{"gene":"DENND4A","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":1994,"finding":"DENND4A (then called IRLB) was identified as a c-myc promoter-binding protein that recognizes the ISRE-like element in the P2 promoter region of human c-myc, demonstrated by DNase footprinting analysis and oligonucleotide-binding specificity assays using a fusion protein expressed in E. coli.","method":"DNase footprinting, oligonucleotide-binding specificity assay, lambda gt11 phage library screening","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct DNA-binding assays (footprinting + specificity assays) in a single study with partial protein only","pmids":["8056341"],"is_preprint":false},{"year":2003,"finding":"Full-length DENND4A (IRLB) was cloned and found to encode a 1865-aa protein containing a tripartite DENN domain, a nuclear localization signal, two PPRs, a calmodulin-binding domain, and the previously identified ISRE-binding domain, predicting interactions with Rab family GTPases.","method":"RT-PCR cloning, bioinformatics/structural domain analysis, genomic mapping","journal":"Genomics","confidence":"Low","confidence_rationale":"Tier 4 / Weak — structural domain prediction and cloning without functional reconstitution of Rab-binding or enzymatic activity","pmids":["12906859"],"is_preprint":false},{"year":2019,"finding":"TDP-43 A315T patient mutant allele specifically enhances translation of Dennd4a mRNA via a specific 3'UTR region, as demonstrated by ribosome profiling and direct binding assays in motor neuron-like cells; this effect was specific to the mutant allele and not observed with wild-type TDP-43.","method":"Ribosome profiling, mRNA direct binding assay, 3'UTR reporter assay, overexpression in motor neuron-like cells","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ribosome profiling plus direct binding plus UTR reporter assay in a single lab, multiple orthogonal methods","pmids":["30357366"],"is_preprint":false},{"year":2025,"finding":"DENND4A directly associates with Retromer and is recruited by Retromer to the endosomal retrieval sub-domain to regulate RAB10 GTPase switching, as revealed by proximity proteomics, X-ray crystallography, in silico predictions, and biochemical/cellular analysis.","method":"Proximity proteomics (BioID), X-ray crystallography, in silico structural predictions, biochemical co-association assays, cellular imaging","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods including structural (X-ray crystallography), proximity proteomics, and biochemical/cellular validation in a single rigorous study; peer-reviewed publication","pmids":["40738907"],"is_preprint":false}],"current_model":"DENND4A is a DENN-domain-containing protein that functions as a RAB10 guanine nucleotide exchange factor (GEF) regulator; it is directly recruited to the endosomal retrieval sub-domain by Retromer to regulate RAB10 GTPase switching as part of cargo recycling, and its Dennd4a mRNA translation is selectively enhanced by the TDP-43 A315T disease mutant via a 3'UTR-dependent mechanism; earlier work also identified it as a c-myc P2 promoter ISRE-like element binding protein."},"narrative":{"mechanistic_narrative":"DENND4A is a large DENN-domain-containing protein that functions in endosomal cargo recycling as a regulator of RAB10 GTPase switching [PMID:40738907]. It directly associates with Retromer and is recruited by Retromer to the endosomal retrieval sub-domain, where it acts on RAB10 nucleotide cycling [PMID:40738907]. The protein additionally carries domains predicted to support nucleic acid and Rab GTPase interactions, including a tripartite DENN domain [PMID:12906859]. Beyond its endosomal role, DENND4A mRNA is a selective target of disease-associated translational dysregulation: the ALS-linked TDP-43 A315T mutant, but not wild-type TDP-43, enhances Dennd4a translation through a specific 3'UTR region [PMID:30357366]. An earlier line of evidence identified DENND4A (then IRLB) as a sequence-specific DNA-binding protein recognizing the ISRE-like element of the human c-myc P2 promoter [PMID:8056341], a nuclear activity whose relationship to its endosomal function has not been resolved in the available corpus.","teleology":[{"year":1994,"claim":"Before any functional annotation, the question was whether this protein had a defined molecular activity; it was first captured as a sequence-specific DNA-binding factor at the c-myc promoter.","evidence":"DNase footprinting and oligonucleotide-binding specificity assays with an E. coli-expressed fusion protein","pmids":["8056341"],"confidence":"Medium","gaps":["Used partial protein only, not full-length DENND4A","No demonstration that DNA binding occurs in cells or regulates c-myc transcription","Relationship to later-defined endosomal function unestablished"]},{"year":2003,"claim":"Cloning the full-length transcript addressed