{"gene":"RAB40C","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2004,"finding":"Rab40c was cloned from an oligodendrocyte cDNA library and found to bind GTPγS (Kd ~21 µM) with higher affinity for GTP than GDP, and is localized in the perinuclear recycling compartment, suggesting involvement in endocytic receptor recycling; the carboxyl-terminal extension contains motifs permitting isoprenylation and palmitoylation.","method":"GTP-binding assay (radiolabeled nucleotide binding), subcellular fractionation/immunolocalization, sequence/structural analysis of domain architecture","journal":"Journal of neuroscience research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct biochemical binding assay plus localization experiment in a single study; no functional mutagenesis or replication across labs","pmids":["15160388"],"is_preprint":false},{"year":2011,"finding":"RAB40C is a direct transcriptional target of the microRNA let-7a; let-7a binds the 3'-UTR of RAB40C mRNA to repress its expression post-transcriptionally, and RAB40C mediates the pro-proliferative effects of let-7a loss in gastric cancer cells.","method":"3'-UTR luciferase reporter assay, let-7a overexpression with RAB40C rescue, in vivo xenograft model","journal":"Carcinogenesis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase reporter directly confirms 3'-UTR binding; rescue experiment places RAB40C downstream of let-7a; single lab","pmids":["21349817"],"is_preprint":false},{"year":2013,"finding":"Rab40c localizes to lipid droplet surfaces (not Golgi or endosomal compartments) and to ERGIC-53-positive structures, is increasingly recruited during lipid droplet formation and maturation, and its knockdown reduces lipid droplet size. Overexpression causes lipid droplet clustering dependent on an intact SOCS box but independent of GTPase activity. Rab40c physically interacts with TIP47 and displays self-interaction; the SOCS box is required for clustering.","method":"GFP-fusion live imaging and co-localization with neutral lipid dyes (Oil Red O, Nile Red), sucrose-density-gradient fractionation, siRNA knockdown with morphometric analysis, Co-IP (Rab40c–TIP47), SOCS-box deletion mutants, GTPase-dead mutants","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (fractionation, imaging, Co-IP, KD phenotype, structure-function mutagenesis) in a single study establishing localization, interaction, and functional requirement","pmids":["23638186"],"is_preprint":false},{"year":2015,"finding":"Rab40C binds the ANKR2 domain of Varp via a direct protein–protein interaction and promotes proteasomal degradation of Varp in a SOCS-box-dependent manner; this reduces Tyrp1 trafficking in melanocytes. Conversely, Rab40C knockdown increases Varp levels and also reduces Tyrp1 signals.","method":"Co-IP (Rab40C–Varp ANKR2 domain), overexpression and knockdown in melanocytes, proteasome inhibitor rescue, immunofluorescence of Tyrp1 trafficking","journal":"Biology open","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal interaction mapping, SOCS-box mutagenesis, proteasome inhibitor rescue, and KD/OE with defined trafficking phenotype in a single focused study","pmids":["25661869"],"is_preprint":false},{"year":2015,"finding":"Methods for analyzing Rab40c association with lipid droplets were established, confirming localization via fluorescence confocal microscopy and sucrose-density centrifugation fractionation, and demonstrating that Rab40c protein level increases during adipocyte differentiation of 3T3-L1 cells.","method":"Fluorescence confocal microscopy (GFP-Rab40c + lipid-dye co-localization), sucrose-density centrifugation fractionation, immunoblot during adipocyte differentiation","journal":"Methods in molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — orthogonal localization methods confirm lipid droplet association; no new functional mechanistic finding beyond PMID:23638186","pmids":["25702114"],"is_preprint":false},{"year":2017,"finding":"DAB2IP, a RasGAP, binds RAB40C primarily through its GAP domain and acts as a GTPase-activating protein (GAP) for RAB40C. DAB2IP overexpression negatively regulates RAB40C's effect on lipid droplet homeostasis; a GAP-defective DAB2IP mutant and siRNA depletion of DAB2IP both confirm this regulatory relationship. RAB40C deletion by CRISPR-Cas9 causes over-accumulation of lipid droplets.","method":"Co-IP (RAB40C–DAB2IP), GAP-defective DAB2IP mutant overexpression, siRNA depletion of DAB2IP, CRISPR-Cas9 knockout of RAB40C with lipid droplet quantification","journal":"Oncotarget","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, gain/loss-of-function with mutants, CRISPR KO) in a single study defining DAB2IP as a GAP for RAB40C","pmids":["29156729"],"is_preprint":false},{"year":2018,"finding":"RAB40C functions as a ubiquitin E3 ligase (via its SOCS box recruiting a CRL complex) responsible for ubiquitination and proteasomal degradation of