for RG biogenesis.","method":"Mouse model analysis (buff mice); siRNA knockdown in As4.1 cells; co-immunoprecipitation of VPS33A with Stx11; renin content assay; electron microscopy","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic mouse model plus KD plus Co-IP in cells; single lab, multiple orthogonal methods","pmids":["40855995"],"is_preprint":false},{"year":2024,"finding":"A domain 3a mutation in C. elegans VPS33A (M376I) suppresses the temperature-sensitive lethality caused by loss of VPS45, another SM protein involved in endosomal SNARE-mediated membrane fusion. This genetic epistasis places VPS33A domain 3a as functionally important for SNARE complex assembly in endosomal trafficking.","method":"Genetic suppressor screen in C. elegans; temperature-sensitive lethality assay","journal":"microPublication biology","confidence":"Low","confidence_rationale":"Tier 2 / Weak — genetic epistasis in C. elegans (ortholog); single genetic screen, no biochemical follow-up","pmids":["38585203"],"is_preprint":false},{"year":2026,"finding":"VPS33A knockdown reduces ULK1 protein levels, suppresses autophagic flux, and increases CCA cell sensitivity to pemigatinib. ULK1 overexpression restores autophagy and reverses the enhanced drug sensitivity caused by VPS33A depletion, placing VPS33A upstream of ULK1 in a pro-autophagic axis.","method":"siRNA knockdown; ULK1 overexpression; GFP-RFP-LC3 autophagic flux assay; CCK-8/EdU proliferation assays; in vivo xenograft","journal":"Digestive diseases and sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, KD + OE epistasis but no direct biochemical interaction between VPS33A and ULK1 demonstrated","pmids":["41718964"],"is_preprint":false}],"current_model":"VPS33A is a Sec1/Munc18-family SM protein and core subunit of both the HOPS and CORVET membrane-tethering complexes, recruited to HOPS through a structurally defined interface with VPS16; it regulates SNARE-mediated fusion of late endosomes, multivesicular bodies, autophagosomes, and lysosome-related organelles (including secretory lysosomes, renin granules, and melanosomes) with lysosomes by engaging specific SNARE complexes (STX17–SNAP29–VAMP7/8, Stx11–Snap23–Vamp8, dSyntaxin16), with STX17 N-peptide phosphorylation providing an additional regulatory checkpoint; loss-of-function or point mutations (e.g., D251E, R498W) destabilize the protein or alter its SNARE/HOPS interactions, leading to lysosomal over-acidification, glycosaminoglycan and sphingolipid accumulation, and organelle-specific trafficking defects underlying Hermansky-Pudlak syndrome–like and mucopolysaccharidosis-plus disease phenotypes."},"narrative":{"mechanistic_narrative":"VPS33A is a Sec1/Munc18 (SM)-family protein and a core subunit of the HOPS membrane-tethering complex that regulates SNARE-mediated fusion of late endosomes, multivesicular bodies, autophagosomes, and lysosome-related organelles with lysosomes [PMID:23901104, PMID:25783203, PMID:19158398]. Crystallographic and structure-guided mutagenesis established that VPS16 recruits VPS33A to HOPS through residues 642–736 of VPS16, an interface necessary and sufficient for the interaction, and disruption of this binding prevents lysosome fusion with both endosomes and autophagosomes [PMID:23901104, PMID:25783203]. VPS33A confers pathway specificity at the lysosomal fusion step by engaging defined SNARE complexes — it binds syntaxin 17 via a motif in the STX17 N-peptide to license the autophagic STX17–SNAP29–VAMP7 trans-SNARE complex, with an STX17 N-peptide phosphoserine acting as a late regulatory checkpoint, and it binds Stx11 to support the Snap23–Stx11–Vamp8 SNARE complex driving renin granule biogenesis [PMID:30655294, PMID:40855995]. Proximity proteomics place VPS33A with both CORVET and HOPS subunits and with class III PI3-kinase complex components, distinguishing it from its paralog VPS33B [PMID:29778605]. Loss-of-function alleles produce organelle-specific trafficking defects: the buff mouse D251E mutation blocks MVB–lysosome and autophagosome–lysosome fusion by altering HOPS-subunit and SNARE associations, causing melanosome, lysosome, and storage-granule biogenesis defects resembling Hermansky-Pudlak syndrome [PMID:12538872, PMID:19566896, PMID:26259518]. A homozygous Arg498Trp mutation destabilizes VPS33A folding and reduces HOPS/CORVET abundance, causing lysosomal over-acidification, glycosaminoglycan and sphingolipid accumulation underlying a mucopolysaccharidosis-plus phenotype [PMID:31070736, PMID:28013294].","teleology":[{"year":2003,"claim":"Established that a mammalian VPS33A defect causes a lysosome-related organelle biogenesis disease, linking the gene to vacuolar/lysosomal trafficking before its biochemistry was known.","evidence":"positional cloning of the buff mouse mutation","pmids":["12538872"],"confidence":"Medium","gaps":["mechanistic role in the tethering complex inferred from yeast/Drosophila homology, not direct mammalian