{"gene":"VPS35L","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2017,"finding":"VPS35L (C16orf62) is a core subunit of the Retriever complex, a heterotrimer composed of DSCR3 (VPS26C), C16orf62 (VPS35L), and VPS29. Retriever is biochemically and functionally distinct from retromer, associates with the cargo adaptor SNX17, and couples with CCC and WASH complexes to prevent lysosomal degradation and promote cell surface recycling of α5β1 integrin and over 120 cell surface proteins.","method":"Co-immunoprecipitation, quantitative proteomic analysis, siRNA knockdown with cargo recycling readout, biochemical fractionation","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, quantitative proteomics, and functional rescue with multiple orthogonal methods in a single foundational study","pmids":["28892079"],"is_preprint":false},{"year":2019,"finding":"CCC and Retriever complexes are closely linked through sharing VPS35L as a common subunit. The integrity of CCC, but not Retriever, is required to maintain normal endosomal levels of PI(3)P; CCC depletion leads to elevated PI(3)P, enhanced WASH activation, excess endosomal F-actin, and trapping of internalized receptors. CCC regulates phosphorylation and endosomal recruitment of the PI(3)P phosphatase MTMR2.","method":"Co-immunoprecipitation, siRNA knockdown, phosphoinositide measurements, fluorescence imaging of endosomal F-actin and receptor trafficking","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (biochemical, imaging, genetic depletion) in a single study establishing VPS35L as shared subunit and PI(3)P regulatory mechanism","pmids":["31537807"],"is_preprint":false},{"year":2023,"finding":"Cryo-EM structure of the human Retriever complex (VPS35L, VPS26C, VPS29) at high resolution reveals a unique assembly mechanism distinct from its paralog retromer. AlphaFold predictions combined with biochemical, cellular, and proteomic analyses elucidate how the Retriever-CCC supercomplex is organized and show that cancer-associated mutations in VPS35L disrupt complex formation and impair membrane protein homeostasis.","method":"Cryogenic electron microscopy, AlphaFold structural prediction, biochemical co-immunoprecipitation, quantitative proteomics, cell-based membrane protein trafficking assays, mutagenesis of cancer-associated variants","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution cryo-EM structure combined with mutagenesis and proteomic validation, peer-reviewed publication","pmids":["38062209"],"is_preprint":false},{"year":2023,"finding":"Cryo-EM structure of Retriever (VPS35L, VPS26C, VPS29) and structural organization of the entire Retriever-CCC complex established, with cancer-associated mutations shown to disrupt complex formation. (Preprint version of PMID:38062209.)","method":"Cryogenic electron microscopy, AlphaFold predictions, biochemical and proteomic analyses","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 1 / Strong — same cryo-EM + mutagenesis + proteomics dataset as the published peer-reviewed version; confidence derived from the replicated peer-reviewed study","pmids":["37333304","37397996"],"is_preprint":true},{"year":2024,"finding":"Structure of the 16-protein Commander complex determined by cryo-EM and mass spectrometry-based proteomics reveals that VPS35L is part of the Retriever subcomplex (with VPS26C and VPS29), which together with DENND10 forms an effector module scaffolded by CCDC22 and CCDC93 onto a stable COMMD1-10 core. Major interaction interfaces are defined, and a strong association with cilium assembly and centrosome/centriole functions is uncovered.","method":"Cryogenic electron microscopy of endogenous complex, mass spectrometry-based proteomics, biochemical interaction mapping","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM of endogenous complex combined with proteomics interaction mapping, peer-reviewed, single lab","pmids":["38459129"],"is_preprint":false},{"year":2019,"finding":"Biallelic loss-of-function variants in VPS35L (compound heterozygous frameshift + missense) cause 3C/Ritscher-Schinzel-like syndrome. The missense variant (p.Ala919Thr) specifically abolishes Retriever complex formation. VPS35L knockout cells show decreased autophagic function under nutrient-rich, starvation, and Torin 1 conditions. Vps35l homozygous knockout mice are embryonic lethal between E7.5 and E10.5.","method":"Exome sequencing, co-immunoprecipitation (complex formation assay), knockout mouse generation, autophagy flux assays (LC3-II/p62), cellular loss-of-function","journal":"Journal of medical genetics","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, knockout mouse, autophagy assays) in a single study with defined phenotypic readouts","pmids":["31712251"],"is_preprint":false},{"year":2014,"finding":"C16orf62 (VPS35L) is part of the CCC complex (COMMD/CCDC22/CCDC93/C16orf62) that is linked to early endosomes via interaction with the WASH complex subunit FAM21. This assembly is required for endosomal trafficking of the copper transporter ATP7A; CCC component depletion prevents copper-dependent movement of ATP7A from endosomes.","method":"Co-immunoprecipitation, siRNA knockdown, fluorescence microscopy of endosomal localization, copper homeostasis assays","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, knockdown with defined trafficking phenotype, replicated in human patient cells with CCDC22 mutations","pmids":["25355947"],"is_preprint":false},{"year":2022,"finding":"VPS35L is a shared subunit between Retriever and CCC complexes in hepatocytes. Liver-specific VPS35L deletion reduces VPS26C levels, minimally impacts CCC composition, decreases cell surface LDLR and LRP1, and raises plasma cholesterol by ~21%. In contrast, VPS26C deletion does not affect VPS35L or CCC, but selectively impairs LRP1 (not LDLR) trafficking and delays postprandial