{"gene":"TBC1D23","run_date":"2026-06-10T10:51:54","timeline":{"discoveries":[{"year":2017,"finding":"TBC1D23 acts as a bridging factor (vesicle-golgin adaptor) for endosome-to-Golgi trafficking: its Rab GAP domain binds a conserved motif at the tips of golgin-245 and golgin-97 at the trans-Golgi, while its C-terminus binds to the WASH complex on endosome-derived vesicles, thereby linking vesicle to target membrane.","method":"Proximity biotinylation of golgin-captured vesicles, Co-IP, knockdown with trafficking assays, ectopic golgin vesicle-capture system","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (proximity biotinylation, Co-IP, functional knockdown, vesicle-capture assay) in a single rigorous study; mechanistic model confirmed by binding domain mapping","pmids":["29084197"],"is_preprint":false},{"year":2017,"finding":"Homozygous truncating mutations in TBC1D23 impair dense core vesicle and lysosomal trafficking dynamics in patient-derived fibroblasts, and knockdown of TBC1D23 by in utero electroporation disrupts cortical neuron positioning in vivo.","method":"Patient fibroblast vesicle/lysosomal trafficking assays, in utero electroporation knockdown in mouse cortex","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two orthogonal methods (cell-based trafficking assay, in vivo electroporation), single lab","pmids":["28823707"],"is_preprint":false},{"year":2019,"finding":"The C-terminal domain of TBC1D23 adopts a Pleckstrin Homology (PH) domain fold, selectively binds PtdIns(4)P on one surface, and binds FAM21 (a WASH complex subunit) via the opposite surface; mutations disrupting either interaction impair endosome-to-TGN trafficking and cause abnormal neuronal growth in zebrafish.","method":"Crystal structure of TBC1D23 C-terminal domain, phosphoinositide binding assays, mutagenesis, Co-IP with FAM21, zebrafish neuronal development assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with mutagenesis, biochemical binding assays, and in vivo zebrafish validation; multiple orthogonal methods in one study","pmids":["31624125"],"is_preprint":false},{"year":2012,"finding":"Tbc1d23 functions as a RAB-GAP to inhibit innate immunity signaling downstream of TLR-signaling adaptors MyD88 and Trif and upstream of the transcription factor XBP1, specifically affecting the maintenance (but not initiation) of inflammatory cytokine production.","method":"Tbc1d23 knockout mice, macrophage overexpression, epistasis analysis with pathway components (MyD88, Trif, XBP1), TLR stimulation assays","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic knockout combined with overexpression and epistasis mapping, single lab","pmids":["22312129"],"is_preprint":false},{"year":2020,"finding":"The crystal structure of the TBC1D23 N-terminus reveals it comprises both TBC and rhodanese domains; the rhodanese domain is catalytically inactive (not a sulfurtransferase or phosphatase) but instead packs against the TBC domain to form a platform that interacts with golgin-97/245. Disrupting golgin binding (but not the putative catalytic site) impairs neuronal growth and brain development in zebrafish.","method":"Crystal structure of TBC1D23 N-terminal domain (TBC + rhodanese), mutagenesis of catalytic site vs. golgin-binding surface, zebrafish developmental assays","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional mutagenesis and in vivo zebrafish validation; multiple orthogonal methods","pmids":["32453802"],"is_preprint":false},{"year":2024,"finding":"TBC1D23 directly interacts with LKB1 and recruits LKB1 to the Golgi apparatus, promoting Golgi-specific activation of AMPK upon energy stress; Golgi-targeted LKB1 expression rescues TBC1D23 deficiency in zebrafish, placing TBC1D23 upstream of LKB1-AMPK signaling at the Golgi.","method":"Co-IP demonstrating direct TBC1D23-LKB1 interaction, Golgi-targeted LKB1 rescue in TBC1D23-deficient zebrafish, AMPK activation assays under energy stress","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP binding, functional rescue in vivo, AMPK activation assay; single lab with two orthogonal methods","pmids":["38413626"],"is_preprint":false},{"year":2024,"finding":"The C-terminal domain of TBC1D23 directly binds the cytoplasmic tails of cargo proteins carboxypeptidase D and syntaxin-16 via a threonine-leucine-tyrosine (TLY) motif adjacent to an acidic cluster; a crystal structure of the TBC1D23 C-terminal domain bound to this acidic TLY motif reveals the binding mechanism, and structure-guided mutations that disrupt motif binding in vitro also block vesicle capture in vivo.","method":"Binding partner screen, direct binding assays, crystal structure of TBC1D23 C-terminus with acidic TLY motif, structure-guided mutagenesis, in vivo vesicle-capture assays","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with mutagenesis, in vitro binding, and in vivo functional rescue in one rigorous