biochemistry","specific SNARE partners not yet identified"]},{"year":2009,"claim":"Resolved how VPS33A achieves pathway specificity, showing it acts at late endosome-to-lysosome and autophagosome-lysosome fusion via syntaxin binding rather than at early endosomes.","evidence":"Drosophila carnation null allele, mosaic analysis, and in vitro dSyntaxin16 binding; mouse buff urothelium ultrastructure and lysosomal enzyme assays; RANKL pull-down and VPS33A knockdown in osteoblasts","pmids":["19158398","19566896","19419298"],"confidence":"Medium","gaps":["mammalian SNARE-binding specificity not directly tested in these studies","RANKL cargo interaction shown by pull-down without structural mapping"]},{"year":2013,"claim":"Defined the atomic basis of VPS33A's incorporation into HOPS, identifying the VPS16(642–736) interface as the recruitment determinant.","evidence":"X-ray crystallography of VPS33A alone and with VPS16, plus in vitro and cell-based interface mutagenesis","pmids":["23901104"],"confidence":"High","gaps":["structure of the full HOPS complex with VPS33A not resolved","did not test functional consequence of interface disruption on fusion"]},{"year":2015,"claim":"Demonstrated functionally that VPS16-mediated recruitment to HOPS is required for fusion, and separated VPS33A/HOPS from the distinct VPS33B/VIPAR complex.","evidence":"structure-guided interface mutants tested in dextran-delivery and autophagosome-lysosome fusion rescue assays with siRNA depletion; co-IP comparisons","pmids":["25783203"],"confidence":"High","gaps":["does not resolve how HOPS engages individual SNAREs at each membrane","in vitro reconstitution of fusion not performed"]},{"year":2015,"claim":"Showed that HOPS assembly controls autophagosomal SNARE engagement, explaining how the D251E mutation selectively impairs autophagy.","evidence":"co-IP of VPS33A(D251E) and Y440D mutants with HOPS subunits and the STX17–VAMP8–SNAP29 SNARE complex; autophagy and endocytic flux assays; buff brain histology","pmids":["26259518"],"confidence":"Medium","gaps":["enhanced versus deficient SNARE association as the disease driver not biochemically dissected","single lab"]},{"year":2017,"claim":"Uncovered a role for VPS33A in lysosomal pH homeostasis and glycosaminoglycan catabolism, defining the mucopolysaccharidosis-plus disease mechanism.","evidence":"exome sequencing of Arg498Trp patients, lysosomal pH measurement, GAG quantification, and RNAi knockdown","pmids":["28013294"],"confidence":"Medium","gaps":["molecular link between VPS33A loss and over-acidification not defined","endocytic/autophagic pathways reported unaffected, conflicting with other models of the same mutation"]},{"year":2018,"claim":"Mapped the proximity interactome of VPS33A, distinguishing it from VPS33B and placing it with both CORVET/HOPS and class III PI3-kinase machinery.","evidence":"BioID proximity biotinylation-mass spectrometry with gel filtration and reciprocal validation","pmids":["29778605"],"confidence":"Medium","gaps":["proximity does not establish direct binary interactions","functional significance of PI3KC3 association not tested"]},{"year":2019,"claim":"Identified an N-peptide phosphorylation checkpoint on STX17 controlling fusion competency, and confirmed Arg498Trp destabilizes folding and depletes HOPS/CORVET.","evidence":"FLIM-FRET in live HeLa cells with STX17 N-peptide and phosphomimetic mutants; crystal-structure-based stability prediction with proteasome-inhibitor rescue and lipidomics","pmids":["30655294","31070736"],"confidence":"Medium","gaps":["kinase responsible for STX17 N-peptide phosphorylation not identified","VAMP7 versus VAMP8 usage differs between studies"]},{"year":2025,"claim":"Extended VPS33A's SNARE-engaging role to a new lysosome-related organelle, showing it supports renin granule biogenesis via Stx11.","evidence":"buff mouse analysis, As4.1 knockdown, co-IP of VPS33A with Stx11, renin assays, and electron microscopy","pmids":["40855995"],"confidence":"Medium","gaps":["how D251E enhances Stx11 binding yet impairs the Snap23–Stx11–Vamp8 complex mechanistically unresolved","single lab"]},{"year":2024,"claim":"Genetic epistasis implicated VPS33A domain 3a in SNARE complex assembly during endosomal trafficking.","evidence":"C. elegans suppressor screen of vps-45 temperature-sensitive lethality","pmids":["38585203"],"confidence":"Low","gaps":["genetic interaction in ortholog with no biochemical follow-up","domain 3a contribution not tested in mammalian VPS33A"]},{"year":2026,"claim":"Positioned VPS33A upstream of ULK1 in a pro-autophagic axis relevant to cancer drug sensitivity.","evidence":"siRNA knockdown and ULK1 overexpression rescue with LC3 flux, proliferation assays, and xenograft in cholangiocarcinoma cells","pmids":["41718964"],"confidence":"Low","gaps":["no direct VPS33A–ULK1 biochemical interaction shown","mechanism by which VPS33A loss reduces ULK1 levels unknown","single lab"]},{"year":null,"claim":"How