triglyceride clearance.","method":"Somatic CRISPR/Cas9 liver-specific gene editing in mice, cell surface biotinylation, plasma lipid measurements, quantitative proteomics of complex composition","journal":"Arteriosclerosis, thrombosis, and vascular biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — in vivo CRISPR/Cas9 knockout with biochemical and physiological readouts, single lab with multiple orthogonal approaches","pmids":["36353989"],"is_preprint":false},{"year":2022,"finding":"VPS35L ablation in patient-derived cells decreases cell surface levels of LRP1 and LDLR, resulting in reduced LDL cellular uptake, establishing the molecular mechanism of hypercholesterolaemia in VPS35L-associated Ritscher-Schinzel syndrome.","method":"Patient-derived cell lines, flow cytometry for cell surface receptor levels, LDL uptake assay","journal":"Journal of medical genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — patient cell-based experiment with defined readout, single lab, single method per endpoint","pmids":["36113987"],"is_preprint":false},{"year":2018,"finding":"C16orf62 (VPS35L) is part of the core CCC complex (CCDC22, CCDC93, C16orf62); COMMD protein deficiency destabilizes this core complex and reduces cell surface LDLR and LRP1, leading to hypercholesterolaemia. CCDC22 deletion via CRISPR/Cas9 somatic editing similarly destabilizes the entire CCC complex including C16orf62.","method":"Liver-specific knockout mice (Commd1/6/9), CRISPR/Cas9 somatic gene editing (Ccdc22), quantitative targeted proteomics, cell surface receptor measurements","journal":"Circulation research","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo mouse knockouts replicated across multiple COMMD members, quantitative proteomics of complex composition, CRISPR validation","pmids":["29545368"],"is_preprint":false},{"year":2021,"finding":"HPV16 L2 minor capsid protein directly interacts with the C16orf62 (VPS35L) subunit of Retriever during infection, in a manner similar to L2's interaction with VPS35 of retromer. This interaction mediates Retriever recruitment during retrograde trafficking of the viral genome; knockdown of VPS35L impairs HPV infection.","method":"Co-immunoprecipitation of L2 with retriever subunits, siRNA knockdown of VPS35L with infectivity readout, colocalization imaging","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP of interaction combined with knockdown infectivity assay and colocalization, single lab","pmids":["33177206"],"is_preprint":false},{"year":2024,"finding":"C16orf62 (VPS35L) knockout via genome-wide CRISPR/Cas9 screen dramatically reduces binding and internalization of porcine deltacoronavirus (PDCoV) into host cells, and this effect is mediated through downregulation of the PDCoV receptor APN (aminopeptidase N) at the cell surface, consistent with VPS35L's role in endosomal recycling. No direct interaction between C16orf62 and the viral spike protein was detected.","method":"Genome-wide CRISPR/Cas9 library screen, gene knockout validation, virus binding/internalization assays, cell surface APN quantification","journal":"Emerging microbes & infections","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR knockout with defined mechanistic readout (surface receptor levels + viral entry), single lab","pmids":["39222358"],"is_preprint":false},{"year":2024,"finding":"SNX17 directly interacts with Retriever through its C-terminal region binding the interface of VPS35L and VPS26C subunits. This interaction is enhanced by SNX17 cargo binding (which relieves an intramolecular autoinhibitory interaction) and by SNX17 binding to PI(3)P-containing membranes, revealing dual activation mechanisms for Retriever recruitment to endosomes.","method":"Biophysical assays with recombinant proteins, structural model-guided mutagenesis, liposome binding assays","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with recombinant proteins, mutagenesis, and liposome assays establishing direct interaction and mechanism, single lab","pmids":["39653850"],"is_preprint":false},{"year":2026,"finding":"VPS35L (Vps35l) deficiency in RAW264.7 cells impairs LRP1 expression at the plasma membrane and impairs osteoclast differentiation, demonstrating that Retriever-mediated endosome-to-plasma membrane recycling is required for maintenance of Siglec-15 ligands and osteoclast precursor function.","method":"Genome-wide knockout screen (CRISPR/Cas9), flow cytometry for Siglec-15 ligand and LRP1 surface levels, osteoclast differentiation assay","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR knockout with defined surface receptor and differentiation phenotype readouts, genome-wide screen context","pmids":["41569849"],"is_preprint":false}],"current_model":"VPS35L (C16orf62) is a core structural subunit of the Retriever complex (VPS35L–VPS26C–VPS29) and is shared with the CCC complex, forming the larger Commander supercomplex; its cryo-EM structure reveals an assembly mechanism distinct from retromer, and it functions as the central scaffold for SNX17-mediated cargo recognition and endosomal recycling of integrins, lipoprotein receptors (LDLR, LRP1), and other transmembrane proteins back to the cell surface, with loss-of-function causing hypercholesterolaemia, impaired autophagy, and the developmental disorder Ritscher-Schinzel syndrome."