the scaffolding protein RACK1; RAB40C-mediated control of RACK1 levels affects cancer cell growth and T-cell migration.","method":"siRNA screen identifying RAB40C, ubiquitination assay, RACK1 stability assay following RAB40C knockdown, functional readouts (cell growth, T-cell migration)","journal":"Future science OA","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — ubiquitination assay and siRNA KD with functional readout, single lab, limited mechanistic detail in abstract","pmids":["30112187"],"is_preprint":false},{"year":2022,"finding":"Rab40c forms a Cullin5-based ubiquitin E3 ligase complex (Rab40c/CRL5), binds the PP6 phosphatase complex subunit ANKRD28, and promotes its ubiquitylation leading to lysosomal degradation. This reduces PP6 activity, increases phosphorylation of FAK and MOB1, and regulates focal adhesion number, size, and distribution in migrating MDA-MB-231 cells.","method":"Rab40c knockout cells (CRISPR), Co-IP (Rab40c–PP6 complex/ANKRD28), mass spectrometry identification of ubiquitylation, phosphoproteomics (FAK, MOB1 phosphorylation), immunofluorescence of focal adhesions","journal":"Life science alliance","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — CRISPR KO + Co-IP + MS-based ubiquitylation + phosphoproteomics, multiple orthogonal methods in a single study with defined substrate and downstream pathway","pmids":["35512830"],"is_preprint":false},{"year":2025,"finding":"RAB40C is a downstream transcriptional target of STAT3 and promotes K63-linked ubiquitination of EGFR at Lys713 by recruiting the E3 ligase TRIM21, thereby stabilizing EGFR protein and sustaining downstream EGFR signaling in hepatocellular carcinoma cells.","method":"Co-immunoprecipitation (RAB40C–TRIM21–EGFR), mass spectrometry identification of ubiquitination site (Lys713), ubiquitination assay (K63-linked), STAT3 ChIP/reporter linking STAT3 to RAB40C transcription, cell growth/migration and xenograft assays","journal":"Cell communication and signaling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, MS-identified ubiquitination site, and functional assays in a single study; single lab, no independent replication","pmids":["41350889"],"is_preprint":false},{"year":2026,"finding":"RAB40C interacts with SNX9 and promotes its degradation via the ubiquitin-proteasome pathway; silencing RAB40C increases SNX9 levels. This RAB40C–SNX9 axis influences Hippo signaling pathway target proteins and modulates proliferation, migration, and invasion of prostate adenocarcinoma cells.","method":"Co-IP (RAB40C–SNX9), siRNA knockdown of RAB40C with SNX9 immunoblot, proteasome inhibitor rescue, double-knockdown epistasis, Hippo pathway target immunoblot","journal":"Central-European journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP and KD with pathway readout in a single lab; limited methodological detail in abstract","pmids":["42245125"],"is_preprint":false}],"current_model":"RAB40C is an atypical small GTPase that uses its SOCS box to recruit Cullin5, forming a CRL5 ubiquitin E3 ligase complex that ubiquitylates and targets multiple substrates (Varp, RACK1, ANKRD28, SNX9, EGFR via TRIM21) for proteasomal or lysosomal degradation, thereby regulating lipid droplet biogenesis (modulated by the GAP activity of DAB2IP), focal adhesion dynamics (via PP6/FAK/Hippo signaling), melanogenic enzyme trafficking, cancer cell growth and migration, and it is itself transcriptionally regulated by STAT3 and post-transcriptionally repressed by the microRNA let-7a."},"narrative":{"mechanistic_narrative":"RAB40C is an atypical small GTPase that couples Rab-family membrane-targeting features to a SOCS box, allowing it to nucleate a Cullin5-based CRL ubiquitin E3 ligase that selects substrates for degradation and thereby controls lipid storage, cell adhesion, and cancer cell behavior [PMID:35512830, PMID:23638186]. The protein binds GTP preferentially over GDP and carries a C-terminal extension permitting isoprenylation and palmitoylation, consistent with its membrane localization to the perinuclear recycling compartment and, prominently, to the surface of lipid droplets where recruitment increases during droplet formation and adipocyte differentiation [PMID:15160388, PMID:23638186, PMID:25702114]. At lipid droplets, RAB40C drives clustering in a manner dependent on an intact SOCS box but independent of GTPase activity, and its loss causes over-accumulation of lipid droplets; DAB2IP acts as a GTPase-activating protein for RAB40C and negatively regulates this lipid droplet homeostasis function [PMID:23638186, PMID:29156729]. As the substrate-recognition module of a CRL5 complex, RAB40C ubiquitylates and degrades multiple targets: it binds the ANKR2 domain of Varp to promote its proteasomal degradation and limit Tyrp1 trafficking in melanocytes [PMID:25661869], targets the PP6 subunit ANKRD28 for lysosomal degradation to derepress FAK and MOB1 phosphorylation and remodel