HOPS-incorporated VPS33A selects among distinct SNARE sets at different organelles and how phosphoregulation is coordinated across pathways remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["no reconstituted fusion assay defining VPS33A's catalytic contribution to SNARE zippering","kinase/phosphatase governing STX17 N-peptide switch unidentified","structure of VPS33A within an assembled HOPS-SNARE intermediate lacking"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[9,11]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[6,9]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[4,8]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[2,7]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,10]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[1,6,9]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,2,4]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[5,11]}],"complexes":["HOPS","CORVET"],"partners":["VPS16","STX17","SNAP29","VAMP7","STX11","VPS41","VPS39","VPS11"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96AX1","full_name":"Vacuolar protein sorting-associated protein 33A","aliases":[],"length_aa":596,"mass_kda":67.6,"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:23351085, PubMed:24554770, PubMed:25266290, PubMed:25783203). Required for fusion of endosomes and autophagosomes with lysosomes; the function is dependent on its association with VPS16 but not VIPAS39 (PubMed:25783203). The function in autophagosome-lysosome fusion implicates STX17 but not UVRAG (PubMed:24554770)","subcellular_location":"Cytoplasmic vesicle; Late endosome membrane; Lysosome membrane; Early endosome; Cytoplasmic vesicle, autophagosome; Cytoplasmic vesicle, clathrin-coated vesicle","url":"https://www.uniprot.org/uniprotkb/Q96AX1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/VPS33A","classification":"Common Essential","n_dependent_lines":875,"n_total_lines":1208,"dependency_fraction":0.7243377483443708},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000139719","cell_line_id":"CID001859","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"vesicles","grade":3},{"compartment":"nucleoplasm","grade":1}],"interactors":[{"gene":"VPS16","stoichiometry":10.0},{"gene":"VPS18","stoichiometry":10.0},{"gene":"NRIP1","stoichiometry":0.2},{"gene":"TGFBRAP1","stoichiometry":0.2},{"gene":"VPS11","stoichiometry":0.2},{"gene":"VPS41","stoichiometry":0.2},{"gene":"VPS8","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001859","total_profiled":1310},"omim":[{"mim_id":"619389","title":"SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 29; SCAR29","url":"https://www.omim.org/entry/619389"},{"mim_id":"617303","title":"MUCOPOLYSACCHARIDOSIS-PLUS SYNDROME; MPSPS","url":"https://www.omim.org/entry/617303"},{"mim_id":"613401","title":"VPS33B-INTERACTING PROTEIN, APICAL-BASOLATERAL POLARITY REGULATOR, SPE39 HOMOLOG; VIPAS39","url":"https://www.omim.org/entry/613401"},{"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"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/VPS33A"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q96AX1","domains":[{"cath_id":"3.40.50.2060","chopping":"2-142","consensus_level":"high","plddt":94.566,"start":2,"end":142},{"cath_id":"3.40.50.1910","chopping":"143-235_471-596","consensus_level":"medium","plddt":93.5479,"start":143,"end":596},{"cath_id":"3.90.830.10","chopping":"245-271_281-366","consensus_level":"medium","plddt":94.5366,"start":245,"end":366},{"cath_id":"1.25.40.850","chopping":"368-417_419-459","consensus_level":"medium","plddt":96.901,"start":368,"end":459}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96AX1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96AX1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96AX1-F1-predicted_aligned_error_v6.png","plddt_mean":93.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=VPS33A","jax_strain_url":"https://www.jax.org/strain/search?query=VPS33A"},"sequence":{"accession":"Q96AX1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96AX1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96AX1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96AX1"}},"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":"12538872","id":"PMC_12538872","title":"The mouse organellar biogenesis mutant buff results from a mutation in Vps33a, a homologue of yeast vps33 and Drosophila carnation.","date":"2003","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/12538872","citation_count":107,"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":"19158398","id":"PMC_19158398","title":"The SM protein Car/Vps33A regulates SNARE-mediated trafficking to lysosomes and lysosome-related organelles.","date":"2009","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/19158398","citation_count":79,"is_preprint":false},{"pmid":"28013294","id":"PMC_28013294","title":"Mutation in VPS33A affects metabolism of glycosaminoglycans: a new type of mucopolysaccharidosis with