},"narrative":{"mechanistic_narrative":"VPS35L (C16orf62) is the central scaffolding subunit of an endosomal recycling machinery that returns internalized transmembrane proteins to the cell surface and prevents their lysosomal degradation [PMID:28892079]. It is the core component of the Retriever heterotrimer (VPS35L–VPS26C–VPS29), a complex that is biochemically distinct from retromer and that couples with the CCC and WASH complexes to recycle α5β1 integrin and over 120 cell surface proteins [PMID:28892079]. Cryo-EM structures show that Retriever assembles through a mechanism unlike its retromer paralog, and that VPS35L sits within the larger Commander supercomplex as part of a Retriever–DENND10 effector module scaffolded by CCDC22 and CCDC93 onto a COMMD1-10 core [PMID:38062209, PMID:38459129]. VPS35L is the shared subunit bridging Retriever and the CCC complex [PMID:31537807, PMID:36353989], and cargo recognition is mediated by SNX17, which binds directly at the VPS35L–VPS26C interface in a reaction activated both by cargo engagement and by SNX17 association with PI(3)P membranes [PMID:39653850]. Within the CCC complex, VPS35L participates in regulating endosomal PI(3)P levels and WASH-dependent F-actin, controlling receptor retention versus recycling [PMID:31537807], and supports trafficking of the copper transporter ATP7A [PMID:25355947]. Physiologically, VPS35L is required to maintain cell surface LDLR and LRP1, and its loss reduces LDL uptake and raises plasma cholesterol [PMID:36353989, PMID:36113987]. Biallelic loss-of-function variants in VPS35L cause 3C/Ritscher-Schinzel-like syndrome, with a missense variant that abolishes Retriever assembly, impaired autophagy in knockout cells, and embryonic lethality in homozygous knockout mice [PMID:31712251]. VPS35L is also exploited by pathogens, supporting HPV16 retrograde trafficking via direct binding of the L2 capsid protein and enabling coronavirus entry by maintaining surface levels of the receptor APN [PMID:33177206, PMID:39222358].","teleology":[{"year":2014,"claim":"Before VPS35L was assigned to any complex, it was unclear how COMMD/CCDC proteins linked to endosomal trafficking; this work placed C16orf62 within the CCC complex tethered to endosomes via WASH subunit FAM21 and required for ATP7A copper-dependent trafficking.","evidence":"Co-immunoprecipitation, siRNA knockdown, fluorescence microscopy and copper homeostasis assays in human cells","pmids":["25355947"],"confidence":"High","gaps":["Did not resolve whether C16orf62 has a distinct second complex beyond CCC","No structural basis for assembly","Cargo repertoire beyond ATP7A undefined"]},{"year":2017,"claim":"It was unknown how cargo internalized via SNX17 escaped lysosomal degradation; this study defined the Retriever heterotrimer (VPS35L–VPS26C–VPS29) as a retromer-distinct machine that, with SNX17, CCC, and WASH, recycles integrin and >120 surface proteins.","evidence":"Reciprocal Co-IP, quantitative proteomics, and siRNA knockdown with cargo recycling readouts","pmids":["28892079"],"confidence":"High","gaps":["Molecular mechanism of SNX17–Retriever coupling not resolved","No structure of the complex","Direct versus indirect SNX17 contacts unclear"]},{"year":2019,"claim":"The functional relationship between CCC and Retriever was undefined; this work established VPS35L as the shared subunit and showed CCC integrity (not Retriever) controls endosomal PI(3)P via MTMR2, governing WASH/F-actin and receptor retention.","evidence":"Co-IP, siRNA knockdown, phosphoinositide measurements, imaging of endosomal F-actin and receptors","pmids":["31537807"],"confidence":"High","gaps":["Mechanism by which CCC controls MTMR2 phosphorylation incomplete","How shared VPS35L is partitioned between complexes unknown"]},{"year":2019,"claim":"Whether VPS35L disruption causes human disease was unknown; biallelic loss-of-function variants were shown to cause Ritscher-Schinzel-like syndrome, with a missense allele abolishing Retriever assembly, impaired autophagy, and embryonic lethality in null mice.","evidence":"Exome sequencing, Co-IP complex-formation assay, knockout mouse, autophagy flux assays","pmids":["31712251"],"confidence":"High","gaps":["Mechanistic link between Retriever loss and autophagy defect not detailed","Tissue-specific contributions to syndrome phenotypes unresolved"]},{"year":2018,"claim":"How endosomal recycling controls plasma lipids was unclear; in vivo work showed the CCC core including C16orf62 is required to maintain surface LDLR and LRP1, and its destabilization causes hypercholesterolaemia.","evidence":"Liver-specific COMMD knockout mice, CRISPR/Cas9 somatic CCDC22 editing, targeted proteomics, surface receptor measurements","pmids":["29545368"],"confidence":"High","gaps":["Direct role of VPS35L versus COMMD/CCDC partners not isolated here","Receptor selectivity mechanism undefined"]},{"year":2021,"claim":"It was unknown whether Retriever is hijacked during viral entry; HPV16 L2 was shown to bind VPS35L directly to recruit Retriever during retrograde genome trafficking.","evidence":"Co-IP of L2 with Retriever subunits, siRNA knockdown infectivity assay, colocalization imaging","pmids":["33177206"],"confidence":"Medium","gaps":["Binding interface on VPS35L not mapped","Single lab, no structural validation"]},{"year":2022,"claim":"The specific contributions of VPS35L versus VPS26C to lipoprotein receptor trafficking were unresolved; in vivo deletions showed VPS35L loss reduces both LDLR and LRP1 and raises cholesterol, whereas VPS26C loss selectively affects LRP1.","evidence":"Somatic CRISPR/Cas9 liver-specific editing in mice, surface biotinylation, plasma lipid and proteomic analyses","pmids":["36353989","36113987"],"confidence":"High","gaps":["Why VPS35L and VPS26C differ in receptor selectivity unexplained","Patient-cell LDL uptake endpoint relies on single method per readout"]},{"year":2023,"claim":"The structural basis of Retriever assembly was unknown; cryo-EM revealed a unique assembly distinct from retromer and showed cancer-associated VPS35L mutations disrupt complex formation and membrane protein homeostasis.","evidence":"Cryo-EM, AlphaFold modeling, Co-IP, proteomics, trafficking assays, variant mutagenesis","pmids":["38062209","37333304","37397996"],"confidence":"High","gaps":["Cargo-bound conformations not captured","Dynamics of CCC coupling