study","pmids":["38552021"],"is_preprint":false},{"year":2023,"finding":"TBC1D23 directly interacts with FAM91A1; the crystal structure of the FAM91A1-TBC1D23 complex shows TBC1D23 binds a conserved surface on FAM91A1 in a Z-shaped conformation; this interaction is required for cooperative regulation of endosome-to-Golgi trafficking of KIAA0319L.","method":"Crystal structure of FAM91A1-TBC1D23 complex, Co-IP, zebrafish developmental assays, KIAA0319L trafficking assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with biochemical Co-IP validation and in vivo zebrafish functional evidence; multiple orthogonal methods","pmids":["37903274"],"is_preprint":false},{"year":2025,"finding":"A truncating TBC1D23 frameshift variant that partially escapes nonsense-mediated decay produces a stable truncated protein with aberrant cytoplasmic (non-Golgi) distribution that inhibits cell proliferation, demonstrating that normal Golgi localization is required for TBC1D23 function and that cytoplasmic mislocalization is itself cytotoxic.","method":"Patient variant characterization, NMD assay, subcellular localization by immunofluorescence, cell proliferation assay, zebrafish model","journal":"Human genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct localization experiment with functional consequence (cell proliferation), single lab, limited mechanistic depth","pmids":["40581672"],"is_preprint":false},{"year":2026,"finding":"TBC1D23 regulates EGFR trafficking by enhancing receptor recycling and membrane localization while suppressing lysosomal degradation, thereby sustaining EGFR/ERK signaling and driving VEGF-C upregulation and lymphangiogenesis in pancreatic ductal adenocarcinoma cells.","method":"siRNA knockdown in PDAC cell lines, EGFR trafficking assays, ERK signaling readouts, VEGF-C secretion assays, orthotopic xenograft model","journal":"Cellular oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional knockdown with mechanistic trafficking assays and signaling readouts, single lab with in vitro and in vivo evidence","pmids":["41920243"],"is_preprint":false}],"current_model":"TBC1D23 is a catalytically inactive TBC-domain protein that functions as a molecular bridge between the WASH/FAM21 complex on endosome-derived vesicles and golgin-97/golgin-245 at the trans-Golgi network; its N-terminal TBC-rhodanese domain platform binds the golgins while its C-terminal PH-like domain binds both PtdIns(4)P and FAM21, and additionally recognizes a shared acidic TLY cargo motif on vesicle cargo proteins (e.g., carboxypeptidase D, syntaxin-16) to confer cargo-selective vesicle tethering; it also recruits LKB1 to the Golgi to enable Golgi-specific AMPK activation, and its Golgi localization is essential for function, as cytoplasmic mislocalization caused by truncating mutations impairs endosome-to-Golgi trafficking and underlies pontocerebellar hypoplasia."},"narrative":{"mechanistic_narrative":"TBC1D23 is a catalytically inactive TBC-domain protein that acts as a vesicle-golgin bridging adaptor mediating endosome-to-trans-Golgi network (TGN) trafficking [PMID:29084197]. Its N-terminus comprises a TBC domain packed against a catalytically inactive rhodanese domain, which together form a platform that binds the coiled-coil golgins golgin-97 and golgin-245 at the TGN [PMID:32453802], while its C-terminal domain adopts a Pleckstrin Homology (PH) fold that engages PtdIns(4)P on one surface and the WASH-complex subunit FAM21 on the opposite surface to capture endosome-derived vesicles [PMID:29084197, PMID:31624125]. The same C-terminal domain directly recognizes a threonine-leucine-tyrosine (TLY) motif adjacent to an acidic cluster in the cytoplasmic tails of cargo proteins such as carboxypeptidase D and syntaxin-16, conferring cargo-selective vesicle tethering [PMID:38552021], and TBC1D23 cooperates with its direct binding partner FAM91A1 to route specific cargo including KIAA0319L [PMID:37903274]. Beyond trafficking, TBC1D23 directly binds LKB1 and recruits it to the Golgi to enable Golgi-localized, energy-stress-induced AMPK activation [PMID:38413626], and it sustains EGFR recycling and downstream ERK signaling to promote VEGF-C-driven lymphangiogenesis in pancreatic ductal adenocarcinoma [PMID:41920243]. Correct Golgi localization is essential for all of these functions: homozygous truncating mutations that mislocalize the protein to the cytoplasm impair endosome-to-Golgi and lysosomal trafficking, disrupt cortical neuron positioning, and cause pontocerebellar hypoplasia [PMID:28823707, PMID:40581672].","teleology":[{"year":2012,"claim":"Established an early functional readout for TBC1D23, placing it as a RAB-GAP-domain protein that restrains innate immune signaling, before its trafficking role was understood.","evidence":"Tbc1d23 knockout mice and macrophage overexpression with epistasis mapping against MyD88, Trif, and XBP1 under TLR