{"gene":"DENND6A","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2012,"finding":"FAM116A (DENND6A) is a Rab14 GDP-GTP exchange factor (GEF) that localizes to and acts on an intermediate endocytic recycling compartment positioned after Rab5/Rab4 and before Rab11 in the transferrin-recycling pathway; loss of FAM116A causes ADAM10 accumulation in a transferrin-positive endosomal compartment, reduces cell-surface ADAM10 levels, and impairs N-cadherin shedding, thereby preventing resolution of cell-cell junctions during migration.","method":"Functional GEF screen, siRNA knockdown with transferrin recycling assays, co-localization/fractionation, ADAM10 cell-surface level measurement, N-cadherin shedding assay, cell migration assay","journal":"Developmental Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (GEF activity assay, subcellular localization, cell-surface proteolysis readout, migration phenotype) in a single focused study; widely cited","pmids":["22595670"],"is_preprint":false},{"year":2024,"finding":"DENND6A acts as a GEF for Rab34, which recruits a RILP/dynein complex to lysosomes to promote retrograde lysosomal transport; DENND6A is also an effector of Arl8b, which recruits DENND6A to peripheral lysosomes to activate Rab34 and initiate retrograde transport, thereby regulating nutrient-dependent juxtanuclear lysosomal repositioning and autophagic flux.","method":"Cell-based Rab GEF screen (all known Rabs), Co-IP, knockdown/knockout with lysosomal positioning assays, autophagic flux assays (LC3-II, p62), live imaging of lysosome movement, epistasis with Arl8b dominant-negative and constitutively active mutants","journal":"Nature Communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (GEF screen, Co-IP, loss-of-function with defined phenotypic readouts, epistasis with Arl8b) in a single peer-reviewed study with specific mechanistic pathway placement","pmids":["38296963"],"is_preprint":false},{"year":2026,"finding":"DENND6A exhibits strong Arf-GAP activity towards ARL8B in vitro, suggesting that its role in lysosome positioning may be explained by GAP activity toward ARL8B rather than (or in addition to) GEF activity toward Rab34; this places DENND6A in a family of 'DENN GAP' proteins.","method":"Computational protein-protein interaction screen, in vitro Arf-GAP activity assay, functional cell migration experiments","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro GAP assay is high-quality but single preprint lab, not yet peer-reviewed; contradicts prior GEF model and lower confidence warranted pending replication","pmids":["41542567"],"is_preprint":true},{"year":2024,"finding":"DENND6A physically interacts with RAB25, and this interaction affects cell migration, as identified by APEX2 proximity labeling and follow-up interaction studies.","method":"APEX2 proximity labeling (BioID-type), physical interaction validation, cell migration assay","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — proximity labeling is not direct binding evidence; single preprint with limited mechanistic follow-up on DENND6A specifically","pmids":["bio_10.1101_2024.11.05.621850"],"is_preprint":true}],"current_model":"DENND6A (FAM116A) is a DENN-domain protein that functions as a GEF for Rab14 on an intermediate endocytic recycling compartment to regulate ADAM10 surface trafficking and N-cadherin shedding during cell migration, and as an effector of Arl8b on peripheral lysosomes where it activates Rab34 to recruit a RILP/dynein complex for retrograde lysosomal transport and autophagy; a recent preprint additionally proposes that DENND6A possesses Arf-GAP activity toward ARL8B, which may provide an alternative mechanistic explanation for its role in lysosome positioning."},"narrative":{"mechanistic_narrative":"DENND6A (FAM116A) is a DENN-domain guanine nucleotide exchange factor that controls discrete steps of membrane traffic governing cell migration and lysosome positioning [PMID:22595670, PMID:38296963]. In the endocytic recycling pathway it acts as a GEF for Rab14 on an intermediate recycling compartment located after Rab5/Rab4 and before Rab11; loss of DENND6A traps ADAM10 in a transferrin-positive endosomal compartment, lowers surface ADAM10, and impairs N-cadherin shedding, thereby preventing resolution of cell-cell junctions during migration [PMID:22595670]. On lysosomes, DENND6A serves as an effector of Arl8b that is recruited to peripheral lysosomes, where it functions as a GEF for Rab34 to assemble a RILP/dynein complex driving retrograde, dynein-dependent juxtanuclear repositioning and supporting autophagic flux under nutrient control [PMID:38296963]. An in vitro reassessment additionally identifies DENND6A as a DENN-domain Arf-GAP acting on ARL8B, offering an alternative biochemical account of its lysosome-positioning role [PMID:41542567].","teleology":[{"year":2012,"claim":"Established