at atomic resolution incomplete"]},{"year":2024,"claim":"The architecture of the full higher-order assembly was undefined; cryo-EM of the endogenous 16-protein Commander complex placed the VPS35L Retriever module with DENND10 on a CCDC22/CCDC93-scaffolded COMMD1-10 core and linked it to cilium and centrosome functions.","evidence":"Cryo-EM of endogenous complex, mass spectrometry proteomics, interaction mapping","pmids":["38459129"],"confidence":"High","gaps":["Functional consequences of cilium/centrosome association not mechanistically dissected","Stoichiometry dynamics in cells unresolved"]},{"year":2024,"claim":"How SNX17 recruits Retriever to endosomes was unknown; reconstitution showed SNX17 binds the VPS35L–VPS26C interface, with the interaction activated both by cargo binding relieving autoinhibition and by PI(3)P membrane association.","evidence":"Biophysical assays with recombinant proteins, structure-guided mutagenesis, liposome binding","pmids":["39653850"],"confidence":"High","gaps":["In vivo validation of the dual-activation model limited","Quantitative contribution of each input to recruitment unmeasured"]},{"year":2024,"claim":"Whether VPS35L mediates other viral entry routes was open; a genome-wide screen showed VPS35L knockout reduces coronavirus entry by lowering surface levels of the receptor APN, without direct spike interaction.","evidence":"Genome-wide CRISPR/Cas9 screen, knockout validation, virus binding/internalization assays, surface APN quantification","pmids":["39222358"],"confidence":"Medium","gaps":["Whether APN is a direct Retriever cargo not established","Single host-cell system"]},{"year":2026,"claim":"The physiological breadth of Retriever recycling was extending; VPS35L deficiency was shown to impair LRP1 surface expression and Siglec-15 ligand maintenance, blocking osteoclast differentiation.","evidence":"Genome-wide CRISPR/Cas9 knockout screen, flow cytometry of surface receptors, osteoclast differentiation assay","pmids":["41569849"],"confidence":"Medium","gaps":["Direct cargo relationship between Retriever and Siglec-15 ligands not biochemically confirmed","In vivo bone phenotype not tested"]},{"year":null,"claim":"How VPS35L is partitioned between the CCC and Retriever assemblies within the Commander supercomplex, and how this partitioning sets cargo selectivity in different tissues, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No mechanism defining cargo-specific routing","Tissue-specific regulation of complex assembly unknown","Structural basis of CCC–Retriever switching incomplete"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,12]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[2,4]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[1,6]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[7,8]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,6]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[0,7]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[5,8]}],"complexes":["Retriever","CCC complex","Commander complex"],"partners":["VPS26C","VPS29","SNX17","CCDC22","CCDC93","FAM21","DENND10"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q7Z3J2","full_name":"VPS35 endosomal protein-sorting factor-like","aliases":["Esophageal cancer-associated protein"],"length_aa":963,"mass_kda":109.6,"function":"Acts as a component of the retriever complex. The retriever complex is a heterotrimeric complex related to retromer cargo-selective complex (CSC) and essential for retromer-independent retrieval and recycling of numerous cargos such as integrin alpha-5/beta-1 (ITGA5:ITGB1) (PubMed:28892079). The recruitment of the retriever complex to the endosomal membrane involves CCC and WASH complexes (PubMed:28892079). In the endosomes, drives the retrieval and recycling of NxxY-motif-containing cargo proteins by coupling to SNX17, a cargo essential for the homeostatic maintenance of numerous cell surface proteins associated with processes that include cell migration, cell adhesion, nutrient supply and cell signaling (PubMed:28892079). Involved in copper-dependent ATP7A trafficking between the trans-Golgi network and vesicles in the cell periphery; the function is proposed to depend on its association with the CCC complex and cooperation with the WASH complex on early endosomes. Does not seem to be required for CCC complex stability (PubMed:25355947) (Microbial infection) The heterotrimeric retriever complex, in collaboration with the CCC complex, mediates the exit of human papillomavirus to the cell surface","subcellular_location":"Membrane; Endosome","url":"https://www.uniprot.org/uniprotkb/Q7Z3J2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/VPS35L","classification":"Not Classified","n_dependent_lines":124,"n_total_lines":1208,"dependency_fraction":0.10264900662251655},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CCDC22","stoichiometry":10.0},{"gene":"CCDC93","stoichiometry":10.0},{"gene":"COMMD1","stoichiometry":10.0},{"gene":"COMMD2","stoichiometry":10.0},{"gene":"COMMD4","stoichiometry":10.0},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"COMMD6","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/VPS35L","total_profiled":1310},"omim":[{"mim_id":"620553","title":"COILED-COIL DOMAIN-CONTAINING PROTEIN 93; CCDC93","url":"https://www.omim.org/entry/620553"},{"mim_id":"619135","title":"RITSCHER-SCHINZEL SYNDROME 3; RTSC3","url":"https://www.omim.org/entry/619135"},{"mim_id":"618981","title":"VPS35 ENDOSOMAL PROTEIN-SORTING FACTOR-LIKE; VPS35L","url":"https://www.omim.org/entry/618981"},{"mim_id":"612377","title":"COMM DOMAIN-CONTAINING PROTEIN 6; COMMD6","url":"https://www.omim.org/entry/612377"},{"mim_id":"612299","title":"COMM DOMAIN-CONTAINING PROTEIN 9; COMMD9","url":"https://www.omim.org/entry/612299"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Mitochondria","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/VPS35L"},"hgnc":{"alias_symbol":["MGC16824"],"prev_symbol":["C16orf62"]},"alphafold":{"accession":"Q7Z3J2","domains":[{"cath_id":"-","chopping":"883-963","consensus_level":"medium","plddt":86.7473,"start":883,"end":963}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z3J2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z3J2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z3J2-F1-predicted_aligned_error_v6.png","plddt_mean":84.