{"gene":"TBC1D31","run_date":"2026-06-10T10:51:54","timeline":{"discoveries":[{"year":2021,"finding":"TBC1D31 assembles a novel complex at centrosomes comprising the E3 ubiquitin ligase praja2, protein kinase A (PKA), and OFD1. Upon GPCR-cAMP stimulation, PKA phosphorylates OFD1 at Ser735, promoting OFD1 proteolysis via the praja2-ubiquitin-proteasome system, a pathway essential for primary ciliogenesis.","method":"Co-immunoprecipitation, centrosome localization assays, phospho-mutant analysis (non-phosphorylatable OFD1 S735A), in vivo knockdown in Medaka fish","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, phospho-site mutagenesis, in vivo vertebrate model replication, multiple orthogonal methods in one rigorous study","pmids":["33934390"],"is_preprint":false},{"year":2021,"finding":"TBC1D31 is essential for primary ciliogenesis; loss of TBC1D31 function impairs cilium biogenesis both in cultured cells and in vivo in Medaka fish, resulting in developmental defects.","method":"Loss-of-function (knockdown/depletion) in cell lines and in vivo Medaka fish model with cilium morphology and developmental phenotype readouts","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean knockdown with defined cellular phenotype replicated in two systems (cell culture and in vivo vertebrate)","pmids":["33934390"],"is_preprint":false},{"year":2025,"finding":"WDR67 (alias TBC1D31) localizes to the A-C linker of centrioles, where it forms a complex with CCDC77 and MIIP connecting adjacent microtubule triplets at the proximal region. Depletion of A-C linker components disrupts microtubule triplet cohesion, causing breakage at the proximal end; co-depletion with inner scaffold components demonstrates their joint role in centriole architecture. The A-C linker also regulates centriole duplication through torus regulation.","method":"Ultrastructure expansion microscopy (U-ExM), protein depletion (siRNA/KO), co-localization and complex characterization, epistasis by co-depletion with inner scaffold","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — ultrastructure expansion microscopy with functional depletion phenotypes and epistasis experiments, replicated in preprint and peer-reviewed publication","pmids":["40707486"],"is_preprint":false},{"year":2024,"finding":"TBC1D31 acts as a Rab GTPase-activating protein (Rab-GAP) that catalyzes GTP hydrolysis for Rab22A, thereby reducing Rab22A-mediated endolysosomal trafficking and degradation of EGFR, leading to sustained EGFR signaling and promoting HCC growth and metastasis.","method":"In vitro GAP activity assay, overexpression and knockdown in HCC cell lines and xenograft models, endolysosomal trafficking assays, EGFR degradation assays","journal":"Advanced science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — GAP activity assay plus in vitro and in vivo functional studies from a single lab with multiple readouts","pmids":["39206796"],"is_preprint":false},{"year":2024,"finding":"ZSCAN16 transcriptionally activates TBC1D31 expression in hepatocellular carcinoma cells, as demonstrated by ChIP-qPCR and dual-luciferase reporter assays. TBC1D31 overexpression rescues the inhibitory effects of ZSCAN16 knockdown on HCC cell proliferation, migration, invasion, and in vivo tumor growth.","method":"ChIP-qPCR, dual-luciferase assay, lentiviral knockdown/overexpression, functional rescue experiments, xenograft tumor model","journal":"Cell division","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct transcriptional regulation confirmed by ChIP and luciferase in a single lab with functional rescue validation","pmids":["39511655"],"is_preprint":false},{"year":2024,"finding":"Elevated TBC1D31 expression is causally associated with a glycolytic metabolic phenotype in triple-negative breast cancer (TNBC) cell lines, as demonstrated by transcriptomics/metabolomics correlation and functional knockdown experiments.","method":"Transcriptomics/metabolomics correlation, siRNA knockdown with metabolic phenotype readout in TNBC cell lines","journal":"Cell death & disease","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, knockdown with metabolic phenotype readout but limited mechanistic pathway placement for TBC1D31 specifically","pmids":["39231952"],"is_preprint":false}],"current_model":"TBC1D31 (also known as WDR67) is a multifunctional centrosomal/centriolar protein that (1) scaffolds a centrosomal complex with praja2, PKA, and OFD1 to link GPCR-cAMP signaling to PKA-mediated phosphorylation of OFD1 (Ser735) and its praja2-dependent ubiquitin-proteasome degradation, thereby controlling primary ciliogenesis; (2) localizes to the centriolar A-C linker as part of a CCDC77/WDR67/MIIP complex that maintains microtubule triplet cohesion and regulates centriole duplication; and (3) functions as a Rab22A GTPase-activating protein (Rab-GAP) that suppresses endolysosomal trafficking and degradation of EGFR, with its expression transcriptionally activated by ZSCAN16 in hepatocellular carcinoma."},"narrative":{"mechanistic_narrative":"TBC1D31 (also called WDR67) is a centrosomal/centriolar scaffold that couples signaling and structural control of the centriole to primary ciliogenesis [PMID:33934390, PMID:40707486]. At the centrosome it assembles a complex with the E3 ubiquitin ligase praja2, protein kinase A (PKA), and OFD1; upon GPCR-cAMP stimulation PKA phosphorylates OFD1 at Ser735, driving its praja2-dependent ubiquitin-proteasome degradation, a step required for cilium biogenesis, with loss of TBC1D31 impairing ciliogenesis in cultured cells and in vivo in Medaka [PMID:33934390]. Structurally, it localizes to the centriolar A-C linker in a complex with CCDC77 and MIIP that bridges adjacent microtubule triplets at the proximal region to maintain triplet cohesion and regulate centriole duplication [PMID:40707486]. Independently, TBC1D31 acts as a Rab22A GTPase-activating protein that suppresses Rab22A-mediated endolysosomal trafficking and degradation of EGFR, sustaining EGFR signaling and promoting hepatocellular carcinoma growth, where its expression is transcriptionally activated by ZSCAN16 [PMID:39206796, PMID:39511655].","teleology":[{"year":2021,"claim":"Established TBC1D31 as a centrosomal scaffold that links GPCR-cAMP/PKA signaling to controlled OFD1 turnover, answering how a signaling input gates ciliogenesis.","evidence":"Reciprocal Co-IP, centrosome localization, OFD1 S735A phospho-mutant analysis, and in vivo knockdown in Medaka","pmids":["33934390"],"confidence":"High","gaps":["Does not define how TBC1D31 itself is recruited to the centrosome","Stoichiometry and assembly order of the praja2/PKA/OFD1 complex unresolved"]},{"year":2021,"claim":"Demonstrated that TBC1D31 is functionally required for primary ciliogenesis, moving it from a complex component to an essential biogenesis factor.","evidence":"Loss-of-function depletion in cell lines and Medaka with cilium morphology and developmental readouts","pmids":["33934390"],"confidence":"High","gaps":["Whether ciliogenesis defects derive solely from OFD1 dysregulation or other pathways","No human disease/genetic link established in the corpus"]},{"year":2024,"claim":"Identified a distinct cytoplasmic role for TBC1D31 as a Rab22A GAP controlling EGFR trafficking, explaining a pro-tumorigenic function separate from its centriolar role.","evidence":"In vitro GAP activity assay, knockdown/overexpression in HCC cells and xenografts, endolysosomal and EGFR degradation assays","pmids":["39206796"],"confidence":"Medium","gaps":["Single-lab findings without independent replication","Relationship between Rab-GAP function and centriolar localization unclear"]},{"year":2024,"claim":"Placed TBC1D31 downstream of a defined transcriptional activator in cancer, showing ZSCAN16 drives its expression to sustain HCC malignancy.","evidence":"ChIP-qPCR, dual-luciferase reporter, lentiviral knockdown/overexpression with functional rescue and xenograft models","pmids":["39511655"],"confidence":"Medium","gaps":["Whether ZSCAN16-driven expression operates through the Rab22A/EGFR axis specifically not resolved","Single-lab evidence"]},{"year":2024,"claim":"Associated elevated TBC1D31 with a glycolytic metabolic phenotype in TNBC, broadening its cancer relevance beyond HCC.","evidence":"Transcriptomics/metabolomics correlation and siRNA knockdown with metabolic readouts in TNBC cell lines","pmids":["39231952"],"confidence":"Low","gaps":["No mechanistic pathway connecting TBC1D31 to glycolysis established","Correlative, single-lab