severe systemic symptoms.","date":"2017","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28013294","citation_count":55,"is_preprint":false},{"pmid":"26259518","id":"PMC_26259518","title":"Impairment of autophagosome-lysosome fusion in the buff mutant mice with the VPS33A(D251E) mutation.","date":"2015","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/26259518","citation_count":44,"is_preprint":false},{"pmid":"31070736","id":"PMC_31070736","title":"The lysosomal disease caused by mutant VPS33A.","date":"2019","source":"Human molecular 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Research","url":"https://pubmed.ncbi.nlm.nih.gov/19419298","citation_count":31,"is_preprint":false},{"pmid":"30655294","id":"PMC_30655294","title":"A VPS33A-binding motif on syntaxin 17 controls autophagy completion in mammalian cells.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30655294","citation_count":31,"is_preprint":false},{"pmid":"29778605","id":"PMC_29778605","title":"Proteomic and Biochemical Comparison of the Cellular Interaction Partners of Human VPS33A and VPS33B.","date":"2018","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/29778605","citation_count":23,"is_preprint":false},{"pmid":"19254700","id":"PMC_19254700","title":"The Vps33a gene regulates behavior and cerebellar Purkinje cell number.","date":"2009","source":"Brain research","url":"https://pubmed.ncbi.nlm.nih.gov/19254700","citation_count":22,"is_preprint":false},{"pmid":"36153662","id":"PMC_36153662","title":"Juvenile mucopolysaccharidosis plus disease caused by a missense mutation in VPS33A.","date":"2022","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/36153662","citation_count":12,"is_preprint":false},{"pmid":"36232726","id":"PMC_36232726","title":"Mucopolysaccharidosis-Plus Syndrome: Report on a Polish Patient with a Novel VPS33A Variant with Comparison with Other Described Patients.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36232726","citation_count":10,"is_preprint":false},{"pmid":"40758165","id":"PMC_40758165","title":"Cellular and molecular changes in mucopolysaccharidosis-plus syndrome caused by a homozygous c.599G > C (p.Arg200Pro) variant of the VPS33A gene.","date":"2025","source":"Journal of applied genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40758165","citation_count":3,"is_preprint":false},{"pmid":"41718964","id":"PMC_41718964","title":"VPS33A Promotes Pemigatinib Resistance in Cholangiocarcinoma via Autophagy.","date":"2026","source":"Digestive diseases and sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41718964","citation_count":1,"is_preprint":false},{"pmid":"38585203","id":"PMC_38585203","title":"Domain 3a mutation of VPS33A suppresses larval arrest phenotype in the loss of VPS45 in Caenorhabditis elegans.","date":"2024","source":"microPublication biology","url":"https://pubmed.ncbi.nlm.nih.gov/38585203","citation_count":0,"is_preprint":false},{"pmid":"40855995","id":"PMC_40855995","title":"Impaired biogenesis of renin granules in juxtaglomerular cells of Vps33a (D251E) mutant mice.","date":"2025","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/40855995","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11173,"output_tokens":3996,"usd":0.04673,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11864,"output_tokens":3923,"usd":0.078698,"stage2_stop_reason":"end_turn"},"total_usd":0.125428,"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\": 2013,\n      \"finding\": \"Crystal structure of human VPS33A confirmed its identity as a Sec1/Munc18 (SM) family member. VPS16 recruits VPS33A to the HOPS complex via residues 642–736 of VPS16, which are necessary and sufficient for the VPS33A–VPS16 interaction. Mutations at the binding interface disrupt the interaction both in vitro and in cells, preventing VPS33A recruitment to HOPS.\",\n      \"method\": \"X-ray crystallography (crystal structures of VPS33A alone and in complex with VPS16(642–736)); in vitro binding assays; cell-based interaction assays with interface mutants\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution crystal structures combined with mutagenesis validated in vitro and in cells; replicated functionally in a second study (PMID:25783203)\",\n      \"pmids\": [\"23901104\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Recruitment of VPS33A to HOPS by VPS16 is required for lysosome fusion with endosomes and autophagosomes. VPS16 and VPS33A interface mutants (designed from the crystal structure) that no longer bind each other fail to rescue lysosome–endosome and lysosome–autophagosome fusion in cells depleted of endogenous proteins. VPS33B and VIPAR, paralogs of VPS33A and VPS16 respectively, form a complex distinct from HOPS and are not required for these fusion events.