focal adhesions in migrating cells [PMID:35512830], and controls levels of the scaffold RACK1 [PMID:30112187] and of SNX9, the latter linking RAB40C to Hippo pathway output [PMID:42245125]. RAB40C expression is repressed post-transcriptionally by the microRNA let-7a and activated transcriptionally by STAT3, and in this STAT3-driven context it recruits the E3 ligase TRIM21 to promote K63-linked ubiquitination of EGFR at Lys713, stabilizing EGFR and sustaining its signaling [PMID:21349817, PMID:41350889]. Through these activities RAB40C modulates cancer cell proliferation, migration, and invasion across gastric, breast, prostate, and hepatocellular models [PMID:21349817, PMID:35512830, PMID:42245125, PMID:41350889].","teleology":[{"year":2004,"claim":"Establishing RAB40C as a bona fide GTP-binding protein with membrane-targeting motifs answered whether this atypical Rab is a functional small GTPase and where it acts.","evidence":"GTP-binding assay, subcellular fractionation/immunolocalization, and domain architecture analysis after cloning from oligodendrocyte cDNA","pmids":["15160388"],"confidence":"Medium","gaps":["No functional mutagenesis to test nucleotide-state-dependent activity","Role of the SOCS box not yet appreciated","Perinuclear recycling localization not linked to a specific pathway"]},{"year":2011,"claim":"Identifying RAB40C as a direct let-7a target placed it in a defined regulatory circuit and connected its expression to tumor cell proliferation.","evidence":"3'-UTR luciferase reporter, let-7a overexpression with RAB40C rescue, and xenograft assay in gastric cancer cells","pmids":["21349817"],"confidence":"Medium","gaps":["Molecular effector mechanism by which RAB40C drives proliferation not defined here","Single cancer context","No link yet to its later-defined E3 ligase activity"]},{"year":2013,"claim":"Defining RAB40C as a lipid droplet-associated protein whose clustering requires the SOCS box but not GTPase activity reframed it from a conventional Rab to a SOCS-box-dependent scaffold at lipid droplets.","evidence":"GFP live imaging with lipid dyes, sucrose-density fractionation, siRNA knockdown morphometrics, Co-IP with TIP47, and SOCS-box/GTPase-dead mutants","pmids":["23638186"],"confidence":"High","gaps":["Identity of the SOCS-box-recruited ligase machinery not yet established","Functional consequence of the TIP47 interaction unresolved","Mechanism linking clustering to droplet biology unclear"]},{"year":2015,"claim":"Demonstrating SOCS-box-dependent proteasomal degradation of Varp and downstream Tyrp1 trafficking gave RAB40C its first defined substrate and tied its SOCS box to ubiquitin-mediated degradation.","evidence":"Co-IP mapping to the Varp ANKR2 domain, SOCS-box mutagenesis, proteasome inhibitor rescue, and Tyrp1 immunofluorescence in melanocytes","pmids":["25661869"],"confidence":"High","gaps":["Identity of the full E3 ligase complex (Cullin partner) not yet shown","Generality beyond melanocyte trafficking unknown"]},{"year":2017,"claim":"Identifying DAB2IP as a GAP for RAB40C and showing CRISPR knockout causes lipid droplet over-accumulation established upstream regulation and a clear loss-of-function phenotype.","evidence":"Co-IP, GAP-defective DAB2IP mutant, siRNA depletion, and CRISPR knockout with lipid droplet quantification","pmids":["29156729"],"confidence":"High","gaps":["How GTPase state intersects with SOCS-box-dependent function not reconciled","Substrate degraded to control droplets not identified here"]},{"year":2018,"claim":"Showing RAB40C ubiquitylates and degrades RACK1 generalized its E3 ligase role beyond Varp and connected it to cancer growth and immune cell migration.","evidence":"siRNA screen, ubiquitination and RACK1 stability assays, and functional readouts of cell growth and T-cell migration","pmids":["30112187"],"confidence":"Medium","gaps":["Limited mechanistic detail on the ligase complex composition","Ubiquitin linkage type and degradation route not detailed","Single lab"]},{"year":2022,"claim":"Defining the Rab40c/CRL5 complex that degrades ANKRD28 to suppress PP6 and elevate FAK/MOB1 phosphorylation provided the first complete enzyme-substrate-pathway axis for RAB40C in focal adhesion and migration control.","evidence":"CRISPR knockout, Co-IP with the PP6 complex/ANKRD28, MS-identified ubiquitylation, phosphoproteomics, and focal adhesion imaging in MDA-MB-231 cells","pmids":["35512830"],"confidence":"High","gaps":["Whether the same CRL5 assembly handles all RAB40C substrates not established","Spatial coordination with lipid droplet pool unresolved"]},{"year":2025,"claim":"Placing RAB40C downstream of STAT3 and showing it recruits TRIM21 to K63-ubiquitylate and stabilize EGFR revealed a non-degradative, signal-sustaining mode distinct from its degradative substrates.","evidence":"Co-IP, MS-identified Lys713 ubiquitination site, K63-linkage ubiquitination assay, STAT3 ChIP/reporter, and