evidence"]},{"year":2025,"claim":"Resolved the structural role of TBC1D31/WDR67 at the centriolar A-C linker, showing it physically bridges microtubule triplets and supports centriole architecture and duplication.","evidence":"Ultrastructure expansion microscopy, siRNA/KO depletion, co-localization, and co-depletion epistasis with inner scaffold components","pmids":["40707486"],"confidence":"High","gaps":["Molecular basis of triplet bridging by the CCDC77/WDR67/MIIP complex not defined","How the A-C linker role integrates with the praja2/PKA/OFD1 signaling function unknown"]},{"year":null,"claim":"It remains unknown how TBC1D31's centriolar structural/ciliogenic functions and its cytoplasmic Rab22A-GAP/EGFR-trafficking role are coordinated within a single protein.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure-function mapping separating GAP, scaffold, and A-C linker activities","No data on whether the two functions are spatially or temporally exclusive"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[0,2]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[2]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,3]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[3]}],"complexes":["praja2/PKA/OFD1 centrosomal complex","CCDC77/WDR67/MIIP A-C linker complex"],"partners":["PRKACA","OFD1","PJA2","CCDC77","MIIP","RAB22A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96DN5","full_name":"TBC1 domain family member 31","aliases":["WD repeat-containing protein 67"],"length_aa":1066,"mass_kda":124.2,"function":"Molecular adapter which is involved in cilium biogenesis. Part of a functional complex including OFD1 a centriolar protein involved in cilium assembly. Could regulate the cAMP-dependent phosphorylation of OFD1, and its subsequent ubiquitination by PJA2 which ultimately leads to its proteasomal degradation","subcellular_location":"Cytoplasm, cytoskeleton, microtubule organizing center, centrosome; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriolar satellite; Cytoplasm, cytoskeleton, cilium basal body","url":"https://www.uniprot.org/uniprotkb/Q96DN5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TBC1D31","classification":"Not Classified","n_dependent_lines":49,"n_total_lines":1208,"dependency_fraction":0.04056291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TBC1D31","total_profiled":1310},"omim":[{"mim_id":"621444","title":"TBC1 DOMAIN FAMILY, MEMBER 31; TBC1D31","url":"https://www.omim.org/entry/621444"},{"mim_id":"619341","title":"PRAJA RING FINGER UBIQUITIN LIGASE 2; PJA2","url":"https://www.omim.org/entry/619341"},{"mim_id":"608772","title":"MIGRATION AND INVASION INHIBITORY PROTEIN; MIIP","url":"https://www.omim.org/entry/608772"},{"mim_id":"601639","title":"PROTEIN KINASE, cAMP-DEPENDENT, CATALYTIC, ALPHA; PRKACA","url":"https://www.omim.org/entry/601639"},{"mim_id":"300170","title":"OFD1 CENTRIOLE AND CENTRIOLAR SATELLITE PROTEIN; OFD1","url":"https://www.omim.org/entry/300170"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Centrosome","reliability":"Supported"},{"location":"Basal body","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TBC1D31"},"hgnc":{"alias_symbol":["MGC21654","Gm85"],"prev_symbol":["WDR67"]},"alphafold":{"accession":"Q96DN5","domains":[{"cath_id":"1.10.472.80","chopping":"541-662","consensus_level":"medium","plddt":92.1748,"start":541,"end":662},{"cath_id":"1.20.5","chopping":"713-776","consensus_level":"medium","plddt":82.2825,"start":713,"end":776},{"cath_id":"1.20.5","chopping":"779-825","consensus_level":"medium","plddt":79.2809,"start":779,"end":825}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96DN5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96DN5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96DN5-F1-predicted_aligned_error_v6.png","plddt_mean":76.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TBC1D31","jax_strain_url":"https://www.jax.org/strain/search?query=TBC1D31"},"sequence":{"accession":"Q96DN5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96DN5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96DN5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96DN5"}},"corpus_meta":[{"pmid":"33934390","id":"PMC_33934390","title":"The TBC1D31/praja2 complex controls primary ciliogenesis through PKA-directed OFD1 ubiquitylation.","date":"2021","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/33934390","citation_count":33,"is_preprint":false},{"pmid":"40707486","id":"PMC_40707486","title":"The A-C linker controls centriole structural integrity and duplication.