\",\n      \"method\": \"Crystal-structure-guided mutagenesis; fluorescent dextran delivery to lysosomes assay (endocytic pathway); autophagosome–lysosome fusion assay; immunoprecipitation; siRNA depletion\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — structure-guided mutagenesis validated with multiple orthogonal cell-based assays; builds directly on crystal structure paper (PMID:23901104)\",\n      \"pmids\": [\"25783203\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Drosophila VPS33A (carnation/Car) is specifically required for late endosome-to-lysosome fusion and autophagosome–lysosome fusion, but not early endosome function. Car binds dSyntaxin16 (present on lysosomes) in vitro, whereas dVps33B binds the early endosomal Avl Syntaxin, explaining their distinct pathway specificities. dVps33B cannot substitute for Car function.\",\n      \"method\": \"Null allele generation; eye-specific genetic mosaic analysis; fluorescence microscopy of endocytic receptors and autophagosomes; in vitro Syntaxin-binding assay\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — null mutant with specific phenotypic readouts combined with in vitro binding specificity assay; multiple orthogonal methods\",\n      \"pmids\": [\"19158398\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Mouse buff (bf) mutation maps to Vps33a, identifying VPS33A as the first mammalian defect in the class C vacuole/prevacuole-associated t-SNARE complex. The mutation causes defective biogenesis of melanosomes, lysosomes, and storage granules, phenotypically resembling Hermansky-Pudlak syndrome.\",\n      \"method\": \"Positional cloning; genetic mapping; sequence analysis of buff mutant\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — positional cloning firmly links gene to phenotype; mechanistic detail (class C complex member) inferred from yeast/Drosophila homology rather than direct biochemical assay in mammals\",\n      \"pmids\": [\"12538872\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"VPS33A (buff mouse point mutation D251E) is required for fusion of uroplakin-degrading multivesicular bodies (MVBs) with lysosomes in bladder urothelial umbrella cells. In buff mice, fusiform vesicles are replaced by accumulating Rab27b-negative MVBs, accompanied by increased lysosomal enzyme activities, indicating a block at the MVB–lysosome fusion step.\",\n      \"method\": \"Histological and ultrastructural analysis of buff mouse urothelium; fluorescence microscopy; lysosomal enzyme activity assays; protein quantification\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo genetic loss-of-function with specific organellar phenotype; single lab, multiple morphological and biochemical readouts\",\n      \"pmids\": [\"19566896\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"VPS33A interacts with the cytoplasmic tail of RANKL (identified by pull-down) and mediates transport of RANKL from the Golgi apparatus to secretory lysosomes in osteoblastic cells. Knockdown of VPS33A reduces lysosomal storage of RANKL and causes its accumulation in the Golgi, and disrupts regulated cell-surface expression of RANKL.\",\n      \"method\": \"Protein pull-down assay; siRNA knockdown; immunofluorescence microscopy; cell-surface expression assay\",\n      \"journal\": \"Journal of bone and mineral research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — pull-down plus KD with defined trafficking phenotype; single lab, two orthogonal approaches\",\n      \"pmids\": [\"19419298\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The VPS33A(D251E) mutation in buff mice selectively impairs autophagosome–lysosome fusion without compromising the endocytic pathway. Mechanistically, VPS33A(D251E) shows enhanced association with the autophagic SNARE complex (STX17–VAMP8–SNAP29) and enhanced interactions with HOPS subunits VPS41, VPS39, VPS18, and VPS11 (but not VPS16). Reduction of VPS33A–HOPS subunit interactions (via VPS33A(Y440D)) also reduces STX17 association, indicating that HOPS assembly controls autophagosomal SNARE engagement. These defects cause Purkinje cell loss.\",\n      \"method\": \"Co-immunoprecipitation; autophagy flux assays; endocytic pathway assays; histological analysis of buff mouse brain; behavioral testing\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with multiple HOPS subunits plus functional pathway dissection; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"26259518\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The Arg498Trp missense mutation in VPS33A destabilizes protein folding (predicted by 3D crystal structure), reducing abundance of full-length VPS33A and other HOPS/CORVET components. Proteasome inhibitor treatment rescues the mutant protein from degradation. Patient fibroblasts show vacuolation, disordered endosomal/lysosomal compartments, abnormal lactosylceramide trafficking, and elevated β-D-galactosylsphingosine despite normal cognate lysosomal hydrolase activities.