growth/xenograft assays in hepatocellular carcinoma","pmids":["41350889"],"confidence":"Medium","gaps":["How RAB40C reconciles substrate-degrading and substrate-stabilizing activities mechanistically unclear","Whether CRL5 is involved in EGFR stabilization not addressed","Single lab"]},{"year":2026,"claim":"Identifying SNX9 as a RAB40C degradation substrate linked to Hippo signaling extended the substrate repertoire and connected RAB40C to another oncogenic pathway in prostate cancer.","evidence":"Co-IP, siRNA knockdown with SNX9 immunoblot, proteasome inhibitor rescue, double-knockdown epistasis, and Hippo target immunoblot","pmids":["42245125"],"confidence":"Medium","gaps":["Direct ubiquitination of SNX9 by RAB40C not demonstrated biochemically","Mechanistic link to Hippo effectors indirect","Limited methodological detail"]},{"year":null,"claim":"How RAB40C selects among its diverse substrates, and whether its membrane targeting (lipid droplet vs recycling compartment) spatially partitions degradative versus stabilizing E3 ligase activities, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the RAB40C CRL5 complex with substrates","Determinants of K48- vs K63-linkage and proteasomal vs lysosomal routing unknown","Physiological (non-cancer) roles largely uncharacterized in the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[0,5]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[3,6,7]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[6,7,8]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[7,8]}],"localization":[{"term_id":"GO:0005811","term_label":"lipid droplet","supporting_discovery_ids":[2,4]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[3,6,7]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[1,8,9]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[7,8,9]}],"complexes":["CRL5 (Cullin5 ubiquitin E3 ligase)"],"partners":["CUL5","VPS9D1/VARP","ANKRD28","RACK1","SNX9","DAB2IP","TRIM21","TIP47"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96S21","full_name":"Ras-related protein Rab-40C","aliases":["Rar-like protein","Ras-like protein family member 8C","SOCS box-containing protein RAR3"],"length_aa":281,"mass_kda":31.3,"function":"RAB40C small GTPase acts as substrate-recognition component of the ECS(RAB40C) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins (PubMed:15601820, PubMed:35512830). The Rab40 subfamily belongs to the Rab family that are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (PubMed:29156729). As part of the ECS(RAB40C) complex, mediates ANKRD28 ubiquitination and degradation, thereby inhibiting protein phosphatase 6 (PP6) complex activity and focal adhesion assembly during cell migration (PubMed:35512830). Also negatively regulate lipid droplets accumulation in a GTP-dependent manner (PubMed:29156729)","subcellular_location":"Cell membrane; Cytoplasm, cytosol; Golgi apparatus membrane","url":"https://www.uniprot.org/uniprotkb/Q96S21/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RAB40C","classification":"Not Classified","n_dependent_lines":10,"n_total_lines":1208,"dependency_fraction":0.008278145695364239},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RAB40C","total_profiled":1310},"omim":[{"mim_id":"619551","title":"RAB40C, MEMBER RAS ONCOGENE FAMILY; RAB40C","url":"https://www.omim.org/entry/619551"},{"mim_id":"619550","title":"RAB40B, MEMBER RAS ONCOGENE FAMILY; RAB40B","url":"https://www.omim.org/entry/619550"},{"mim_id":"301065","title":"RAB40A, MEMBER RAS ONCOGENE FAMILY; RAB40A","url":"https://www.omim.org/entry/301065"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Vesicles","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RAB40C"},"hgnc":{"alias_symbol":["RARL"],"prev_symbol":["RASL8C"]},"alphafold":{"accession":"Q96S21","domains":[{"cath_id":"3.40.50.300","chopping":"12-182","consensus_level":"high","plddt":85.0799,"start":12,"end":182},{"cath_id":"1.10.10","chopping":"191-235","consensus_level":"high","plddt":75.6229,"start":191,"end":235}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96S21","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96S21-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96S21-F1-predicted_aligned_error_v6.png","plddt_mean":74.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RAB40C","jax_strain_url":"https://www.jax.org/strain/search?query=RAB40C"},"sequence":{"accession":"Q96S21","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96S21.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96S21/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96S21"}},"corpus_meta":[{"pmid":"21349817","id":"PMC_21349817","title":"Low-level expression of let-7a in gastric cancer and its involvement in tumorigenesis by targeting RAB40C.","date":"2011","source":"Carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/21349817","citation_count":90,"is_preprint":false},{"pmid":"23638186","id":"PMC_23638186","title":"Small GTPase Rab40c associates with lipid droplets and modulates the biogenesis of lipid droplets.