stimulation","pmids":["22312129"],"confidence":"Medium","gaps":["Did not connect the immune phenotype to a molecular trafficking mechanism","Whether the TBC domain has genuine GAP catalytic activity was not resolved here","No structural basis for the proposed activity"]},{"year":2017,"claim":"Defined TBC1D23 as a vesicle-golgin bridging adaptor, answering how endosome-derived vesicles are tethered to the trans-Golgi.","evidence":"Proximity biotinylation of golgin-captured vesicles, Co-IP, knockdown trafficking assays, and an ectopic golgin vesicle-capture system","pmids":["29084197"],"confidence":"High","gaps":["Atomic basis of golgin and WASH-complex binding not yet resolved","Did not identify the cargo-recognition determinant","Catalytic status of the TBC domain unaddressed"]},{"year":2017,"claim":"Linked TBC1D23 loss to a human disease mechanism by showing truncating mutations disrupt vesicle/lysosomal trafficking and neuronal positioning.","evidence":"Patient-derived fibroblast trafficking assays and in utero electroporation knockdown in mouse cortex","pmids":["28823707"],"confidence":"Medium","gaps":["Did not establish why truncation abolishes function at the protein level","Single lab; in vivo neuronal phenotype not mechanistically dissected"]},{"year":2019,"claim":"Resolved the C-terminal domain as a PH fold with two distinct binding faces, explaining how TBC1D23 simultaneously reads membrane lipid identity and the WASH complex.","evidence":"Crystal structure of the C-terminal domain, phosphoinositide binding assays, FAM21 Co-IP, and zebrafish neuronal development assays","pmids":["31624125"],"confidence":"High","gaps":["Did not yet identify a direct cargo-binding site","How the N-terminus engages golgins remained structurally undefined"]},{"year":2020,"claim":"Showed the N-terminal TBC-rhodanese module is catalytically inactive and instead forms a golgin-binding platform, redefining TBC1D23 as a scaffold rather than an enzyme.","evidence":"Crystal structure of the N-terminal TBC+rhodanese domains with catalytic-site versus golgin-surface mutagenesis and zebrafish developmental assays","pmids":["32453802"],"confidence":"High","gaps":["Does not reconcile the earlier proposed RAB-GAP immune function with loss of catalysis","Golgin-binding surface mapped but full ternary tethering geometry unresolved"]},{"year":2023,"claim":"Identified FAM91A1 as a direct structural partner, showing TBC1D23 functions within a cooperative complex to route specific cargo.","evidence":"Crystal structure of the FAM91A1-TBC1D23 complex, Co-IP, KIAA0319L trafficking assays, and zebrafish developmental assays","pmids":["37903274"],"confidence":"High","gaps":["Cargo selectivity determinant still unidentified at this stage","How FAM91A1 engagement is coordinated with golgin and FAM21 binding unknown"]},{"year":2024,"claim":"Established the molecular basis of cargo-selective tethering by showing the C-terminal domain reads an acidic TLY motif in cargo cytoplasmic tails.","evidence":"Binding partner screen, direct binding assays, crystal structure of the C-terminal domain bound to the acidic TLY motif, and structure-guided in vivo vesicle-capture assays","pmids":["38552021"],"confidence":"High","gaps":["Full repertoire of TLY-motif cargo not enumerated","How lipid, FAM21, and cargo binding are spatially partitioned on one PH domain not fully resolved"]},{"year":2024,"claim":"Extended TBC1D23 function beyond trafficking by showing it recruits LKB1 to the Golgi to enable compartment-specific AMPK activation.","evidence":"Co-IP of direct TBC1D23-LKB1 interaction, Golgi-targeted LKB1 rescue in deficient zebrafish, and AMPK activation assays under energy stress","pmids":["38413626"],"confidence":"Medium","gaps":["Structural basis of the LKB1 interaction not determined","Relationship between the LKB1-AMPK role and the tethering role unclear"]},{"year":2025,"claim":"Demonstrated that Golgi localization itself is required for function and that cytoplasmic mislocalization of a stable truncated protein is cytotoxic.","evidence":"Patient variant characterization, NMD assay, immunofluorescence localization, cell proliferation assay, and zebrafish model","pmids":["40581672"],"confidence":"Medium","gaps":["Single lab; mechanism of cytoplasmic toxicity not defined","Does not distinguish loss-of-function from gain-of-toxicity contributions to disease"]},{"year":2026,"claim":"Implicated TBC1D23 in disease beyond neurodevelopment by showing it sustains EGFR recycling and signaling to drive lymphangiogenesis in pancreatic cancer.","evidence":"siRNA knockdown in PDAC lines, EGFR trafficking and ERK signaling readouts, VEGF-C secretion assays, and orthotopic xenograft model","pmids":["41920243"],"confidence":"Medium","gaps":["Whether EGFR is a direct TLY-motif cargo not established","Single-lab finding; generality across tumor types untested"]},{"year":null,"claim":"How the