\",\n      \"method\": \"Crystal structure analysis; immunoblotting; proteasome inhibitor treatment; confocal microscopy; lipidomic screening; glycosaminoglycan urinary analysis\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — structural prediction plus biochemical rescue experiment; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"31070736\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"A homozygous VPS33A Arg498Trp mutation causes lysosomal over-acidification and heparan sulphate accumulation (plasma HS ~60× normal) in patient-derived and VPS33A-depleted cells, without affecting endocytic or autophagic pathways, revealing a novel role for VPS33A in controlling lysosomal pH homeostasis and glycosaminoglycan catabolism.\",\n      \"method\": \"Whole exome/Sanger sequencing; lysosomal pH measurement; GAG quantification; RNAi knockdown in cells; endocytic and autophagic pathway assays\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — patient genetics corroborated by siRNA knockdown with specific functional readouts; single lab, multiple methods\",\n      \"pmids\": [\"28013294\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"VPS33A interacts with syntaxin 17 (Stx17) via a VPS33A-binding motif in the Stx17 N-peptide to regulate autophagosome–lysosome fusion. FLIM-FRET in live HeLa cells revealed that Stx17 heterotrimerizes with SNAP29 and VAMP7 (not VAMP8) at the autophagosome. A phosphoserine in the Stx17 N-peptide acts as a master-switch controlling fusion competency, providing a late regulatory checkpoint for autophagy completion.\",\n      \"method\": \"FLIM-FRET in live HeLa cells; Stx17 N-peptide binding assays; phosphomimetic/phospho-null mutant analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — high-resolution in-situ FRET assay with mutagenesis in cells; single lab, novel method with multiple mutants tested\",\n      \"pmids\": [\"30655294\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"BioID proximity biotinylation revealed that VPS33A co-localizes with components of both CORVET and HOPS complexes and with class III PI3-kinase (PI3KC3) complex subunits (PIK3C3, PIK3R4, NRBF2, UVRAG, RUBICON), while VPS33B does not associate with CORVET/HOPS subunits and instead interacts with CCDC22 (a CCC complex member). The VPS33B–VIPAR complex is considerably smaller than CORVET/HOPS.\",\n      \"method\": \"BioID proximity biotinylation–mass spectrometry; gel filtration fractionation; reciprocal interaction validation\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proximity proteomics with gel filtration validation; single lab, two orthogonal approaches\",\n      \"pmids\": [\"29778605\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"VPS33A (as part of the HOPS complex) is required for renin granule (RG) biogenesis in juxtaglomerular cells. The buff mouse VPS33A(D251E) mutation produces smaller RGs and reduced active renin. VPS33A interacts with Stx11 (SNARE), and this interaction is enhanced by the D251E mutation, impairing the SNARE complex (Snap23–Stx11–Vamp8) required for RG biogenesis.\",\n      \"method\": \"Mouse model analysis (buff mice); siRNA knockdown in As4.1 cells; co-immunoprecipitation of VPS33A with Stx11; renin content assay; electron microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic mouse model plus KD plus Co-IP in cells; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"40855995\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"A domain 3a mutation in C. elegans VPS33A (M376I) suppresses the temperature-sensitive lethality caused by loss of VPS45, another SM protein involved in endosomal SNARE-mediated membrane fusion. This genetic epistasis places VPS33A domain 3a as functionally important for SNARE complex assembly in endosomal trafficking.\",\n      \"method\": \"Genetic suppressor screen in C. elegans; temperature-sensitive lethality assay\",\n      \"journal\": \"microPublication biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic epistasis in C. elegans (ortholog); single genetic screen, no biochemical follow-up\",\n      \"pmids\": [\"38585203\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"VPS33A knockdown reduces ULK1 protein levels, suppresses autophagic flux, and increases CCA cell sensitivity to pemigatinib. ULK1 overexpression restores autophagy and reverses the enhanced drug sensitivity caused by VPS33A depletion, placing VPS33A upstream of ULK1 in a pro-autophagic axis.