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=VPS35L","jax_strain_url":"https://www.jax.org/strain/search?query=VPS35L"},"sequence":{"accession":"Q7Z3J2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q7Z3J2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q7Z3J2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z3J2"}},"corpus_meta":[{"pmid":"28892079","id":"PMC_28892079","title":"Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling.","date":"2017","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/28892079","citation_count":282,"is_preprint":false},{"pmid":"23728943","id":"PMC_23728943","title":"Identification of driver genes in hepatocellular carcinoma by exome sequencing.","date":"2013","source":"Hepatology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/23728943","citation_count":245,"is_preprint":false},{"pmid":"25355947","id":"PMC_25355947","title":"COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A.","date":"2014","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/25355947","citation_count":186,"is_preprint":false},{"pmid":"30993794","id":"PMC_30993794","title":"Towards a molecular understanding of endosomal trafficking by Retromer and Retriever.","date":"2019","source":"Traffic (Copenhagen, 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Retriever is biochemically and functionally distinct from retromer, associates with the cargo adaptor SNX17, and couples with CCC and WASH complexes to prevent lysosomal degradation and promote cell surface recycling of α5β1 integrin and over 120 cell surface proteins.\",\n      \"method\": \"Co-immunoprecipitation, quantitative proteomic analysis, siRNA knockdown with cargo recycling readout, biochemical fractionation\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, quantitative proteomics, and functional rescue with multiple orthogonal methods in a single foundational study\",\n      \"pmids\": [\"28892079\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CCC and Retriever complexes are closely linked through sharing VPS35L as a common subunit. The integrity of CCC, but not Retriever, is required to maintain normal endosomal levels of PI(3)P; CCC depletion leads to elevated PI(3)P, enhanced WASH activation, excess endosomal F-actin, and trapping of internalized receptors. CCC regulates phosphorylation and endosomal recruitment of the PI(3)P phosphatase MTMR2.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, phosphoinositide measurements, fluorescence imaging of endosomal F-actin and receptor trafficking\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (biochemical, imaging, genetic depletion) in a single study establishing VPS35L as shared subunit and PI(3)P regulatory mechanism\",\n      \"pmids\": [\"31537807\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Cryo-EM structure of the human Retriever complex (VPS35L, VPS26C, VPS29) at high resolution reveals a unique assembly mechanism distinct from its paralog retromer. AlphaFold predictions combined with biochemical, cellular, and proteomic analyses elucidate how the Retriever-CCC supercomplex is organized and show that cancer-associated mutations in VPS35L disrupt complex formation and impair membrane protein homeostasis.\",\n      \"method\": \"Cryogenic electron microscopy, AlphaFold structural prediction, biochemical co-immunoprecipitation, quantitative proteomics, cell-based membrane protein trafficking assays, mutagenesis of cancer-associated variants\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution cryo-EM structure combined with mutagenesis and proteomic validation, peer-reviewed publication\",\n      \"pmids\": [\"38062209\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Cryo-EM structure of Retriever (VPS35L, VPS26C, VPS29) and structural organization of the entire Retriever-CCC complex established, with cancer-associated mutations shown to disrupt complex formation. (Preprint version of PMID:38062209.)\",\n      \"method\": \"Cryogenic electron microscopy, AlphaFold predictions, biochemical and proteomic analyses\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — same cryo-EM + mutagenesis + proteomics dataset as the published peer-reviewed version; confidence derived from the replicated peer-reviewed study\",\n      \"pmids\": [\"37333304\", \"37397996\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Structure of the 16-protein Commander complex determined by cryo-EM and mass spectrometry-based proteomics reveals that VPS35L is part of the Retriever subcomplex (with VPS26C and VPS29), which together with DENND10 forms an effector module scaffolded by CCDC22 and CCDC93 onto a stable COMMD1-10 core. Major interaction interfaces are defined, and a strong association with cilium assembly and centrosome/centriole functions is uncovered.\",\n      \"method\": \"Cryogenic electron microscopy of endogenous complex, mass spectrometry-based proteomics, biochemical interaction mapping\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM of endogenous complex combined with proteomics interaction mapping, peer-reviewed, single lab\",\n      \"pmids\": [\"38459129\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Biallelic loss-of-function variants in VPS35L (compound heterozygous frameshift + missense) cause 3C/Ritscher-Schinzel-like syndrome. The missense variant (p.Ala919Thr) specifically abolishes Retriever complex formation. VPS35L knockout cells show decreased autophagic function under nutrient-rich, starvation, and Torin 1 conditions. Vps35l homozygous knockout mice are embryonic lethal between E7.5 and E10.5.