catalytically inactive scaffold integrates its multiple binding activities (golgin platform, lipid, FAM21, FAM91A1, cargo TLY motif, LKB1) into a single coordinated tethering and signaling event remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No integrated structure of TBC1D23 simultaneously engaging vesicle and golgin","Reconciliation of the early RAB-GAP immune function with later evidence of catalytic inactivity is incomplete","Whether cargo-selectivity rules generalize across all TBC1D23-dependent trafficking is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,2,6]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[2]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[0,4,5,8]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[0,6]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,6,7]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[0,2]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[5,9]}],"complexes":[],"partners":["GOLGA1","GOLGA4","FAM21","FAM91A1","STX16","CPD","STK11"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NUY8","full_name":"TBC1 domain family member 23","aliases":["HCV non-structural protein 4A-transactivated protein 1"],"length_aa":699,"mass_kda":78.3,"function":"Putative Rab GTPase-activating protein which plays a role in vesicular trafficking (PubMed:28823707). Involved in endosome-to-Golgi trafficking. Acts as a bridging protein by binding simultaneously to golgins, including GOLGA1 and GOLGA4, located at the trans-Golgi, and to the WASH complex, located on endosome-derived vesicles (PubMed:29084197, PubMed:29426865). Together with WDR11 complex facilitates the golgin-mediated capture of vesicles generated using AP-1 (PubMed:29426865). Plays a role in brain development, including in cortical neuron positioning (By similarity). May also be important for neurite outgrowth, possibly through its involvement in membrane trafficking and cargo delivery, 2 processes that are essential for axonal and dendritic growth (By similarity). May act as a general inhibitor of innate immunity signaling, strongly inhibiting multiple TLR and dectin/CLEC7A-signaling pathways. Does not alter initial activation events, but instead affects maintenance of inflammatory gene expression several hours after bacterial lipopolysaccharide (LPS) challenge (By similarity)","subcellular_location":"Golgi apparatus, trans-Golgi network; Cytoplasmic vesicle","url":"https://www.uniprot.org/uniprotkb/Q9NUY8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TBC1D23","classification":"Not Classified","n_dependent_lines":8,"n_total_lines":1208,"dependency_fraction":0.006622516556291391},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"KIF4A","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/TBC1D23","total_profiled":1310},"omim":[{"mim_id":"617695","title":"PONTOCEREBELLAR HYPOPLASIA, TYPE 11; PCH11","url":"https://www.omim.org/entry/617695"},{"mim_id":"617687","title":"TBC1 DOMAIN FAMILY, MEMBER 23; TBC1D23","url":"https://www.omim.org/entry/617687"},{"mim_id":"615867","title":"TBC1 DOMAIN FAMILY, MEMBER 32; TBC1D32","url":"https://www.omim.org/entry/615867"},{"mim_id":"607596","title":"PONTOCEREBELLAR HYPOPLASIA, TYPE 1A; PCH1A","url":"https://www.omim.org/entry/607596"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Golgi apparatus","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TBC1D23"},"hgnc":{"alias_symbol":["FLJ11046"],"prev_symbol":[]},"alphafold":{"accession":"Q9NUY8","domains":[{"cath_id":"1.10.472.80","chopping":"158-311","consensus_level":"medium","plddt":92.3856,"start":158,"end":311},{"cath_id":"3.40.250.10","chopping":"319-447","consensus_level":"high","plddt":89.9823,"start":319,"end":447},{"cath_id":"2.30.29.30","chopping":"579-699","consensus_level":"high","plddt":87.1041,"start":579,"end":699},{"cath_id":"1.10.8","chopping":"48-157","consensus_level":"medium","plddt":92.0732,"start":48,"end":157}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NUY8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NUY8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NUY8-F1-predicted_aligned_error_v6.png","plddt_mean":80.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TBC1D23","jax_strain_url":"https://www.jax.org/strain/search?query=TBC1D23"},"sequence":{"accession":"Q9NUY8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NUY8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NUY8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NUY8"}},"corpus_meta":[{"pmid":"29084197","id":"PMC_29084197","title":"TBC1D23 is a bridging factor for endosomal vesicle capture by golgins at the trans-Golgi.","date":"2017","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/29084197","citation_count":76,"is_preprint":false},{"pmid":"28823707","id":"PMC_28823707","title":"Homozygous Truncating Variants in TBC1D23 Cause Pontocerebellar Hypoplasia and Alter Cortical