{"gene":"DENND4C","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2011,"finding":"DENND4C is the primary guanine nucleotide exchange factor (GEF) for Rab10 required for insulin-stimulated GLUT4 vesicle translocation to the plasma membrane in adipocytes. Knockdown of DENND4C markedly inhibited GLUT4 translocation, ectopic expression slightly stimulated it, and DENND4C was found in isolated GLUT4 vesicles.","method":"siRNA knockdown, ectopic overexpression, GLUT4 translocation assay, subcellular fractionation of GLUT4 vesicles","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function and gain-of-function with defined cellular phenotype, subcellular localization by fractionation, replicated conceptually by independent lab (PMID:23804653)","pmids":["21454697"],"is_preprint":false},{"year":2013,"finding":"Activation of Rab10 by DENND4C (its GEF) does not require insulin stimulation, establishing that DENND4C's GEF activity toward Rab10 is constitutive and that insulin regulation of Rab10 in the GLUT4 translocation pathway operates through suppression of the GAP AS160, not through activation of DENND4C.","method":"Epistasis/pathway analysis in adipocytes; insulin-stimulation experiments combined with Rab10 activation assays","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pathway placement by genetic/pharmacological epistasis in intact cells, single lab but two orthogonal lines of evidence (Rab14/Rab10 hierarchy and insulin-independence of GEF activity)","pmids":["23804653"],"is_preprint":false},{"year":2025,"finding":"Retromer directly associates with and recruits DENND4C (along with DENND4A, TBC1D1, and TBC1D4) to the endosomal retrieval sub-domain to regulate RAB10 GTPase switching, establishing Retromer as a hub linking cargo recycling with RAB GTPase regulation.","method":"Proximity proteomics, X-ray crystallography, in silico structural predictions, biochemical pulldown/co-IP, cellular analysis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — X-ray crystallography combined with proximity proteomics and biochemical/cellular validation in a single rigorous study, peer-reviewed publication","pmids":["40738907"],"is_preprint":false},{"year":2024,"finding":"Retromer directly associates with DENND4C and recruits it to the endosomal retrieval sub-domain for RAB10 regulation (preprint version of the above finding, same data).","method":"Proximity proteomics, X-ray crystallography, biochemical and cellular analysis","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — same dataset as published paper (PMID:40738907); preprint included only for completeness; evidence quality is the same","pmids":["bio_10.1101_2024.11.22.622898"],"is_preprint":true}],"current_model":"DENND4C is a constitutively active GEF for RAB10 that localizes to GLUT4-containing vesicles and is required for insulin-stimulated GLUT4 translocation to the plasma membrane in adipocytes; additionally, DENND4C is directly recruited to the endosomal retrieval sub-domain by Retromer, positioning it as part of a hub that couples endosomal cargo recycling with regulated RAB10 GTPase switching."},"narrative":{"mechanistic_narrative":"DENND4C is a guanine nucleotide exchange factor (GEF) for the small GTPase RAB10 that functions in regulated membrane trafficking, most notably insulin-stimulated GLUT4 vesicle delivery to the plasma membrane in adipocytes [PMID:21454697]. It localizes to GLUT4-containing vesicles, and loss of DENND4C markedly impairs GLUT4 translocation, identifying it as the primary RAB10 GEF in this pathway [PMID:21454697]. Its GEF activity toward RAB10 is constitutive and insulin-independent, so insulin regulation of the pathway is imposed not by activating DENND4C but through suppression of the RAB10 GAP AS160 [PMID:23804653]. DENND4C is also directly bound and recruited by Retromer to the endosomal retrieval sub-domain, placing its RAB10 GTPase-switching activity within an endosomal cargo-recycling hub [PMID:40738907].","teleology":[{"year":2011,"claim":"Established which GEF drives RAB10 activation during regulated GLUT4 trafficking, identifying DENND4C as the molecular link between RAB10 and insulin-responsive glucose uptake.","evidence":"siRNA knockdown, overexpression, GLUT4 translocation assays, and GLUT4-vesicle fractionation in adipocytes","pmids":["21454697"],"confidence":"High","gaps":["Direct nucleotide-exchange kinetics on RAB10 not measured in this study","Domain of DENND4C responsible for GEF activity not mapped","Mechanism of vesicle targeting not defined"]},{"year":2013,"claim":"Resolved where insulin acts in the pathway by showing DENND4C GEF