\",\n      \"method\": \"Exome sequencing, co-immunoprecipitation (complex formation assay), knockout mouse generation, autophagy flux assays (LC3-II/p62), cellular loss-of-function\",\n      \"journal\": \"Journal of medical genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, knockout mouse, autophagy assays) in a single study with defined phenotypic readouts\",\n      \"pmids\": [\"31712251\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"C16orf62 (VPS35L) is part of the CCC complex (COMMD/CCDC22/CCDC93/C16orf62) that is linked to early endosomes via interaction with the WASH complex subunit FAM21. This assembly is required for endosomal trafficking of the copper transporter ATP7A; CCC component depletion prevents copper-dependent movement of ATP7A from endosomes.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, fluorescence microscopy of endosomal localization, copper homeostasis assays\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, knockdown with defined trafficking phenotype, replicated in human patient cells with CCDC22 mutations\",\n      \"pmids\": [\"25355947\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"VPS35L is a shared subunit between Retriever and CCC complexes in hepatocytes. Liver-specific VPS35L deletion reduces VPS26C levels, minimally impacts CCC composition, decreases cell surface LDLR and LRP1, and raises plasma cholesterol by ~21%. In contrast, VPS26C deletion does not affect VPS35L or CCC, but selectively impairs LRP1 (not LDLR) trafficking and delays postprandial triglyceride clearance.\",\n      \"method\": \"Somatic CRISPR/Cas9 liver-specific gene editing in mice, cell surface biotinylation, plasma lipid measurements, quantitative proteomics of complex composition\",\n      \"journal\": \"Arteriosclerosis, thrombosis, and vascular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo CRISPR/Cas9 knockout with biochemical and physiological readouts, single lab with multiple orthogonal approaches\",\n      \"pmids\": [\"36353989\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"VPS35L ablation in patient-derived cells decreases cell surface levels of LRP1 and LDLR, resulting in reduced LDL cellular uptake, establishing the molecular mechanism of hypercholesterolaemia in VPS35L-associated Ritscher-Schinzel syndrome.\",\n      \"method\": \"Patient-derived cell lines, flow cytometry for cell surface receptor levels, LDL uptake assay\",\n      \"journal\": \"Journal of medical genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — patient cell-based experiment with defined readout, single lab, single method per endpoint\",\n      \"pmids\": [\"36113987\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"C16orf62 (VPS35L) is part of the core CCC complex (CCDC22, CCDC93, C16orf62); COMMD protein deficiency destabilizes this core complex and reduces cell surface LDLR and LRP1, leading to hypercholesterolaemia. CCDC22 deletion via CRISPR/Cas9 somatic editing similarly destabilizes the entire CCC complex including C16orf62.\",\n      \"method\": \"Liver-specific knockout mice (Commd1/6/9), CRISPR/Cas9 somatic gene editing (Ccdc22), quantitative targeted proteomics, cell surface receptor measurements\",\n      \"journal\": \"Circulation research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo mouse knockouts replicated across multiple COMMD members, quantitative proteomics of complex composition, CRISPR validation\",\n      \"pmids\": [\"29545368\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HPV16 L2 minor capsid protein directly interacts with the C16orf62 (VPS35L) subunit of Retriever during infection, in a manner similar to L2's interaction with VPS35 of retromer. This interaction mediates Retriever recruitment during retrograde trafficking of the viral genome; knockdown of VPS35L impairs HPV infection.\",\n      \"method\": \"Co-immunoprecipitation of L2 with retriever subunits, siRNA knockdown of VPS35L with infectivity readout, colocalization imaging\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP of interaction combined with knockdown infectivity assay and colocalization, single lab\",\n      \"pmids\": [\"33177206\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"C16orf62 (VPS35L) knockout via genome-wide CRISPR/Cas9 screen dramatically reduces binding and internalization of porcine deltacoronavirus (PDCoV) into host cells, and this effect is mediated through downregulation of the PDCoV receptor APN (aminopeptidase N) at the cell surface, consistent with VPS35L's role in endosomal recycling. No direct interaction between C16orf62 and the viral spike protein was detected.\",\n      \"method\": \"Genome-wide CRISPR/Cas9 library screen, gene knockout validation, virus binding/internalization assays, cell surface APN quantification\",\n      \"journal\": \"Emerging microbes & infections\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR knockout with defined mechanistic readout (surface receptor levels + viral entry), single lab\",\n      \"pmids\": [\"39222358\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SNX17 directly interacts with Retriever through its C-terminal region binding the interface of VPS35L and VPS26C subunits. This interaction is enhanced by SNX17 cargo binding (which relieves an intramolecular autoinhibitory interaction) and by SNX17 binding to PI(3)P-containing membranes, revealing dual activation mechanisms for Retriever recruitment to endosomes.