Development.","date":"2017","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28823707","citation_count":41,"is_preprint":false},{"pmid":"31624125","id":"PMC_31624125","title":"Structural and functional studies of TBC1D23 C-terminal domain provide a link between endosomal trafficking and PCH.","date":"2019","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/31624125","citation_count":28,"is_preprint":false},{"pmid":"22312129","id":"PMC_22312129","title":"Spatiotemporal inhibition of innate immunity signaling by the Tbc1d23 RAB-GAP.","date":"2012","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/22312129","citation_count":22,"is_preprint":false},{"pmid":"38413626","id":"PMC_38413626","title":"TBC1D23 mediates Golgi-specific LKB1 signaling.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38413626","citation_count":20,"is_preprint":false},{"pmid":"32453802","id":"PMC_32453802","title":"Structure of TBC1D23 N-terminus reveals a novel role for rhodanese domain.","date":"2020","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/32453802","citation_count":18,"is_preprint":false},{"pmid":"38552021","id":"PMC_38552021","title":"Cargo selective vesicle tethering: The structural basis for binding of specific cargo proteins by the Golgi tether component TBC1D23.","date":"2024","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/38552021","citation_count":15,"is_preprint":false},{"pmid":"37903274","id":"PMC_37903274","title":"FAM91A1-TBC1D23 complex structure reveals human genetic variations susceptible for PCH.","date":"2023","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/37903274","citation_count":11,"is_preprint":false},{"pmid":"40581672","id":"PMC_40581672","title":"Identification and functional analysis of a novel TBC1D23 pathogenic variant in a Chinese family with pontocerebellar hypoplasia.","date":"2025","source":"Human genomics","url":"https://pubmed.ncbi.nlm.nih.gov/40581672","citation_count":2,"is_preprint":false},{"pmid":"41920243","id":"PMC_41920243","title":"TBC1D23 drives lymphatic metastasis in pancreatic ductal adenocarcinoma by altering EGFR cell surface dynamics and signaling.","date":"2026","source":"Cellular oncology (Dordrecht, Netherlands)","url":"https://pubmed.ncbi.nlm.nih.gov/41920243","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.12.17.628665","title":"A CRISPR/Cas9 screen reveals proteins at the endosome-Golgi interface that modulate cellular ASO activity","date":"2024-12-18","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.17.628665","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7343,"output_tokens":2688,"usd":0.031175,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9946,"output_tokens":3788,"usd":0.072215,"stage2_stop_reason":"end_turn"},"total_usd":0.10339,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2017,\n      \"finding\": \"TBC1D23 acts as a bridging factor (vesicle-golgin adaptor) for endosome-to-Golgi trafficking: its Rab GAP domain binds a conserved motif at the tips of golgin-245 and golgin-97 at the trans-Golgi, while its C-terminus binds to the WASH complex on endosome-derived vesicles, thereby linking vesicle to target membrane.\",\n      \"method\": \"Proximity biotinylation of golgin-captured vesicles, Co-IP, knockdown with trafficking assays, ectopic golgin vesicle-capture system\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (proximity biotinylation, Co-IP, functional knockdown, vesicle-capture assay) in a single rigorous study; mechanistic model confirmed by binding domain mapping\",\n      \"pmids\": [\"29084197\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Homozygous truncating mutations in TBC1D23 impair dense core vesicle and lysosomal trafficking dynamics in patient-derived fibroblasts, and knockdown of TBC1D23 by in utero electroporation disrupts cortical neuron positioning in vivo.\",\n      \"method\": \"Patient fibroblast vesicle/lysosomal trafficking assays, in utero electroporation knockdown in mouse cortex\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two orthogonal methods (cell-based trafficking assay, in vivo electroporation), single lab\",\n      \"pmids\": [\"28823707\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The C-terminal domain of TBC1D23 adopts a Pleckstrin Homology (PH) domain fold, selectively binds PtdIns(4)P on one surface, and binds FAM21 (a WASH complex subunit) via the opposite surface; mutations disrupting either interaction impair endosome-to-TGN trafficking and cause abnormal neuronal growth in zebrafish.\",\n      \"method\": \"Crystal structure of TBC1D23 C-terminal domain, phosphoinositide binding assays, mutagenesis, Co-IP with FAM21, zebrafish neuronal development assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with mutagenesis, biochemical binding assays, and in vivo zebrafish validation; multiple orthogonal methods in one study\",\n      \"pmids\": [\"31624125\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Tbc1d23 functions as a RAB-GAP to inhibit innate immunity signaling downstream of TLR-signaling adaptors MyD88 and Trif and upstream of the transcription factor XBP1, specifically affecting the maintenance (but not initiation) of inflammatory cytokine production.