what kind of protein this is, revealing a multidomain architecture including a tripartite DENN domain that predicted Rab GTPase involvement.","evidence":"RT-PCR cloning, domain/bioinformatic analysis, and genomic mapping","pmids":["12906859"],"confidence":"Low","gaps":["Domain assignments are predictions without functional reconstitution","Rab binding and any enzymatic activity not demonstrated","NLS and calmodulin-binding domain functions untested"]},{"year":2019,"claim":"To connect DENND4A to disease, the question was whether its expression is altered by an ALS mutation; ribosome profiling showed mutant TDP-43 A315T selectively enhances Dennd4a translation via its 3'UTR.","evidence":"Ribosome profiling, direct mRNA-binding assay, and 3'UTR reporter assays with overexpression in motor neuron-like cells","pmids":["30357366"],"confidence":"Medium","gaps":["Single-lab finding in a motor neuron-like cell model","Downstream consequence of elevated DENND4A protein not defined","Mechanism of mutant-specific 3'UTR recognition not resolved"]},{"year":2025,"claim":"The defining mechanistic question — what DENND4A does at the membrane — was answered by showing it directly associates with Retromer and is recruited to regulate RAB10 GTPase switching during endosomal cargo retrieval.","evidence":"Proximity proteomics (BioID), X-ray crystallography, in silico structural prediction, and biochemical/cellular validation","pmids":["40738907"],"confidence":"High","gaps":["Direct GEF catalytic activity of DENND4A on RAB10 not enzymatically quantified","Specific cargoes whose recycling depends on DENND4A not identified","Link to its DNA-binding and TDP-43-regulated translation roles unexplored"]},{"year":null,"claim":"It remains unknown how DENND4A's nuclear DNA-binding activity and its endosomal RAB10/Retromer function relate, and whether disease-driven translational upregulation alters its membrane-trafficking role.","evidence":"No integrating study in the available corpus","pmids":[],"confidence":"Low","gaps":["No reconciliation of nuclear versus endosomal localization and function","No measurement of how TDP-43-driven DENND4A levels affect RAB10 cycling or cargo recycling"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[3]}],"complexes":[],"partners":["RAB10","VPS35"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q7Z401","full_name":"C-myc promoter-binding protein","aliases":["DENN domain-containing protein 4A"],"length_aa":1863,"mass_kda":209.2,"function":"Probable guanine nucleotide exchange factor (GEF) which may activate RAB10. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. According to PubMed:8056341, it may bind to ISRE-like element (interferon-stimulated response element) of MYC P2 promoter","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q7Z401/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DENND4A","classification":"Not Classified","n_dependent_lines":50,"n_total_lines":1208,"dependency_fraction":0.041390728476821195},"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":"MAP4K4","stoichiometry":0.2},{"gene":"UBA1","stoichiometry":0.2},{"gene":"VPS35","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/DENND4A","total_profiled":1310},"omim":[{"mim_id":"600382","title":"MYC PROMOTER-BINDING PROTEIN","url":"https://www.omim.org/entry/600382"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli rim","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Mitotic chromosome","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"retina","ntpm":54.8}],"url":"https://www.proteinatlas.org/search/DENND4A"},"hgnc":{"alias_symbol":["IRLB"],"prev_symbol":["MYCPBP"]},"alphafold":{"accession":"Q7Z401","domains":[{"cath_id":"-","chopping":"2-40_204-359_674-711","consensus_level":"medium","plddt":83.453,"start":2,"end":711},{"cath_id":"2.100.10.50","chopping":"43-201","consensus_level":"medium","plddt":88.3033,"start":43,"end":201},{"cath_id":"-","chopping":"741-867","consensus_level":"medium","plddt":87.7996,"start":741,"end":867},{"cath_id":"-","chopping":"1441-1502_1628-1728","consensus_level":"medium","plddt":86.5239,"start":1441,"end":1728},{"cath_id":"-","chopping":"1732-1863","consensus_level":"medium","plddt":82.5422,"start":1732,"end":1863}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z401","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z401-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q7Z401-F1-predicted_aligned_error_v6.png","plddt_mean":64.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DENND4A","jax_strain_url":"https://www.jax.org/strain/search?query=DENND4A"},"sequence":{"accession":"Q7Z401","fasta_url":"https://rest.uniprot.org/uniprotkb/Q7Z401.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q7Z401/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q7Z401"}},"corpus_meta":[{"pmid":"30357366","id":"PMC_30357366","title":"TDP-43 enhances translation of specific mRNAs linked to neurodegenerative disease.