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/40707486","citation_count":10,"is_preprint":false},{"pmid":"28504162","id":"PMC_28504162","title":"Purification of glucomannan from salep: Part 2. Structural characterization.","date":"2017","source":"Carbohydrate polymers","url":"https://pubmed.ncbi.nlm.nih.gov/28504162","citation_count":9,"is_preprint":false},{"pmid":"39206796","id":"PMC_39206796","title":"Genomic Amplification of TBC1D31 Promotes Hepatocellular Carcinoma Through Reducing the Rab22A-Mediated Endolysosomal Trafficking and Degradation of EGFR.","date":"2024","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/39206796","citation_count":8,"is_preprint":false},{"pmid":"39067134","id":"PMC_39067134","title":"A susceptibility gene signature for ERBB2-driven mammary tumour development and metastasis in collaborative cross mice.","date":"2024","source":"EBioMedicine","url":"https://pubmed.ncbi.nlm.nih.gov/39067134","citation_count":8,"is_preprint":false},{"pmid":"37468454","id":"PMC_37468454","title":"A novel homozygous missense variant in TBC1D31 in a consanguineous family with congenital anomalies of the kidney and urinary tract (CAKUT).","date":"2023","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/37468454","citation_count":4,"is_preprint":false},{"pmid":"39231952","id":"PMC_39231952","title":"TBC1 domain-containing proteins are frequently involved in triple-negative breast cancers in connection with the induction of a glycolytic phenotype.","date":"2024","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/39231952","citation_count":4,"is_preprint":false},{"pmid":"39511655","id":"PMC_39511655","title":"ZSCAN16 expedites hepatocellular carcinoma progression via activating TBC1D31.","date":"2024","source":"Cell division","url":"https://pubmed.ncbi.nlm.nih.gov/39511655","citation_count":2,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.04.616628","title":"The A-C Linker controls centriole cohesion and duplication","date":"2024-10-04","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.04.616628","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6764,"output_tokens":1686,"usd":0.022791,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8460,"output_tokens":2425,"usd":0.051463,"stage2_stop_reason":"end_turn"},"total_usd":0.074254,"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\": 2021,\n      \"finding\": \"TBC1D31 assembles a novel complex at centrosomes comprising the E3 ubiquitin ligase praja2, protein kinase A (PKA), and OFD1. Upon GPCR-cAMP stimulation, PKA phosphorylates OFD1 at Ser735, promoting OFD1 proteolysis via the praja2-ubiquitin-proteasome system, a pathway essential for primary ciliogenesis.\",\n      \"method\": \"Co-immunoprecipitation, centrosome localization assays, phospho-mutant analysis (non-phosphorylatable OFD1 S735A), in vivo knockdown in Medaka fish\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, phospho-site mutagenesis, in vivo vertebrate model replication, multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"33934390\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"TBC1D31 is essential for primary ciliogenesis; loss of TBC1D31 function impairs cilium biogenesis both in cultured cells and in vivo in Medaka fish, resulting in developmental defects.\",\n      \"method\": \"Loss-of-function (knockdown/depletion) in cell lines and in vivo Medaka fish model with cilium morphology and developmental phenotype readouts\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean knockdown with defined cellular phenotype replicated in two systems (cell culture and in vivo vertebrate)\",\n      \"pmids\": [\"33934390\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"WDR67 (alias TBC1D31) localizes to the A-C linker of centrioles, where it forms a complex with CCDC77 and MIIP connecting adjacent microtubule triplets at the proximal region. Depletion of A-C linker components disrupts microtubule triplet cohesion, causing breakage at the proximal end; co-depletion with inner scaffold components demonstrates their joint role in centriole architecture. The A-C linker also regulates centriole duplication through torus regulation.