\",\n      \"method\": \"Tbc1d23 knockout mice, macrophage overexpression, epistasis analysis with pathway components (MyD88, Trif, XBP1), TLR stimulation assays\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic knockout combined with overexpression and epistasis mapping, single lab\",\n      \"pmids\": [\"22312129\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"The crystal structure of the TBC1D23 N-terminus reveals it comprises both TBC and rhodanese domains; the rhodanese domain is catalytically inactive (not a sulfurtransferase or phosphatase) but instead packs against the TBC domain to form a platform that interacts with golgin-97/245. Disrupting golgin binding (but not the putative catalytic site) impairs neuronal growth and brain development in zebrafish.\",\n      \"method\": \"Crystal structure of TBC1D23 N-terminal domain (TBC + rhodanese), mutagenesis of catalytic site vs. golgin-binding surface, zebrafish developmental assays\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional mutagenesis and in vivo zebrafish validation; multiple orthogonal methods\",\n      \"pmids\": [\"32453802\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TBC1D23 directly interacts with LKB1 and recruits LKB1 to the Golgi apparatus, promoting Golgi-specific activation of AMPK upon energy stress; Golgi-targeted LKB1 expression rescues TBC1D23 deficiency in zebrafish, placing TBC1D23 upstream of LKB1-AMPK signaling at the Golgi.\",\n      \"method\": \"Co-IP demonstrating direct TBC1D23-LKB1 interaction, Golgi-targeted LKB1 rescue in TBC1D23-deficient zebrafish, AMPK activation assays under energy stress\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP binding, functional rescue in vivo, AMPK activation assay; single lab with two orthogonal methods\",\n      \"pmids\": [\"38413626\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"The C-terminal domain of TBC1D23 directly binds the cytoplasmic tails of cargo proteins carboxypeptidase D and syntaxin-16 via a threonine-leucine-tyrosine (TLY) motif adjacent to an acidic cluster; a crystal structure of the TBC1D23 C-terminal domain bound to this acidic TLY motif reveals the binding mechanism, and structure-guided mutations that disrupt motif binding in vitro also block vesicle capture in vivo.\",\n      \"method\": \"Binding partner screen, direct binding assays, crystal structure of TBC1D23 C-terminus with acidic TLY motif, structure-guided mutagenesis, in vivo vesicle-capture assays\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with mutagenesis, in vitro binding, and in vivo functional rescue in one rigorous study\",\n      \"pmids\": [\"38552021\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TBC1D23 directly interacts with FAM91A1; the crystal structure of the FAM91A1-TBC1D23 complex shows TBC1D23 binds a conserved surface on FAM91A1 in a Z-shaped conformation; this interaction is required for cooperative regulation of endosome-to-Golgi trafficking of KIAA0319L.\",\n      \"method\": \"Crystal structure of FAM91A1-TBC1D23 complex, Co-IP, zebrafish developmental assays, KIAA0319L trafficking assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with biochemical Co-IP validation and in vivo zebrafish functional evidence; multiple orthogonal methods\",\n      \"pmids\": [\"37903274\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A truncating TBC1D23 frameshift variant that partially escapes nonsense-mediated decay produces a stable truncated protein with aberrant cytoplasmic (non-Golgi) distribution that inhibits cell proliferation, demonstrating that normal Golgi localization is required for TBC1D23 function and that cytoplasmic mislocalization is itself cytotoxic.\",\n      \"method\": \"Patient variant characterization, NMD assay, subcellular localization by immunofluorescence, cell proliferation assay, zebrafish model\",\n      \"journal\": \"Human genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct localization experiment with functional consequence (cell proliferation), single lab, limited mechanistic depth\",\n      \"pmids\": [\"40581672\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"TBC1D23 regulates EGFR trafficking by enhancing receptor recycling and membrane localization while suppressing lysosomal degradation, thereby sustaining EGFR/ERK signaling and driving VEGF-C upregulation and lymphangiogenesis in pancreatic ductal adenocarcinoma cells.