DENND6A's first molecular activity by showing it is a Rab14 GEF acting at a defined station of the endocytic recycling pathway, linking it to surface delivery of the sheddase ADAM10 and to junction remodeling during migration.","evidence":"Functional GEF screen with siRNA knockdown, transferrin recycling and co-localization assays, ADAM10 surface measurement, N-cadherin shedding and migration assays","pmids":["22595670"],"confidence":"High","gaps":["Direct structural basis of Rab14 recognition not resolved","Mechanism recruiting DENND6A to the intermediate recycling compartment not defined","Whether ADAM10 is the only relevant cargo unknown"]},{"year":2024,"claim":"Extended DENND6A function to lysosomes by showing it acts as a Rab34 GEF downstream of Arl8b to recruit RILP/dynein for retrograde transport, placing it in a defined nutrient-responsive lysosome-positioning and autophagy pathway.","evidence":"Cell-based Rab GEF screen, Co-IP, knockdown/knockout lysosome positioning and autophagic flux assays, live imaging, epistasis with Arl8b mutants","pmids":["38296963"],"confidence":"High","gaps":["Structural detail of the Arl8b-DENND6A effector interaction not resolved","How DENND6A toggles between Rab14 (recycling) and Rab34 (lysosomal) roles unknown","Direct vs indirect assembly of the RILP/dynein complex not fully dissected"]},{"year":2024,"claim":"Identified RAB25 as a DENND6A interactor relevant to migration, expanding the candidate partner set beyond Rab14.","evidence":"APEX2 proximity labeling with physical interaction validation and migration assays (preprint)","pmids":["bio_10.1101_2024.11.05.621850"],"confidence":"Low","gaps":["Proximity labeling is not direct binding evidence and lacks reciprocal validation","Functional consequence of the RAB25 interaction on DENND6A activity undefined","Single preprint, not peer-reviewed"]},{"year":2026,"claim":"Challenged the GEF-only model by demonstrating in vitro Arf-GAP activity of DENND6A toward ARL8B, proposing a GAP-based explanation for lysosome positioning.","evidence":"Computational interaction screen, in vitro Arf-GAP activity assay, cell migration experiments (preprint)","pmids":["41542567"],"confidence":"Medium","gaps":["Single preprint lab, not yet peer-reviewed and contradicts prior GEF model","GAP activity shown in vitro; cellular relevance versus Rab34 GEF role not reconciled","No structural basis for ARL8B GAP catalysis"]},{"year":null,"claim":"How DENND6A reconciles GEF activity toward Rab14/Rab34 with proposed GAP activity toward ARL8B, and how it is partitioned between recycling endosomes and lysosomes, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified biochemical model integrating GEF and GAP activities","No structure of DENND6A bound to any partner","Determinants of compartment-specific targeting unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[1]}],"complexes":[],"partners":["RAB14","RAB34","ARL8B","RILP","ADAM10","RAB25"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8IWF6","full_name":"Protein DENND6A","aliases":["DENN domain-containing protein 6A"],"length_aa":608,"mass_kda":69.6,"function":"Guanine nucleotide exchange factor (GEF) for RAB14. Component of an endocytic recycling pathway that is required for the control of ADAM10 transport, shedding of N-cadherin/CDH2 by ADAM9 or ADAM10 and regulation of cell-cell junctions. Required for RAB14 recruitment to recycling endosomes","subcellular_location":"Recycling endosome; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q8IWF6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DENND6A","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/DENND6A","total_profiled":1310},"omim":[{"mim_id":"620561","title":"DENN DOMAIN-CONTAINING PROTEIN 6A; DENND6A","url":"https://www.omim.org/entry/620561"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Vesicles","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/DENND6A"},"hgnc":{"alias_symbol":["FLJ34969","AFI1A"],"prev_symbol":["FAM116A"]},"alphafold":{"accession":"Q8IWF6","domains":[{"cath_id":"3.30.450.200","chopping":"57-218","consensus_level":"high","plddt":88.9349,"start":57,"end":218},{"cath_id":"3.40.50","chopping":"272-432","consensus_level":"medium","plddt":88.6772,"start":272,"end":432},{"cath_id":"-","chopping":"433-512","consensus_level":"medium","plddt":93.8791,"start":433,"end":512},{"cath_id":"-","chopping":"542-606","consensus_level":"high","plddt":86.8872,"start":542,"end":606}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IWF6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IWF6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IWF6-F1-predicted_aligned_error_v6.png","plddt_mean":83.