activity is constitutive, so insulin operates downstream through GAP (AS160) suppression rather than GEF activation.","evidence":"Pathway/epistasis analysis combining insulin stimulation with RAB10 activation assays in adipocytes","pmids":["23804653"],"confidence":"Medium","gaps":["Single-lab pathway placement without reconstituted biochemistry","How DENND4C itself is spatially regulated remains undefined","Interplay with RAB14 hierarchy not fully resolved"]},{"year":2025,"claim":"Defined how DENND4C is positioned at endosomes by showing Retromer directly binds and recruits it to the retrieval sub-domain, coupling cargo recycling to RAB10 GTPase switching.","evidence":"Proximity proteomics, X-ray crystallography, biochemical pulldown/co-IP, and cellular analysis","pmids":["40738907"],"confidence":"High","gaps":["Functional consequence of Retromer recruitment for GLUT4 trafficking not directly tested","Structural basis of the DENND4C-Retromer interface within the full complex not detailed here","Whether recruitment alters RAB10 GEF kinetics not measured"]},{"year":null,"claim":"How constitutive DENND4C GEF activity, vesicle targeting, and Retromer-mediated endosomal recruitment are integrated to spatially restrict RAB10 activation remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of DENND4C catalytic engagement with RAB10","Tissue and cargo specificity of DENND4C function beyond adipocyte GLUT4 not mapped","Regulation of DENND4C localization between GLUT4 vesicles and endosomal sub-domains undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,2]}],"localization":[{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[0]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[0]}],"complexes":[],"partners":["RAB10","VPS35"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5VZ89","full_name":"DENN domain-containing protein 4C","aliases":[],"length_aa":1909,"mass_kda":212.7,"function":"Guanine nucleotide exchange factor (GEF) activating RAB10. Promotes the exchange of GDP to GTP, converting inactive GDP-bound RAB10 into its active GTP-bound form. Thereby, stimulates SLC2A4/GLUT4 glucose transporter-enriched vesicles delivery to the plasma membrane in response to insulin","subcellular_location":"Cytoplasmic vesicle membrane; Cell membrane; Cytoplasm, cytosol","url":"https://www.uniprot.org/uniprotkb/Q5VZ89/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DENND4C","classification":"Not Classified","n_dependent_lines":17,"n_total_lines":1208,"dependency_fraction":0.014072847682119206},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CALM1","stoichiometry":0.2},{"gene":"CALM2","stoichiometry":0.2},{"gene":"CALM3","stoichiometry":0.2},{"gene":"VPS35","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/DENND4C","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Golgi apparatus","reliability":"Supported"},{"location":"Vesicles","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/DENND4C"},"hgnc":{"alias_symbol":["FLJ20686","bA513M16.3","RAB10GEF"],"prev_symbol":["C9orf55B","C9orf55"]},"alphafold":{"accession":"Q5VZ89","domains":[{"cath_id":"3.30.450.200","chopping":"2-40_202-359","consensus_level":"medium","plddt":83.1774,"start":2,"end":359},{"cath_id":"2.100.10.50","chopping":"41-199","consensus_level":"high","plddt":87.3628,"start":41,"end":199},{"cath_id":"-","chopping":"592-657_746-874","consensus_level":"medium","plddt":85.8544,"start":592,"end":874},{"cath_id":"-","chopping":"1482-1499_1516-1545_1677-1689_1698-1778","consensus_level":"medium","plddt":83.4307,"start":1482,"end":1778},{"cath_id":"-","chopping":"1804-1909","consensus_level":"medium","plddt":84.269,"start":1804,"end":1909}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5VZ89","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5VZ89-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5VZ89-F1-predicted_aligned_error_v6.png","plddt_mean":63.97},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DENND4C","jax_strain_url":"https://www.jax.org/strain/search?query=DENND4C"},"sequence":{"accession":"Q5VZ89","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5VZ89.