\",\n      \"method\": \"siRNA knockdown in PDAC cell lines, EGFR trafficking assays, ERK signaling readouts, VEGF-C secretion assays, orthotopic xenograft model\",\n      \"journal\": \"Cellular oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional knockdown with mechanistic trafficking assays and signaling readouts, single lab with in vitro and in vivo evidence\",\n      \"pmids\": [\"41920243\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TBC1D23 is a catalytically inactive TBC-domain protein that functions as a molecular bridge between the WASH/FAM21 complex on endosome-derived vesicles and golgin-97/golgin-245 at the trans-Golgi network; its N-terminal TBC-rhodanese domain platform binds the golgins while its C-terminal PH-like domain binds both PtdIns(4)P and FAM21, and additionally recognizes a shared acidic TLY cargo motif on vesicle cargo proteins (e.g., carboxypeptidase D, syntaxin-16) to confer cargo-selective vesicle tethering; it also recruits LKB1 to the Golgi to enable Golgi-specific AMPK activation, and its Golgi localization is essential for function, as cytoplasmic mislocalization caused by truncating mutations impairs endosome-to-Golgi trafficking and underlies pontocerebellar hypoplasia.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TBC1D23 is a catalytically inactive TBC-domain protein that acts as a vesicle-golgin bridging adaptor mediating endosome-to-trans-Golgi network (TGN) trafficking [#0]. Its N-terminus comprises a TBC domain packed against a catalytically inactive rhodanese domain, which together form a platform that binds the coiled-coil golgins golgin-97 and golgin-245 at the TGN [#4], while its C-terminal domain adopts a Pleckstrin Homology (PH) fold that engages PtdIns(4)P on one surface and the WASH-complex subunit FAM21 on the opposite surface to capture endosome-derived vesicles [#0, #2]. The same C-terminal domain directly recognizes a threonine-leucine-tyrosine (TLY) motif adjacent to an acidic cluster in the cytoplasmic tails of cargo proteins such as carboxypeptidase D and syntaxin-16, conferring cargo-selective vesicle tethering [#6], and TBC1D23 cooperates with its direct binding partner FAM91A1 to route specific cargo including KIAA0319L [#7]. Beyond trafficking, TBC1D23 directly binds LKB1 and recruits it to the Golgi to enable Golgi-localized, energy-stress-induced AMPK activation [#5], and it sustains EGFR recycling and downstream ERK signaling to promote VEGF-C-driven lymphangiogenesis in pancreatic ductal adenocarcinoma [#9]. Correct Golgi localization is essential for all of these functions: homozygous truncating mutations that mislocalize the protein to the cytoplasm impair endosome-to-Golgi and lysosomal trafficking, disrupt cortical neuron positioning, and cause pontocerebellar hypoplasia [#1, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Established an early functional readout for TBC1D23, placing it as a RAB-GAP-domain protein that restrains innate immune signaling, before its trafficking role was understood.\",\n      \"evidence\": \"Tbc1d23 knockout mice and macrophage overexpression with epistasis mapping against MyD88, Trif, and XBP1 under TLR stimulation\",\n      \"pmids\": [\"22312129\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Did not connect the immune phenotype to a molecular trafficking mechanism\",\n        \"Whether the TBC domain has genuine GAP catalytic activity was not resolved here\",\n        \"No structural basis for the proposed activity\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined TBC1D23 as a vesicle-golgin bridging adaptor, answering how endosome-derived vesicles are tethered to the trans-Golgi.\",\n      \"evidence\": \"Proximity biotinylation of golgin-captured vesicles, Co-IP, knockdown trafficking assays, and an ectopic golgin vesicle-capture system\",\n      \"pmids\": [\"29084197\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Atomic basis of golgin and WASH-complex binding not yet resolved\",\n        \"Did not identify the cargo-recognition determinant\",\n        \"Catalytic status of the TBC domain unaddressed\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Linked TBC1D23 loss to a human disease mechanism by showing truncating mutations disrupt vesicle/lysosomal trafficking and neuronal positioning.\",\n      \"evidence\": \"Patient-derived fibroblast trafficking assays and in utero electroporation knockdown in mouse cortex\",\n      \"pmids\": [\"28823707\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Did not establish why truncation abolishes function at the protein level\",\n        \"Single lab; in vivo neuronal phenotype not mechanistically dissected\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Resolved the C-terminal domain as a PH fold with two distinct binding faces, explaining how TBC1D23 simultaneously reads membrane lipid identity and the WASH complex.