\",\n      \"method\": \"Biophysical assays with recombinant proteins, structural model-guided mutagenesis, liposome binding assays\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with recombinant proteins, mutagenesis, and liposome assays establishing direct interaction and mechanism, single lab\",\n      \"pmids\": [\"39653850\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"VPS35L (Vps35l) deficiency in RAW264.7 cells impairs LRP1 expression at the plasma membrane and impairs osteoclast differentiation, demonstrating that Retriever-mediated endosome-to-plasma membrane recycling is required for maintenance of Siglec-15 ligands and osteoclast precursor function.\",\n      \"method\": \"Genome-wide knockout screen (CRISPR/Cas9), flow cytometry for Siglec-15 ligand and LRP1 surface levels, osteoclast differentiation assay\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR knockout with defined surface receptor and differentiation phenotype readouts, genome-wide screen context\",\n      \"pmids\": [\"41569849\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"VPS35L (C16orf62) is a core structural subunit of the Retriever complex (VPS35L–VPS26C–VPS29) and is shared with the CCC complex, forming the larger Commander supercomplex; its cryo-EM structure reveals an assembly mechanism distinct from retromer, and it functions as the central scaffold for SNX17-mediated cargo recognition and endosomal recycling of integrins, lipoprotein receptors (LDLR, LRP1), and other transmembrane proteins back to the cell surface, with loss-of-function causing hypercholesterolaemia, impaired autophagy, and the developmental disorder Ritscher-Schinzel syndrome.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"VPS35L (C16orf62) is the central scaffolding subunit of an endosomal recycling machinery that returns internalized transmembrane proteins to the cell surface and prevents their lysosomal degradation [#0]. It is the core component of the Retriever heterotrimer (VPS35L–VPS26C–VPS29), a complex that is biochemically distinct from retromer and that couples with the CCC and WASH complexes to recycle α5β1 integrin and over 120 cell surface proteins [#0]. Cryo-EM structures show that Retriever assembles through a mechanism unlike its retromer paralog, and that VPS35L sits within the larger Commander supercomplex as part of a Retriever–DENND10 effector module scaffolded by CCDC22 and CCDC93 onto a COMMD1-10 core [#2, #4]. VPS35L is the shared subunit bridging Retriever and the CCC complex [#1, #7], and cargo recognition is mediated by SNX17, which binds directly at the VPS35L–VPS26C interface in a reaction activated both by cargo engagement and by SNX17 association with PI(3)P membranes [#12]. Within the CCC complex, VPS35L participates in regulating endosomal PI(3)P levels and WASH-dependent F-actin, controlling receptor retention versus recycling [#1], and supports trafficking of the copper transporter ATP7A [#6]. Physiologically, VPS35L is required to maintain cell surface LDLR and LRP1, and its loss reduces LDL uptake and raises plasma cholesterol [#7, #8]. Biallelic loss-of-function variants in VPS35L cause 3C/Ritscher-Schinzel-like syndrome, with a missense variant that abolishes Retriever assembly, impaired autophagy in knockout cells, and embryonic lethality in homozygous knockout mice [#5]. VPS35L is also exploited by pathogens, supporting HPV16 retrograde trafficking via direct binding of the L2 capsid protein and enabling coronavirus entry by maintaining surface levels of the receptor APN [#10, #11].\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Before VPS35L was assigned to any complex, it was unclear how COMMD/CCDC proteins linked to endosomal trafficking; this work placed C16orf62 within the CCC complex tethered to endosomes via WASH subunit FAM21 and required for ATP7A copper-dependent trafficking.\",\n      \"evidence\": \"Co-immunoprecipitation, siRNA knockdown, fluorescence microscopy and copper homeostasis assays in human cells\",\n      \"pmids\": [\"25355947\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve whether C16orf62 has a distinct second complex beyond CCC\", \"No structural basis for assembly\", \"Cargo repertoire beyond ATP7A undefined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"It was unknown how cargo internalized via SNX17 escaped lysosomal degradation; this study defined the Retriever heterotrimer (VPS35L–VPS26C–VPS29) as a retromer-distinct machine that, with SNX17, CCC, and WASH, recycles integrin and >120 surface proteins.\",\n      \"evidence\": \"Reciprocal Co-IP, quantitative proteomics, and siRNA knockdown with cargo recycling readouts\",\n      \"pmids\": [\"28892079\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism of SNX17–Retriever coupling not resolved\", \"No structure of the complex\", \"Direct versus indirect SNX17 contacts unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"The functional relationship between CCC and Retriever was undefined; this work established VPS35L as the shared subunit and showed CCC integrity (not Retriever) controls endosomal PI(3)P via MTMR2, governing WASH/F-actin and receptor retention.\",\n      \"evidence\": \"Co-IP, siRNA knockdown, phosphoinositide measurements, imaging of endosomal F-actin and receptors\",\n      \"pmids\": [\"31537807\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which CCC controls MTMR2 phosphorylation incomplete\", \"How shared VPS35L is partitioned between complexes unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Whether VPS35L disruption causes human disease was unknown; biallelic loss-of-function variants were shown to cause Ritscher-Schinzel-like syndrome, with a missense allele abolishing Retriever assembly, impaired autophagy, and embryonic lethality in null mice.