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23638186","citation_count":35,"is_preprint":false},{"pmid":"15160388","id":"PMC_15160388","title":"Vesicle transport in oligodendrocytes: probable role of Rab40c protein.","date":"2004","source":"Journal of neuroscience research","url":"https://pubmed.ncbi.nlm.nih.gov/15160388","citation_count":33,"is_preprint":false},{"pmid":"25661869","id":"PMC_25661869","title":"Rab40C is a novel Varp-binding protein that promotes proteasomal degradation of Varp in melanocytes.","date":"2015","source":"Biology open","url":"https://pubmed.ncbi.nlm.nih.gov/25661869","citation_count":24,"is_preprint":false},{"pmid":"30112187","id":"PMC_30112187","title":"RAB40C regulates RACK1 stability via the ubiquitin-proteasome system.","date":"2018","source":"Future science OA","url":"https://pubmed.ncbi.nlm.nih.gov/30112187","citation_count":17,"is_preprint":false},{"pmid":"35512830","id":"PMC_35512830","title":"Rab40c regulates focal adhesions and PP6 activity by controlling ANKRD28 ubiquitylation.","date":"2022","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/35512830","citation_count":13,"is_preprint":false},{"pmid":"35349758","id":"PMC_35349758","title":"Small GTPase Rab40C is upregulated by 20-hydroxyecdysone and insulin pathways to regulate ovarian development and fecundity.","date":"2022","source":"Insect science","url":"https://pubmed.ncbi.nlm.nih.gov/35349758","citation_count":11,"is_preprint":false},{"pmid":"29156729","id":"PMC_29156729","title":"A RasGAP, DAB2IP, regulates lipid droplet homeostasis by serving as GAP toward RAB40C.","date":"2017","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/29156729","citation_count":11,"is_preprint":false},{"pmid":"34305407","id":"PMC_34305407","title":"RAB40C Gene Polymorphisms Were Associated with Alcohol-Induced Osteonecrosis of the Femoral Head.","date":"2021","source":"International journal of general medicine","url":"https://pubmed.ncbi.nlm.nih.gov/34305407","citation_count":5,"is_preprint":false},{"pmid":"25702114","id":"PMC_25702114","title":"Analysis of biogenesis of lipid droplets by examining Rab40c associating with lipid droplets.","date":"2015","source":"Methods in molecular biology (Clifton, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/25702114","citation_count":5,"is_preprint":false},{"pmid":"32656896","id":"PMC_32656896","title":"RAB40C gene polymorphisms rs62030917 and rs2269556 are associated with an increased risk of lumbar disc herniation development in the Chinese Han population.","date":"2021","source":"The journal of gene medicine","url":"https://pubmed.ncbi.nlm.nih.gov/32656896","citation_count":4,"is_preprint":false},{"pmid":"41350889","id":"PMC_41350889","title":"RAB40C recruiting TRIM21 facilitates the progression of hepatocellular carcinoma by stabilizing EGFR.","date":"2025","source":"Cell communication and signaling : CCS","url":"https://pubmed.ncbi.nlm.nih.gov/41350889","citation_count":0,"is_preprint":false},{"pmid":"42245125","id":"PMC_42245125","title":"RAB40C regulates SNX9 stability via the ubiquitin-proteasome system and modulates the Hippo signaling pathway of prostate adenocarcinoma.","date":"2026","source":"Central-European journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/42245125","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8191,"output_tokens":2870,"usd":0.033812,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10184,"output_tokens":3796,"usd":0.07291,"stage2_stop_reason":"end_turn"},"total_usd":0.106722,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2004,\n      \"finding\": \"Rab40c was cloned from an oligodendrocyte cDNA library and found to bind GTPγS (Kd ~21 µM) with higher affinity for GTP than GDP, and is localized in the perinuclear recycling compartment, suggesting involvement in endocytic receptor recycling; the carboxyl-terminal extension contains motifs permitting isoprenylation and palmitoylation.\",\n      \"method\": \"GTP-binding assay (radiolabeled nucleotide binding), subcellular fractionation/immunolocalization, sequence/structural analysis of domain architecture\",\n      \"journal\": \"Journal of neuroscience research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct biochemical binding assay plus localization experiment in a single study; no functional mutagenesis or replication across labs\",\n      \"pmids\": [\"15160388\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"RAB40C is a direct transcriptional target of the microRNA let-7a; let-7a binds the 3'-UTR of RAB40C mRNA to repress its expression post-transcriptionally, and RAB40C mediates the pro-proliferative effects of let-7a loss in gastric cancer cells.