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/30357366","citation_count":53,"is_preprint":false},{"pmid":"38200816","id":"PMC_38200816","title":"Genome-Wide Association Studies Reveal Candidate Genes Associated with Pigmentation Patterns of Single Feathers of Tianfu Nonghua Ducks.","date":"2023","source":"Animals : an open access journal from MDPI","url":"https://pubmed.ncbi.nlm.nih.gov/38200816","citation_count":8,"is_preprint":false},{"pmid":"32112984","id":"PMC_32112984","title":"High-throughput transcriptome analysis reveals potentially important relationships between lncRNAs and genes in broilers affected by Valgus-varus Deformity (Gallus gallus).","date":"2020","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/32112984","citation_count":7,"is_preprint":false},{"pmid":"8056341","id":"PMC_8056341","title":"Cloning of a cDNA encoding a human protein which binds a sequence in the c-myc gene similar to the interferon-stimulated response element.","date":"1994","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/8056341","citation_count":7,"is_preprint":false},{"pmid":"12906859","id":"PMC_12906859","title":"Molecular cloning, structural analysis, and expression of a human IRLB, MYC promoter-binding protein: new DENN domain-containing protein family emerges.","date":"2003","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/12906859","citation_count":5,"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":"40551051","id":"PMC_40551051","title":"Epigenetic Insights into Vascular Cognitive Impairment: DNA Methylation in the Human Brain Tissue.","date":"2025","source":"Molecular neurobiology","url":"https://pubmed.ncbi.nlm.nih.gov/40551051","citation_count":3,"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":5905,"output_tokens":1030,"usd":0.016583,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7538,"output_tokens":1844,"usd":0.041895,"stage2_stop_reason":"end_turn"},"total_usd":0.058478,"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\": 1994,\n      \"finding\": \"DENND4A (then called IRLB) was identified as a c-myc promoter-binding protein that recognizes the ISRE-like element in the P2 promoter region of human c-myc, demonstrated by DNase footprinting analysis and oligonucleotide-binding specificity assays using a fusion protein expressed in E. coli.\",\n      \"method\": \"DNase footprinting, oligonucleotide-binding specificity assay, lambda gt11 phage library screening\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct DNA-binding assays (footprinting + specificity assays) in a single study with partial protein only\",\n      \"pmids\": [\"8056341\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Full-length DENND4A (IRLB) was cloned and found to encode a 1865-aa protein containing a tripartite DENN domain, a nuclear localization signal, two PPRs, a calmodulin-binding domain, and the previously identified ISRE-binding domain, predicting interactions with Rab family GTPases.\",\n      \"method\": \"RT-PCR cloning, bioinformatics/structural domain analysis, genomic mapping\",\n      \"journal\": \"Genomics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — structural domain prediction and cloning without functional reconstitution of Rab-binding or enzymatic activity\",\n      \"pmids\": [\"12906859\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TDP-43 A315T patient mutant allele specifically enhances translation of Dennd4a mRNA via a specific 3'UTR region, as demonstrated by ribosome profiling and direct binding assays in motor neuron-like cells; this effect was specific to the mutant allele and not observed with wild-type TDP-43.\",\n      \"method\": \"Ribosome profiling, mRNA direct binding assay, 3'UTR reporter assay, overexpression in motor neuron-like cells\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ribosome profiling plus direct binding plus UTR reporter assay in a single lab, multiple orthogonal methods\",\n      \"pmids\": [\"30357366\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DENND4A directly associates with Retromer and is recruited by Retromer to the endosomal retrieval sub-domain to regulate RAB10 GTPase switching, as revealed by proximity proteomics, X-ray crystallography, in silico predictions, and biochemical/cellular analysis.\",\n      \"method\": \"Proximity proteomics (BioID), X-ray crystallography, in silico structural predictions, biochemical co-association assays, cellular imaging\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods including structural (X-ray crystallography), proximity proteomics, and biochemical/cellular validation in a single rigorous study; peer-reviewed publication\",\n      \"pmids\": [\"40738907\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DENND4A is a DENN-domain-containing protein that functions as a RAB10 guanine nucleotide exchange factor (GEF) regulator; it is directly recruited to the endosomal retrieval sub-domain by Retromer to regulate RAB10 GTPase switching as part of cargo recycling, and its Dennd4a mRNA translation is selectively enhanced by the TDP-43 A315T disease mutant via a 3'UTR-dependent mechanism; earlier work also identified it as a c-myc P2 promoter ISRE-like element binding protein.