\",\n      \"evidence\": \"Crystal structure of the C-terminal domain, phosphoinositide binding assays, FAM21 Co-IP, and zebrafish neuronal development assays\",\n      \"pmids\": [\"31624125\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Did not yet identify a direct cargo-binding site\",\n        \"How the N-terminus engages golgins remained structurally undefined\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed the N-terminal TBC-rhodanese module is catalytically inactive and instead forms a golgin-binding platform, redefining TBC1D23 as a scaffold rather than an enzyme.\",\n      \"evidence\": \"Crystal structure of the N-terminal TBC+rhodanese domains with catalytic-site versus golgin-surface mutagenesis and zebrafish developmental assays\",\n      \"pmids\": [\"32453802\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Does not reconcile the earlier proposed RAB-GAP immune function with loss of catalysis\",\n        \"Golgin-binding surface mapped but full ternary tethering geometry unresolved\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified FAM91A1 as a direct structural partner, showing TBC1D23 functions within a cooperative complex to route specific cargo.\",\n      \"evidence\": \"Crystal structure of the FAM91A1-TBC1D23 complex, Co-IP, KIAA0319L trafficking assays, and zebrafish developmental assays\",\n      \"pmids\": [\"37903274\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Cargo selectivity determinant still unidentified at this stage\",\n        \"How FAM91A1 engagement is coordinated with golgin and FAM21 binding unknown\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established the molecular basis of cargo-selective tethering by showing the C-terminal domain reads an acidic TLY motif in cargo cytoplasmic tails.\",\n      \"evidence\": \"Binding partner screen, direct binding assays, crystal structure of the C-terminal domain bound to the acidic TLY motif, and structure-guided in vivo vesicle-capture assays\",\n      \"pmids\": [\"38552021\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Full repertoire of TLY-motif cargo not enumerated\",\n        \"How lipid, FAM21, and cargo binding are spatially partitioned on one PH domain not fully resolved\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended TBC1D23 function beyond trafficking by showing it recruits LKB1 to the Golgi to enable compartment-specific AMPK activation.\",\n      \"evidence\": \"Co-IP of direct TBC1D23-LKB1 interaction, Golgi-targeted LKB1 rescue in deficient zebrafish, and AMPK activation assays under energy stress\",\n      \"pmids\": [\"38413626\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Structural basis of the LKB1 interaction not determined\",\n        \"Relationship between the LKB1-AMPK role and the tethering role unclear\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated that Golgi localization itself is required for function and that cytoplasmic mislocalization of a stable truncated protein is cytotoxic.\",\n      \"evidence\": \"Patient variant characterization, NMD assay, immunofluorescence localization, cell proliferation assay, and zebrafish model\",\n      \"pmids\": [\"40581672\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single lab; mechanism of cytoplasmic toxicity not defined\",\n        \"Does not distinguish loss-of-function from gain-of-toxicity contributions to disease\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Implicated TBC1D23 in disease beyond neurodevelopment by showing it sustains EGFR recycling and signaling to drive lymphangiogenesis in pancreatic cancer.\",\n      \"evidence\": \"siRNA knockdown in PDAC lines, EGFR trafficking and ERK signaling readouts, VEGF-C secretion assays, and orthotopic xenograft model\",\n      \"pmids\": [\"41920243\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether EGFR is a direct TLY-motif cargo not established\",\n        \"Single-lab finding; generality across tumor types untested\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the catalytically inactive scaffold integrates its multiple binding activities (golgin platform, lipid, FAM21, FAM91A1, cargo TLY motif, LKB1) into a single coordinated tethering and signaling event remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No integrated structure of TBC1D23 simultaneously engaging vesicle and golgin\",\n        \"Reconciliation of the early RAB-GAP immune function with later evidence of catalytic inactivity is incomplete\",\n        \"Whether cargo-selectivity rules generalize across all TBC1D23-dependent trafficking is unknown\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2, 6]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [0, 4, 5, 8]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-199991\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 6, 7]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [5, 9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"GOLGA1\", \"GOLGA4\", \"FAM21\", \"FAM91A1\", \"STX16\", \"CPD\", \"STK11\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}