\",\n      \"method\": \"3'-UTR luciferase reporter assay, let-7a overexpression with RAB40C rescue, in vivo xenograft model\",\n      \"journal\": \"Carcinogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase reporter directly confirms 3'-UTR binding; rescue experiment places RAB40C downstream of let-7a; single lab\",\n      \"pmids\": [\"21349817\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Rab40c localizes to lipid droplet surfaces (not Golgi or endosomal compartments) and to ERGIC-53-positive structures, is increasingly recruited during lipid droplet formation and maturation, and its knockdown reduces lipid droplet size. Overexpression causes lipid droplet clustering dependent on an intact SOCS box but independent of GTPase activity. Rab40c physically interacts with TIP47 and displays self-interaction; the SOCS box is required for clustering.\",\n      \"method\": \"GFP-fusion live imaging and co-localization with neutral lipid dyes (Oil Red O, Nile Red), sucrose-density-gradient fractionation, siRNA knockdown with morphometric analysis, Co-IP (Rab40c–TIP47), SOCS-box deletion mutants, GTPase-dead mutants\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (fractionation, imaging, Co-IP, KD phenotype, structure-function mutagenesis) in a single study establishing localization, interaction, and functional requirement\",\n      \"pmids\": [\"23638186\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Rab40C binds the ANKR2 domain of Varp via a direct protein–protein interaction and promotes proteasomal degradation of Varp in a SOCS-box-dependent manner; this reduces Tyrp1 trafficking in melanocytes. Conversely, Rab40C knockdown increases Varp levels and also reduces Tyrp1 signals.\",\n      \"method\": \"Co-IP (Rab40C–Varp ANKR2 domain), overexpression and knockdown in melanocytes, proteasome inhibitor rescue, immunofluorescence of Tyrp1 trafficking\",\n      \"journal\": \"Biology open\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal interaction mapping, SOCS-box mutagenesis, proteasome inhibitor rescue, and KD/OE with defined trafficking phenotype in a single focused study\",\n      \"pmids\": [\"25661869\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Methods for analyzing Rab40c association with lipid droplets were established, confirming localization via fluorescence confocal microscopy and sucrose-density centrifugation fractionation, and demonstrating that Rab40c protein level increases during adipocyte differentiation of 3T3-L1 cells.\",\n      \"method\": \"Fluorescence confocal microscopy (GFP-Rab40c + lipid-dye co-localization), sucrose-density centrifugation fractionation, immunoblot during adipocyte differentiation\",\n      \"journal\": \"Methods in molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — orthogonal localization methods confirm lipid droplet association; no new functional mechanistic finding beyond PMID:23638186\",\n      \"pmids\": [\"25702114\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"DAB2IP, a RasGAP, binds RAB40C primarily through its GAP domain and acts as a GTPase-activating protein (GAP) for RAB40C. DAB2IP overexpression negatively regulates RAB40C's effect on lipid droplet homeostasis; a GAP-defective DAB2IP mutant and siRNA depletion of DAB2IP both confirm this regulatory relationship. RAB40C deletion by CRISPR-Cas9 causes over-accumulation of lipid droplets.\",\n      \"method\": \"Co-IP (RAB40C–DAB2IP), GAP-defective DAB2IP mutant overexpression, siRNA depletion of DAB2IP, CRISPR-Cas9 knockout of RAB40C with lipid droplet quantification\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (Co-IP, gain/loss-of-function with mutants, CRISPR KO) in a single study defining DAB2IP as a GAP for RAB40C\",\n      \"pmids\": [\"29156729\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RAB40C functions as a ubiquitin E3 ligase (via its SOCS box recruiting a CRL complex) responsible for ubiquitination and proteasomal degradation of the scaffolding protein RACK1; RAB40C-mediated control of RACK1 levels affects cancer cell growth and T-cell migration.\",\n      \"method\": \"siRNA screen identifying RAB40C, ubiquitination assay, RACK1 stability assay following RAB40C knockdown, functional readouts (cell growth, T-cell migration)\",\n      \"journal\": \"Future science OA\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — ubiquitination assay and siRNA KD with functional readout, single lab, limited mechanistic detail in abstract\",\n      \"pmids\": [\"30112187\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Rab40c forms a Cullin5-based ubiquitin E3 ligase complex (Rab40c/CRL5), binds the PP6 phosphatase complex subunit ANKRD28, and promotes its ubiquitylation leading to lysosomal degradation. This reduces PP6 activity, increases phosphorylation of FAK and MOB1, and regulates focal adhesion number, size, and distribution in migrating MDA-MB-231 cells.