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DENND4A is a large DENN-domain-containing protein that functions in endosomal cargo recycling as a regulator of RAB10 GTPase switching [#3]. It directly associates with Retromer and is recruited by Retromer to the endosomal retrieval sub-domain, where it acts on RAB10 nucleotide cycling [#3]. The protein additionally carries domains predicted to support nucleic acid and Rab GTPase interactions, including a tripartite DENN domain [#1]. Beyond its endosomal role, DENND4A mRNA is a selective target of disease-associated translational dysregulation: the ALS-linked TDP-43 A315T mutant, but not wild-type TDP-43, enhances Dennd4a translation through a specific 3'UTR region [#2]. An earlier line of evidence identified DENND4A (then IRLB) as a sequence-specific DNA-binding protein recognizing the ISRE-like element of the human c-myc P2 promoter [#0], a nuclear activity whose relationship to its endosomal function has not been resolved in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 1994,\n      \"claim\": \"Before any functional annotation, the question was whether this protein had a defined molecular activity; it was first captured as a sequence-specific DNA-binding factor at the c-myc promoter.\",\n      \"evidence\": \"DNase footprinting and oligonucleotide-binding specificity assays with an E. coli-expressed fusion protein\",\n      \"pmids\": [\"8056341\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Used partial protein only, not full-length DENND4A\",\n        \"No demonstration that DNA binding occurs in cells or regulates c-myc transcription\",\n        \"Relationship to later-defined endosomal function unestablished\"\n      ]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Cloning the full-length transcript addressed what kind of protein this is, revealing a multidomain architecture including a tripartite DENN domain that predicted Rab GTPase involvement.\",\n      \"evidence\": \"RT-PCR cloning, domain/bioinformatic analysis, and genomic mapping\",\n      \"pmids\": [\"12906859\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Domain assignments are predictions without functional reconstitution\",\n        \"Rab binding and any enzymatic activity not demonstrated\",\n        \"NLS and calmodulin-binding domain functions untested\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"To connect DENND4A to disease, the question was whether its expression is altered by an ALS mutation; ribosome profiling showed mutant TDP-43 A315T selectively enhances Dennd4a translation via its 3'UTR.\",\n      \"evidence\": \"Ribosome profiling, direct mRNA-binding assay, and 3'UTR reporter assays with overexpression in motor neuron-like cells\",\n      \"pmids\": [\"30357366\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab finding in a motor neuron-like cell model\",\n        \"Downstream consequence of elevated DENND4A protein not defined\",\n        \"Mechanism of mutant-specific 3'UTR recognition not resolved\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The defining mechanistic question — what DENND4A does at the membrane — was answered by showing it directly associates with Retromer and is recruited to regulate RAB10 GTPase switching during endosomal cargo retrieval.\",\n      \"evidence\": \"Proximity proteomics (BioID), X-ray crystallography, in silico structural prediction, and biochemical/cellular validation\",\n      \"pmids\": [\"40738907\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct GEF catalytic activity of DENND4A on RAB10 not enzymatically quantified\",\n        \"Specific cargoes whose recycling depends on DENND4A not identified\",\n        \"Link to its DNA-binding and TDP-43-regulated translation roles unexplored\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how DENND4A's nuclear DNA-binding activity and its endosomal RAB10/Retromer function relate, and whether disease-driven translational upregulation alters its membrane-trafficking role.\",\n      \"evidence\": \"No integrating study in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No reconciliation of nuclear versus endosomal localization and function\",\n        \"No measurement of how TDP-43-driven DENND4A levels affect RAB10 cycling or cargo recycling\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RAB10\", \"VPS35\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":3,"faith_total":4,"faith_pct":75.0}}