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DENND6A","jax_strain_url":"https://www.jax.org/strain/search?query=DENND6A"},"sequence":{"accession":"Q8IWF6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8IWF6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8IWF6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IWF6"}},"corpus_meta":[{"pmid":"22595670","id":"PMC_22595670","title":"Rab14 and its exchange factor FAM116 link endocytic recycling and adherens junction stability in migrating cells.","date":"2012","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/22595670","citation_count":111,"is_preprint":false},{"pmid":"38296963","id":"PMC_38296963","title":"DENND6A links Arl8b to a Rab34/RILP/dynein complex, regulating lysosomal positioning and autophagy.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38296963","citation_count":17,"is_preprint":false},{"pmid":"41542567","id":"PMC_41542567","title":"Avl9 defines a family of GTPase-activating proteins that regulate diverse cell biological functions.","date":"2026","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41542567","citation_count":2,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.11.05.621850","title":"A Proximity MAP of RAB GTPases","date":"2024-11-06","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.05.621850","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3894,"output_tokens":1230,"usd":0.015066,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7800,"output_tokens":2035,"usd":0.044937,"stage2_stop_reason":"end_turn"},"total_usd":0.060003,"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\": 2012,\n      \"finding\": \"FAM116A (DENND6A) is a Rab14 GDP-GTP exchange factor (GEF) that localizes to and acts on an intermediate endocytic recycling compartment positioned after Rab5/Rab4 and before Rab11 in the transferrin-recycling pathway; loss of FAM116A causes ADAM10 accumulation in a transferrin-positive endosomal compartment, reduces cell-surface ADAM10 levels, and impairs N-cadherin shedding, thereby preventing resolution of cell-cell junctions during migration.\",\n      \"method\": \"Functional GEF screen, siRNA knockdown with transferrin recycling assays, co-localization/fractionation, ADAM10 cell-surface level measurement, N-cadherin shedding assay, cell migration assay\",\n      \"journal\": \"Developmental Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (GEF activity assay, subcellular localization, cell-surface proteolysis readout, migration phenotype) in a single focused study; widely cited\",\n      \"pmids\": [\"22595670\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DENND6A acts as a GEF for Rab34, which recruits a RILP/dynein complex to lysosomes to promote retrograde lysosomal transport; DENND6A is also an effector of Arl8b, which recruits DENND6A to peripheral lysosomes to activate Rab34 and initiate retrograde transport, thereby regulating nutrient-dependent juxtanuclear lysosomal repositioning and autophagic flux.\",\n      \"method\": \"Cell-based Rab GEF screen (all known Rabs), Co-IP, knockdown/knockout with lysosomal positioning assays, autophagic flux assays (LC3-II, p62), live imaging of lysosome movement, epistasis with Arl8b dominant-negative and constitutively active mutants\",\n      \"journal\": \"Nature Communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (GEF screen, Co-IP, loss-of-function with defined phenotypic readouts, epistasis with Arl8b) in a single peer-reviewed study with specific mechanistic pathway placement\",\n      \"pmids\": [\"38296963\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"DENND6A exhibits strong Arf-GAP activity towards ARL8B in vitro, suggesting that its role in lysosome positioning may be explained by GAP activity toward ARL8B rather than (or in addition to) GEF activity toward Rab34; this places DENND6A in a family of 'DENN GAP' proteins.\",\n      \"method\": \"Computational protein-protein interaction screen, in vitro Arf-GAP activity assay, functional cell migration experiments\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro GAP assay is high-quality but single preprint lab, not yet peer-reviewed; contradicts prior GEF model and lower confidence warranted pending replication\",\n      \"pmids\": [\"41542567\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DENND6A physically interacts with RAB25, and this interaction affects cell migration, as identified by APEX2 proximity labeling and follow-up interaction studies.\",\n      \"method\": \"APEX2 proximity labeling (BioID-type), physical interaction validation, cell migration assay\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — proximity labeling is not direct binding evidence; single preprint with limited mechanistic follow-up on DENND6A specifically\",\n      \"pmids\": [\"bio_10.1101_2024.11.05.621850\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"DENND6A (FAM116A) is a DENN-domain protein that functions as a GEF for Rab14 on an intermediate endocytic recycling compartment to regulate ADAM10 surface trafficking and N-cadherin shedding during cell migration, and as an effector of Arl8b on peripheral lysosomes where it activates Rab34 to recruit a RILP/dynein complex for retrograde lysosomal transport and autophagy; a recent preprint additionally proposes that DENND6A possesses Arf-GAP activity toward ARL8B, which may provide an alternative mechanistic explanation for its role in lysosome positioning.