\",\n      \"method\": \"Ultrastructure expansion microscopy (U-ExM), protein depletion (siRNA/KO), co-localization and complex characterization, epistasis by co-depletion with inner scaffold\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — ultrastructure expansion microscopy with functional depletion phenotypes and epistasis experiments, replicated in preprint and peer-reviewed publication\",\n      \"pmids\": [\"40707486\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TBC1D31 acts as a Rab GTPase-activating protein (Rab-GAP) that catalyzes GTP hydrolysis for Rab22A, thereby reducing Rab22A-mediated endolysosomal trafficking and degradation of EGFR, leading to sustained EGFR signaling and promoting HCC growth and metastasis.\",\n      \"method\": \"In vitro GAP activity assay, overexpression and knockdown in HCC cell lines and xenograft models, endolysosomal trafficking assays, EGFR degradation assays\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — GAP activity assay plus in vitro and in vivo functional studies from a single lab with multiple readouts\",\n      \"pmids\": [\"39206796\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ZSCAN16 transcriptionally activates TBC1D31 expression in hepatocellular carcinoma cells, as demonstrated by ChIP-qPCR and dual-luciferase reporter assays. TBC1D31 overexpression rescues the inhibitory effects of ZSCAN16 knockdown on HCC cell proliferation, migration, invasion, and in vivo tumor growth.\",\n      \"method\": \"ChIP-qPCR, dual-luciferase assay, lentiviral knockdown/overexpression, functional rescue experiments, xenograft tumor model\",\n      \"journal\": \"Cell division\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct transcriptional regulation confirmed by ChIP and luciferase in a single lab with functional rescue validation\",\n      \"pmids\": [\"39511655\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Elevated TBC1D31 expression is causally associated with a glycolytic metabolic phenotype in triple-negative breast cancer (TNBC) cell lines, as demonstrated by transcriptomics/metabolomics correlation and functional knockdown experiments.\",\n      \"method\": \"Transcriptomics/metabolomics correlation, siRNA knockdown with metabolic phenotype readout in TNBC cell lines\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, knockdown with metabolic phenotype readout but limited mechanistic pathway placement for TBC1D31 specifically\",\n      \"pmids\": [\"39231952\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TBC1D31 (also known as WDR67) is a multifunctional centrosomal/centriolar protein that (1) scaffolds a centrosomal complex with praja2, PKA, and OFD1 to link GPCR-cAMP signaling to PKA-mediated phosphorylation of OFD1 (Ser735) and its praja2-dependent ubiquitin-proteasome degradation, thereby controlling primary ciliogenesis; (2) localizes to the centriolar A-C linker as part of a CCDC77/WDR67/MIIP complex that maintains microtubule triplet cohesion and regulates centriole duplication; and (3) functions as a Rab22A GTPase-activating protein (Rab-GAP) that suppresses endolysosomal trafficking and degradation of EGFR, with its expression transcriptionally activated by ZSCAN16 in hepatocellular carcinoma.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TBC1D31 (also called WDR67) is a centrosomal/centriolar scaffold that couples signaling and structural control of the centriole to primary ciliogenesis [#0, #1, #2]. At the centrosome it assembles a complex with the E3 ubiquitin ligase praja2, protein kinase A (PKA), and OFD1; upon GPCR-cAMP stimulation PKA phosphorylates OFD1 at Ser735, driving its praja2-dependent ubiquitin-proteasome degradation, a step required for cilium biogenesis, with loss of TBC1D31 impairing ciliogenesis in cultured cells and in vivo in Medaka [#0, #1]. Structurally, it localizes to the centriolar A-C linker in a complex with CCDC77 and MIIP that bridges adjacent microtubule triplets at the proximal region to maintain triplet cohesion and regulate centriole duplication [#2]. Independently, TBC1D31 acts as a Rab22A GTPase-activating protein that suppresses Rab22A-mediated endolysosomal trafficking and degradation of EGFR, sustaining EGFR signaling and promoting hepatocellular carcinoma growth, where its expression is transcriptionally activated by ZSCAN16 [#3, #4].