\",\n      \"method\": \"Rab40c knockout cells (CRISPR), Co-IP (Rab40c–PP6 complex/ANKRD28), mass spectrometry identification of ubiquitylation, phosphoproteomics (FAK, MOB1 phosphorylation), immunofluorescence of focal adhesions\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — CRISPR KO + Co-IP + MS-based ubiquitylation + phosphoproteomics, multiple orthogonal methods in a single study with defined substrate and downstream pathway\",\n      \"pmids\": [\"35512830\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RAB40C is a downstream transcriptional target of STAT3 and promotes K63-linked ubiquitination of EGFR at Lys713 by recruiting the E3 ligase TRIM21, thereby stabilizing EGFR protein and sustaining downstream EGFR signaling in hepatocellular carcinoma cells.\",\n      \"method\": \"Co-immunoprecipitation (RAB40C–TRIM21–EGFR), mass spectrometry identification of ubiquitination site (Lys713), ubiquitination assay (K63-linked), STAT3 ChIP/reporter linking STAT3 to RAB40C transcription, cell growth/migration and xenograft assays\",\n      \"journal\": \"Cell communication and signaling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, MS-identified ubiquitination site, and functional assays in a single study; single lab, no independent replication\",\n      \"pmids\": [\"41350889\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"RAB40C interacts with SNX9 and promotes its degradation via the ubiquitin-proteasome pathway; silencing RAB40C increases SNX9 levels. This RAB40C–SNX9 axis influences Hippo signaling pathway target proteins and modulates proliferation, migration, and invasion of prostate adenocarcinoma cells.\",\n      \"method\": \"Co-IP (RAB40C–SNX9), siRNA knockdown of RAB40C with SNX9 immunoblot, proteasome inhibitor rescue, double-knockdown epistasis, Hippo pathway target immunoblot\",\n      \"journal\": \"Central-European journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP and KD with pathway readout in a single lab; limited methodological detail in abstract\",\n      \"pmids\": [\"42245125\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RAB40C is an atypical small GTPase that uses its SOCS box to recruit Cullin5, forming a CRL5 ubiquitin E3 ligase complex that ubiquitylates and targets multiple substrates (Varp, RACK1, ANKRD28, SNX9, EGFR via TRIM21) for proteasomal or lysosomal degradation, thereby regulating lipid droplet biogenesis (modulated by the GAP activity of DAB2IP), focal adhesion dynamics (via PP6/FAK/Hippo signaling), melanogenic enzyme trafficking, cancer cell growth and migration, and it is itself transcriptionally regulated by STAT3 and post-transcriptionally repressed by the microRNA let-7a.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RAB40C is an atypical small GTPase that couples Rab-family membrane-targeting features to a SOCS box, allowing it to nucleate a Cullin5-based CRL ubiquitin E3 ligase that selects substrates for degradation and thereby controls lipid storage, cell adhesion, and cancer cell behavior [#7, #2]. The protein binds GTP preferentially over GDP and carries a C-terminal extension permitting isoprenylation and palmitoylation, consistent with its membrane localization to the perinuclear recycling compartment and, prominently, to the surface of lipid droplets where recruitment increases during droplet formation and adipocyte differentiation [#0, #2, #4]. At lipid droplets, RAB40C drives clustering in a manner dependent on an intact SOCS box but independent of GTPase activity, and its loss causes over-accumulation of lipid droplets; DAB2IP acts as a GTPase-activating protein for RAB40C and negatively regulates this lipid droplet homeostasis function [#2, #5]. As the substrate-recognition module of a CRL5 complex, RAB40C ubiquitylates and degrades multiple targets: it binds the ANKR2 domain of Varp to promote its proteasomal degradation and limit Tyrp1 trafficking in melanocytes [#3], targets the PP6 subunit ANKRD28 for lysosomal degradation to derepress FAK and MOB1 phosphorylation and remodel focal adhesions in migrating cells [#7], and controls levels of the scaffold RACK1 [#6] and of SNX9, the latter linking RAB40C to Hippo pathway output [#9]. RAB40C expression is repressed post-transcriptionally by the microRNA let-7a and activated transcriptionally by STAT3, and in this STAT3-driven context it recruits the E3 ligase TRIM21 to promote K63-linked ubiquitination of EGFR at Lys713, stabilizing EGFR and sustaining its signaling [#1, #8]. Through these activities RAB40C modulates cancer cell proliferation, migration, and invasion across gastric, breast, prostate, and hepatocellular models [#1, #7, #9, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Establishing RAB40C as a bona fide GTP-binding protein with membrane-targeting motifs answered whether this atypical Rab is a functional small GTPase and where it acts.