\",\n      \"method\": \"siRNA knockdown; ULK1 overexpression; GFP-RFP-LC3 autophagic flux assay; CCK-8/EdU proliferation assays; in vivo xenograft\",\n      \"journal\": \"Digestive diseases and sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, KD + OE epistasis but no direct biochemical interaction between VPS33A and ULK1 demonstrated\",\n      \"pmids\": [\"41718964\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"VPS33A is a Sec1/Munc18-family SM protein and core subunit of both the HOPS and CORVET membrane-tethering complexes, recruited to HOPS through a structurally defined interface with VPS16; it regulates SNARE-mediated fusion of late endosomes, multivesicular bodies, autophagosomes, and lysosome-related organelles (including secretory lysosomes, renin granules, and melanosomes) with lysosomes by engaging specific SNARE complexes (STX17–SNAP29–VAMP7/8, Stx11–Snap23–Vamp8, dSyntaxin16), with STX17 N-peptide phosphorylation providing an additional regulatory checkpoint; loss-of-function or point mutations (e.g., D251E, R498W) destabilize the protein or alter its SNARE/HOPS interactions, leading to lysosomal over-acidification, glycosaminoglycan and sphingolipid accumulation, and organelle-specific trafficking defects underlying Hermansky-Pudlak syndrome–like and mucopolysaccharidosis-plus disease phenotypes.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"VPS33A is a Sec1/Munc18 (SM)-family protein and a core subunit of the HOPS membrane-tethering complex that regulates SNARE-mediated fusion of late endosomes, multivesicular bodies, autophagosomes, and lysosome-related organelles with lysosomes [#0, #1, #2]. Crystallographic and structure-guided mutagenesis established that VPS16 recruits VPS33A to HOPS through residues 642\\u2013736 of VPS16, an interface necessary and sufficient for the interaction, and disruption of this binding prevents lysosome fusion with both endosomes and autophagosomes [#0, #1]. VPS33A confers pathway specificity at the lysosomal fusion step by engaging defined SNARE complexes \\u2014 it binds syntaxin 17 via a motif in the STX17 N-peptide to license the autophagic STX17\\u2013SNAP29\\u2013VAMP7 trans-SNARE complex, with an STX17 N-peptide phosphoserine acting as a late regulatory checkpoint, and it binds Stx11 to support the Snap23\\u2013Stx11\\u2013Vamp8 SNARE complex driving renin granule biogenesis [#9, #11]. Proximity proteomics place VPS33A with both CORVET and HOPS subunits and with class III PI3-kinase complex components, distinguishing it from its paralog VPS33B [#10]. Loss-of-function alleles produce organelle-specific trafficking defects: the buff mouse D251E mutation blocks MVB\\u2013lysosome and autophagosome\\u2013lysosome fusion by altering HOPS-subunit and SNARE associations, causing melanosome, lysosome, and storage-granule biogenesis defects resembling Hermansky-Pudlak syndrome [#3, #4, #6]. A homozygous Arg498Trp mutation destabilizes VPS33A folding and reduces HOPS/CORVET abundance, causing lysosomal over-acidification, glycosaminoglycan and sphingolipid accumulation underlying a mucopolysaccharidosis-plus phenotype [#7, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2003,\n      \"claim\": \"Established that a mammalian VPS33A defect causes a lysosome-related organelle biogenesis disease, linking the gene to vacuolar/lysosomal trafficking before its biochemistry was known.\",\n      \"evidence\": \"positional cloning of the buff mouse mutation\",\n      \"pmids\": [\"12538872\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"mechanistic role in the tethering complex inferred from yeast/Drosophila homology, not direct mammalian biochemistry\", \"specific SNARE partners not yet identified\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Resolved how VPS33A achieves pathway specificity, showing it acts at late endosome-to-lysosome and autophagosome-lysosome fusion via syntaxin binding rather than at early endosomes.\",\n      \"evidence\": \"Drosophila carnation null allele, mosaic analysis, and in vitro dSyntaxin16 binding; mouse buff urothelium ultrastructure and lysosomal enzyme assays; RANKL pull-down and VPS33A knockdown in osteoblasts\",\n      \"pmids\": [\"19158398\", \"19566896\", \"19419298\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"mammalian SNARE-binding specificity not directly tested in these studies\", \"RANKL cargo interaction shown by pull-down without structural mapping\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Defined the atomic basis of VPS33A's incorporation into HOPS, identifying the VPS16(642\\u2013736) interface as the recruitment determinant.\",\n      \"evidence\": \"X-ray crystallography of VPS33A alone and with VPS16, plus in vitro and cell-based interface mutagenesis\",\n      \"pmids\": [\"23901104\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"structure of the full HOPS complex with VPS33A not resolved\", \"did not test functional consequence of interface disruption on fusion\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrated functionally that VPS16-mediated recruitment to HOPS is required for fusion, and separated VPS33A/HOPS from the distinct VPS33B/VIPAR complex.\",\n      \"evidence\": \"structure-guided interface mutants tested in dextran-delivery and autophagosome-lysosome fusion rescue assays with siRNA depletion; co-IP comparisons\",\n      \"pmids\": [\"25783203\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"does not resolve how HOPS engages individual SNAREs at each membrane\", \"in vitro reconstitution of fusion not performed\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed that HOPS assembly controls autophagosomal SNARE engagement, explaining how the D251E mutation selectively impairs autophagy.