\",\n  \"teleology\": [\n    {\n      \"year\": 2021,\n      \"claim\": \"Established TBC1D31 as a centrosomal scaffold that links GPCR-cAMP/PKA signaling to controlled OFD1 turnover, answering how a signaling input gates ciliogenesis.\",\n      \"evidence\": \"Reciprocal Co-IP, centrosome localization, OFD1 S735A phospho-mutant analysis, and in vivo knockdown in Medaka\",\n      \"pmids\": [\"33934390\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define how TBC1D31 itself is recruited to the centrosome\", \"Stoichiometry and assembly order of the praja2/PKA/OFD1 complex unresolved\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Demonstrated that TBC1D31 is functionally required for primary ciliogenesis, moving it from a complex component to an essential biogenesis factor.\",\n      \"evidence\": \"Loss-of-function depletion in cell lines and Medaka with cilium morphology and developmental readouts\",\n      \"pmids\": [\"33934390\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ciliogenesis defects derive solely from OFD1 dysregulation or other pathways\", \"No human disease/genetic link established in the corpus\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified a distinct cytoplasmic role for TBC1D31 as a Rab22A GAP controlling EGFR trafficking, explaining a pro-tumorigenic function separate from its centriolar role.\",\n      \"evidence\": \"In vitro GAP activity assay, knockdown/overexpression in HCC cells and xenografts, endolysosomal and EGFR degradation assays\",\n      \"pmids\": [\"39206796\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab findings without independent replication\", \"Relationship between Rab-GAP function and centriolar localization unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed TBC1D31 downstream of a defined transcriptional activator in cancer, showing ZSCAN16 drives its expression to sustain HCC malignancy.\",\n      \"evidence\": \"ChIP-qPCR, dual-luciferase reporter, lentiviral knockdown/overexpression with functional rescue and xenograft models\",\n      \"pmids\": [\"39511655\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ZSCAN16-driven expression operates through the Rab22A/EGFR axis specifically not resolved\", \"Single-lab evidence\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Associated elevated TBC1D31 with a glycolytic metabolic phenotype in TNBC, broadening its cancer relevance beyond HCC.\",\n      \"evidence\": \"Transcriptomics/metabolomics correlation and siRNA knockdown with metabolic readouts in TNBC cell lines\",\n      \"pmids\": [\"39231952\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mechanistic pathway connecting TBC1D31 to glycolysis established\", \"Correlative, single-lab evidence\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Resolved the structural role of TBC1D31/WDR67 at the centriolar A-C linker, showing it physically bridges microtubule triplets and supports centriole architecture and duplication.\",\n      \"evidence\": \"Ultrastructure expansion microscopy, siRNA/KO depletion, co-localization, and co-depletion epistasis with inner scaffold components\",\n      \"pmids\": [\"40707486\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of triplet bridging by the CCDC77/WDR67/MIIP complex not defined\", \"How the A-C linker role integrates with the praja2/PKA/OFD1 signaling function unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how TBC1D31's centriolar structural/ciliogenic functions and its cytoplasmic Rab22A-GAP/EGFR-trafficking role are coordinated within a single protein.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure-function mapping separating GAP, scaffold, and A-C linker activities\", \"No data on whether the two functions are spatially or temporally exclusive\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\"praja2/PKA/OFD1 centrosomal complex\", \"CCDC77/WDR67/MIIP A-C linker complex\"],\n    \"partners\": [\"PRKACA\", \"OFD1\", \"PJA2\", \"CCDC77\", \"MIIP\", \"RAB22A\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}