\",\n      \"evidence\": \"Exome sequencing, Co-IP complex-formation assay, knockout mouse, autophagy flux assays\",\n      \"pmids\": [\"31712251\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic link between Retriever loss and autophagy defect not detailed\", \"Tissue-specific contributions to syndrome phenotypes unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"How endosomal recycling controls plasma lipids was unclear; in vivo work showed the CCC core including C16orf62 is required to maintain surface LDLR and LRP1, and its destabilization causes hypercholesterolaemia.\",\n      \"evidence\": \"Liver-specific COMMD knockout mice, CRISPR/Cas9 somatic CCDC22 editing, targeted proteomics, surface receptor measurements\",\n      \"pmids\": [\"29545368\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct role of VPS35L versus COMMD/CCDC partners not isolated here\", \"Receptor selectivity mechanism undefined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"It was unknown whether Retriever is hijacked during viral entry; HPV16 L2 was shown to bind VPS35L directly to recruit Retriever during retrograde genome trafficking.\",\n      \"evidence\": \"Co-IP of L2 with Retriever subunits, siRNA knockdown infectivity assay, colocalization imaging\",\n      \"pmids\": [\"33177206\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding interface on VPS35L not mapped\", \"Single lab, no structural validation\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"The specific contributions of VPS35L versus VPS26C to lipoprotein receptor trafficking were unresolved; in vivo deletions showed VPS35L loss reduces both LDLR and LRP1 and raises cholesterol, whereas VPS26C loss selectively affects LRP1.\",\n      \"evidence\": \"Somatic CRISPR/Cas9 liver-specific editing in mice, surface biotinylation, plasma lipid and proteomic analyses\",\n      \"pmids\": [\"36353989\", \"36113987\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why VPS35L and VPS26C differ in receptor selectivity unexplained\", \"Patient-cell LDL uptake endpoint relies on single method per readout\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The structural basis of Retriever assembly was unknown; cryo-EM revealed a unique assembly distinct from retromer and showed cancer-associated VPS35L mutations disrupt complex formation and membrane protein homeostasis.\",\n      \"evidence\": \"Cryo-EM, AlphaFold modeling, Co-IP, proteomics, trafficking assays, variant mutagenesis\",\n      \"pmids\": [\"38062209\", \"37333304\", \"37397996\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cargo-bound conformations not captured\", \"Dynamics of CCC coupling at atomic resolution incomplete\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"The architecture of the full higher-order assembly was undefined; cryo-EM of the endogenous 16-protein Commander complex placed the VPS35L Retriever module with DENND10 on a CCDC22/CCDC93-scaffolded COMMD1-10 core and linked it to cilium and centrosome functions.\",\n      \"evidence\": \"Cryo-EM of endogenous complex, mass spectrometry proteomics, interaction mapping\",\n      \"pmids\": [\"38459129\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequences of cilium/centrosome association not mechanistically dissected\", \"Stoichiometry dynamics in cells unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"How SNX17 recruits Retriever to endosomes was unknown; reconstitution showed SNX17 binds the VPS35L–VPS26C interface, with the interaction activated both by cargo binding relieving autoinhibition and by PI(3)P membrane association.\",\n      \"evidence\": \"Biophysical assays with recombinant proteins, structure-guided mutagenesis, liposome binding\",\n      \"pmids\": [\"39653850\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo validation of the dual-activation model limited\", \"Quantitative contribution of each input to recruitment unmeasured\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Whether VPS35L mediates other viral entry routes was open; a genome-wide screen showed VPS35L knockout reduces coronavirus entry by lowering surface levels of the receptor APN, without direct spike interaction.\",\n      \"evidence\": \"Genome-wide CRISPR/Cas9 screen, knockout validation, virus binding/internalization assays, surface APN quantification\",\n      \"pmids\": [\"39222358\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether APN is a direct Retriever cargo not established\", \"Single host-cell system\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"The physiological breadth of Retriever recycling was extending; VPS35L deficiency was shown to impair LRP1 surface expression and Siglec-15 ligand maintenance, blocking osteoclast differentiation.\",\n      \"evidence\": \"Genome-wide CRISPR/Cas9 knockout screen, flow cytometry of surface receptors, osteoclast differentiation assay\",\n      \"pmids\": [\"41569849\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct cargo relationship between Retriever and Siglec-15 ligands not biochemically confirmed\", \"In vivo bone phenotype not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How VPS35L is partitioned between the CCC and Retriever assemblies within the Commander supercomplex, and how this partitioning sets cargo selectivity in different tissues, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No mechanism defining cargo-specific routing\", \"Tissue-specific regulation of complex assembly unknown\", \"Structural basis of CCC–Retriever switching incomplete\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 12]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [2, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [1, 6]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [7, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [5, 8]}\n    ],\n    \"complexes\": [\"Retriever\", \"CCC complex\", \"Commander complex\"],\n    \"partners\": [\"VPS26C\", \"VPS29\", \"SNX17\", \"CCDC22\", \"CCDC93\", \"FAM21\", \"DENND10\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}