\",\n      \"evidence\": \"co-IP of VPS33A(D251E) and Y440D mutants with HOPS subunits and the STX17\\u2013VAMP8\\u2013SNAP29 SNARE complex; autophagy and endocytic flux assays; buff brain histology\",\n      \"pmids\": [\"26259518\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"enhanced versus deficient SNARE association as the disease driver not biochemically dissected\", \"single lab\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Uncovered a role for VPS33A in lysosomal pH homeostasis and glycosaminoglycan catabolism, defining the mucopolysaccharidosis-plus disease mechanism.\",\n      \"evidence\": \"exome sequencing of Arg498Trp patients, lysosomal pH measurement, GAG quantification, and RNAi knockdown\",\n      \"pmids\": [\"28013294\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"molecular link between VPS33A loss and over-acidification not defined\", \"endocytic/autophagic pathways reported unaffected, conflicting with other models of the same mutation\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Mapped the proximity interactome of VPS33A, distinguishing it from VPS33B and placing it with both CORVET/HOPS and class III PI3-kinase machinery.\",\n      \"evidence\": \"BioID proximity biotinylation-mass spectrometry with gel filtration and reciprocal validation\",\n      \"pmids\": [\"29778605\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"proximity does not establish direct binary interactions\", \"functional significance of PI3KC3 association not tested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified an N-peptide phosphorylation checkpoint on STX17 controlling fusion competency, and confirmed Arg498Trp destabilizes folding and depletes HOPS/CORVET.\",\n      \"evidence\": \"FLIM-FRET in live HeLa cells with STX17 N-peptide and phosphomimetic mutants; crystal-structure-based stability prediction with proteasome-inhibitor rescue and lipidomics\",\n      \"pmids\": [\"30655294\", \"31070736\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"kinase responsible for STX17 N-peptide phosphorylation not identified\", \"VAMP7 versus VAMP8 usage differs between studies\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended VPS33A's SNARE-engaging role to a new lysosome-related organelle, showing it supports renin granule biogenesis via Stx11.\",\n      \"evidence\": \"buff mouse analysis, As4.1 knockdown, co-IP of VPS33A with Stx11, renin assays, and electron microscopy\",\n      \"pmids\": [\"40855995\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"how D251E enhances Stx11 binding yet impairs the Snap23\\u2013Stx11\\u2013Vamp8 complex mechanistically unresolved\", \"single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Genetic epistasis implicated VPS33A domain 3a in SNARE complex assembly during endosomal trafficking.\",\n      \"evidence\": \"C. elegans suppressor screen of vps-45 temperature-sensitive lethality\",\n      \"pmids\": [\"38585203\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"genetic interaction in ortholog with no biochemical follow-up\", \"domain 3a contribution not tested in mammalian VPS33A\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Positioned VPS33A upstream of ULK1 in a pro-autophagic axis relevant to cancer drug sensitivity.\",\n      \"evidence\": \"siRNA knockdown and ULK1 overexpression rescue with LC3 flux, proliferation assays, and xenograft in cholangiocarcinoma cells\",\n      \"pmids\": [\"41718964\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"no direct VPS33A\\u2013ULK1 biochemical interaction shown\", \"mechanism by which VPS33A loss reduces ULK1 levels unknown\", \"single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How HOPS-incorporated VPS33A selects among distinct SNARE sets at different organelles and how phosphoregulation is coordinated across pathways remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"no reconstituted fusion assay defining VPS33A's catalytic contribution to SNARE zippering\", \"kinase/phosphatase governing STX17 N-peptide switch unidentified\", \"structure of VPS33A within an assembled HOPS-SNARE intermediate lacking\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [9, 11]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [6, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [4, 8]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [2, 7]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 10]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [1, 6, 9]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 2, 4]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [5, 11]}\n    ],\n    \"complexes\": [\"HOPS\", \"CORVET\"],\n    \"partners\": [\"VPS16\", \"STX17\", \"SNAP29\", \"VAMP7\", \"Stx11\", \"VPS41\", \"VPS39\", \"VPS11\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}