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5VZ89/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5VZ89"}},"corpus_meta":[{"pmid":"21454697","id":"PMC_21454697","title":"Insulin-stimulated GLUT4 protein translocation in adipocytes requires the Rab10 guanine nucleotide exchange factor Dennd4C.","date":"2011","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21454697","citation_count":67,"is_preprint":false},{"pmid":"23804653","id":"PMC_23804653","title":"Specialized sorting of GLUT4 and its recruitment to the cell surface are independently regulated by distinct Rabs.","date":"2013","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/23804653","citation_count":58,"is_preprint":false},{"pmid":"31296839","id":"PMC_31296839","title":"KHDRBS3 regulates the permeability of blood-tumor barrier via cDENND4C/miR-577 axis.","date":"2019","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/31296839","citation_count":36,"is_preprint":false},{"pmid":"38412628","id":"PMC_38412628","title":"Circ DENND4C inhibits pyroptosis and alleviates ischemia-reperfusion acute kidney injury by exosomes secreted from human urine-derived stem cells.","date":"2024","source":"Chemico-biological interactions","url":"https://pubmed.ncbi.nlm.nih.gov/38412628","citation_count":24,"is_preprint":false},{"pmid":"32669971","id":"PMC_32669971","title":"Circ-DENND4C up-regulates TCF4 expression to modulate hepatocellular carcinoma cell proliferation and apoptosis via activating Wnt/β-catenin signal pathway.","date":"2020","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/32669971","citation_count":15,"is_preprint":false},{"pmid":"40738907","id":"PMC_40738907","title":"Mapping of endosomal proximity proteomes reveals Retromer as a hub for RAB GTPase regulation.","date":"2025","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/40738907","citation_count":5,"is_preprint":false},{"pmid":"29958078","id":"PMC_29958078","title":"Identification of nine novel loci related to hematological traits in a Japanese population.","date":"2018","source":"Physiological genomics","url":"https://pubmed.ncbi.nlm.nih.gov/29958078","citation_count":5,"is_preprint":false},{"pmid":"33090893","id":"PMC_33090893","title":"Circular RNA-DENND4C in H9c2 cells relieves OGD/R-induced injury by down regulation of microRNA-320.","date":"2020","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/33090893","citation_count":3,"is_preprint":false},{"pmid":"41358261","id":"PMC_41358261","title":"Circular RNA DENND4C Regulates Cell Malignant Behaviors in Breast Cancer Through the miR-26a-5p/HSPA8 Axis.","date":"2025","source":"Breast cancer (Dove Medical Press)","url":"https://pubmed.ncbi.nlm.nih.gov/41358261","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.11.22.622898","title":"Mapping the endosomal proximity proteome reveals Retromer as a hub for RAB GTPase regulation","date":"2024-11-22","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.22.622898","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7599,"output_tokens":1059,"usd":0.019341,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7570,"output_tokens":1541,"usd":0.038187,"stage2_stop_reason":"end_turn"},"total_usd":0.057528,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"DENND4C is the primary guanine nucleotide exchange factor (GEF) for Rab10 required for insulin-stimulated GLUT4 vesicle translocation to the plasma membrane in adipocytes. Knockdown of DENND4C markedly inhibited GLUT4 translocation, ectopic expression slightly stimulated it, and DENND4C was found in isolated GLUT4 vesicles.\",\n      \"method\": \"siRNA knockdown, ectopic overexpression, GLUT4 translocation assay, subcellular fractionation of GLUT4 vesicles\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function and gain-of-function with defined cellular phenotype, subcellular localization by fractionation, replicated conceptually by independent lab (PMID:23804653)\",\n      \"pmids\": [\"21454697\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Activation of Rab10 by DENND4C (its GEF) does not require insulin stimulation, establishing that DENND4C's GEF activity toward Rab10 is constitutive and that insulin regulation of Rab10 in the GLUT4 translocation pathway operates through suppression of the GAP AS160, not through activation of DENND4C.\",\n      \"method\": \"Epistasis/pathway analysis in adipocytes; insulin-stimulation experiments combined with Rab10 activation assays\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pathway placement by genetic/pharmacological epistasis in intact cells, single lab but two orthogonal lines of evidence (Rab14/Rab10 hierarchy and insulin-independence of GEF activity)\",\n      \"pmids\": [\"23804653\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Retromer directly associates with and recruits DENND4C (along with DENND4A, TBC1D1, and TBC1D4) to the endosomal retrieval sub-domain to regulate RAB10 GTPase switching, establishing Retromer as a hub linking cargo recycling with RAB GTPase regulation.