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DENND6A (FAM116A) is a DENN-domain guanine nucleotide exchange factor that controls discrete steps of membrane traffic governing cell migration and lysosome positioning [#0, #1]. In the endocytic recycling pathway it acts as a GEF for Rab14 on an intermediate recycling compartment located after Rab5/Rab4 and before Rab11; loss of DENND6A traps ADAM10 in a transferrin-positive endosomal compartment, lowers surface ADAM10, and impairs N-cadherin shedding, thereby preventing resolution of cell-cell junctions during migration [#0]. On lysosomes, DENND6A serves as an effector of Arl8b that is recruited to peripheral lysosomes, where it functions as a GEF for Rab34 to assemble a RILP/dynein complex driving retrograde, dynein-dependent juxtanuclear repositioning and supporting autophagic flux under nutrient control [#1]. An in vitro reassessment additionally identifies DENND6A as a DENN-domain Arf-GAP acting on ARL8B, offering an alternative biochemical account of its lysosome-positioning role [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Established DENND6A's first molecular activity by showing it is a Rab14 GEF acting at a defined station of the endocytic recycling pathway, linking it to surface delivery of the sheddase ADAM10 and to junction remodeling during migration.\",\n      \"evidence\": \"Functional GEF screen with siRNA knockdown, transferrin recycling and co-localization assays, ADAM10 surface measurement, N-cadherin shedding and migration assays\",\n      \"pmids\": [\"22595670\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct structural basis of Rab14 recognition not resolved\",\n        \"Mechanism recruiting DENND6A to the intermediate recycling compartment not defined\",\n        \"Whether ADAM10 is the only relevant cargo unknown\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended DENND6A function to lysosomes by showing it acts as a Rab34 GEF downstream of Arl8b to recruit RILP/dynein for retrograde transport, placing it in a defined nutrient-responsive lysosome-positioning and autophagy pathway.\",\n      \"evidence\": \"Cell-based Rab GEF screen, Co-IP, knockdown/knockout lysosome positioning and autophagic flux assays, live imaging, epistasis with Arl8b mutants\",\n      \"pmids\": [\"38296963\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural detail of the Arl8b-DENND6A effector interaction not resolved\",\n        \"How DENND6A toggles between Rab14 (recycling) and Rab34 (lysosomal) roles unknown\",\n        \"Direct vs indirect assembly of the RILP/dynein complex not fully dissected\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified RAB25 as a DENND6A interactor relevant to migration, expanding the candidate partner set beyond Rab14.\",\n      \"evidence\": \"APEX2 proximity labeling with physical interaction validation and migration assays (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.11.05.621850\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Proximity labeling is not direct binding evidence and lacks reciprocal validation\",\n        \"Functional consequence of the RAB25 interaction on DENND6A activity undefined\",\n        \"Single preprint, not peer-reviewed\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Challenged the GEF-only model by demonstrating in vitro Arf-GAP activity of DENND6A toward ARL8B, proposing a GAP-based explanation for lysosome positioning.\",\n      \"evidence\": \"Computational interaction screen, in vitro Arf-GAP activity assay, cell migration experiments (preprint)\",\n      \"pmids\": [\"41542567\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single preprint lab, not yet peer-reviewed and contradicts prior GEF model\",\n        \"GAP activity shown in vitro; cellular relevance versus Rab34 GEF role not reconciled\",\n        \"No structural basis for ARL8B GAP catalysis\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How DENND6A reconciles GEF activity toward Rab14/Rab34 with proposed GAP activity toward ARL8B, and how it is partitioned between recycling endosomes and lysosomes, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No unified biochemical model integrating GEF and GAP activities\",\n        \"No structure of DENND6A bound to any partner\",\n        \"Determinants of compartment-specific targeting unknown\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RAB14\", \"RAB34\", \"ARL8B\", \"RILP\", \"ADAM10\", \"RAB25\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}