\",\n      \"method\": \"Proximity proteomics, X-ray crystallography, in silico structural predictions, biochemical pulldown/co-IP, cellular analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — X-ray crystallography combined with proximity proteomics and biochemical/cellular validation in a single rigorous study, peer-reviewed publication\",\n      \"pmids\": [\"40738907\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Retromer directly associates with DENND4C and recruits it to the endosomal retrieval sub-domain for RAB10 regulation (preprint version of the above finding, same data).\",\n      \"method\": \"Proximity proteomics, X-ray crystallography, biochemical and cellular analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — same dataset as published paper (PMID:40738907); preprint included only for completeness; evidence quality is the same\",\n      \"pmids\": [\"bio_10.1101_2024.11.22.622898\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"DENND4C is a constitutively active GEF for RAB10 that localizes to GLUT4-containing vesicles and is required for insulin-stimulated GLUT4 translocation to the plasma membrane in adipocytes; additionally, DENND4C is directly recruited to the endosomal retrieval sub-domain by Retromer, positioning it as part of a hub that couples endosomal cargo recycling with regulated RAB10 GTPase switching.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DENND4C is a guanine nucleotide exchange factor (GEF) for the small GTPase RAB10 that functions in regulated membrane trafficking, most notably insulin-stimulated GLUT4 vesicle delivery to the plasma membrane in adipocytes [#0]. It localizes to GLUT4-containing vesicles, and loss of DENND4C markedly impairs GLUT4 translocation, identifying it as the primary RAB10 GEF in this pathway [#0]. Its GEF activity toward RAB10 is constitutive and insulin-independent, so insulin regulation of the pathway is imposed not by activating DENND4C but through suppression of the RAB10 GAP AS160 [#1]. DENND4C is also directly bound and recruited by Retromer to the endosomal retrieval sub-domain, placing its RAB10 GTPase-switching activity within an endosomal cargo-recycling hub [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Established which GEF drives RAB10 activation during regulated GLUT4 trafficking, identifying DENND4C as the molecular link between RAB10 and insulin-responsive glucose uptake.\",\n      \"evidence\": \"siRNA knockdown, overexpression, GLUT4 translocation assays, and GLUT4-vesicle fractionation in adipocytes\",\n      \"pmids\": [\"21454697\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct nucleotide-exchange kinetics on RAB10 not measured in this study\", \"Domain of DENND4C responsible for GEF activity not mapped\", \"Mechanism of vesicle targeting not defined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Resolved where insulin acts in the pathway by showing DENND4C GEF activity is constitutive, so insulin operates downstream through GAP (AS160) suppression rather than GEF activation.\",\n      \"evidence\": \"Pathway/epistasis analysis combining insulin stimulation with RAB10 activation assays in adipocytes\",\n      \"pmids\": [\"23804653\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab pathway placement without reconstituted biochemistry\", \"How DENND4C itself is spatially regulated remains undefined\", \"Interplay with RAB14 hierarchy not fully resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined how DENND4C is positioned at endosomes by showing Retromer directly binds and recruits it to the retrieval sub-domain, coupling cargo recycling to RAB10 GTPase switching.\",\n      \"evidence\": \"Proximity proteomics, X-ray crystallography, biochemical pulldown/co-IP, and cellular analysis\",\n      \"pmids\": [\"40738907\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of Retromer recruitment for GLUT4 trafficking not directly tested\", \"Structural basis of the DENND4C-Retromer interface within the full complex not detailed here\", \"Whether recruitment alters RAB10 GEF kinetics not measured\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How constitutive DENND4C GEF activity, vesicle targeting, and Retromer-mediated endosomal recruitment are integrated to spatially restrict RAB10 activation remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural model of DENND4C catalytic engagement with RAB10\", \"Tissue and cargo specificity of DENND4C function beyond adipocyte GLUT4 not mapped\", \"Regulation of DENND4C localization between GLUT4 vesicles and endosomal sub-domains undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RAB10\", \"VPS35\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}