\",\n      \"evidence\": \"GTP-binding assay, subcellular fractionation/immunolocalization, and domain architecture analysis after cloning from oligodendrocyte cDNA\",\n      \"pmids\": [\"15160388\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional mutagenesis to test nucleotide-state-dependent activity\", \"Role of the SOCS box not yet appreciated\", \"Perinuclear recycling localization not linked to a specific pathway\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identifying RAB40C as a direct let-7a target placed it in a defined regulatory circuit and connected its expression to tumor cell proliferation.\",\n      \"evidence\": \"3'-UTR luciferase reporter, let-7a overexpression with RAB40C rescue, and xenograft assay in gastric cancer cells\",\n      \"pmids\": [\"21349817\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular effector mechanism by which RAB40C drives proliferation not defined here\", \"Single cancer context\", \"No link yet to its later-defined E3 ligase activity\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Defining RAB40C as a lipid droplet-associated protein whose clustering requires the SOCS box but not GTPase activity reframed it from a conventional Rab to a SOCS-box-dependent scaffold at lipid droplets.\",\n      \"evidence\": \"GFP live imaging with lipid dyes, sucrose-density fractionation, siRNA knockdown morphometrics, Co-IP with TIP47, and SOCS-box/GTPase-dead mutants\",\n      \"pmids\": [\"23638186\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the SOCS-box-recruited ligase machinery not yet established\", \"Functional consequence of the TIP47 interaction unresolved\", \"Mechanism linking clustering to droplet biology unclear\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrating SOCS-box-dependent proteasomal degradation of Varp and downstream Tyrp1 trafficking gave RAB40C its first defined substrate and tied its SOCS box to ubiquitin-mediated degradation.\",\n      \"evidence\": \"Co-IP mapping to the Varp ANKR2 domain, SOCS-box mutagenesis, proteasome inhibitor rescue, and Tyrp1 immunofluorescence in melanocytes\",\n      \"pmids\": [\"25661869\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the full E3 ligase complex (Cullin partner) not yet shown\", \"Generality beyond melanocyte trafficking unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identifying DAB2IP as a GAP for RAB40C and showing CRISPR knockout causes lipid droplet over-accumulation established upstream regulation and a clear loss-of-function phenotype.\",\n      \"evidence\": \"Co-IP, GAP-defective DAB2IP mutant, siRNA depletion, and CRISPR knockout with lipid droplet quantification\",\n      \"pmids\": [\"29156729\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How GTPase state intersects with SOCS-box-dependent function not reconciled\", \"Substrate degraded to control droplets not identified here\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Showing RAB40C ubiquitylates and degrades RACK1 generalized its E3 ligase role beyond Varp and connected it to cancer growth and immune cell migration.\",\n      \"evidence\": \"siRNA screen, ubiquitination and RACK1 stability assays, and functional readouts of cell growth and T-cell migration\",\n      \"pmids\": [\"30112187\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Limited mechanistic detail on the ligase complex composition\", \"Ubiquitin linkage type and degradation route not detailed\", \"Single lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defining the Rab40c/CRL5 complex that degrades ANKRD28 to suppress PP6 and elevate FAK/MOB1 phosphorylation provided the first complete enzyme-substrate-pathway axis for RAB40C in focal adhesion and migration control.\",\n      \"evidence\": \"CRISPR knockout, Co-IP with the PP6 complex/ANKRD28, MS-identified ubiquitylation, phosphoproteomics, and focal adhesion imaging in MDA-MB-231 cells\",\n      \"pmids\": [\"35512830\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the same CRL5 assembly handles all RAB40C substrates not established\", \"Spatial coordination with lipid droplet pool unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placing RAB40C downstream of STAT3 and showing it recruits TRIM21 to K63-ubiquitylate and stabilize EGFR revealed a non-degradative, signal-sustaining mode distinct from its degradative substrates.\",\n      \"evidence\": \"Co-IP, MS-identified Lys713 ubiquitination site, K63-linkage ubiquitination assay, STAT3 ChIP/reporter, and growth/xenograft assays in hepatocellular carcinoma\",\n      \"pmids\": [\"41350889\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How RAB40C reconciles substrate-degrading and substrate-stabilizing activities mechanistically unclear\", \"Whether CRL5 is involved in EGFR stabilization not addressed\", \"Single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identifying SNX9 as a RAB40C degradation substrate linked to Hippo signaling extended the substrate repertoire and connected RAB40C to another oncogenic pathway in prostate cancer.\",\n      \"evidence\": \"Co-IP, siRNA knockdown with SNX9 immunoblot, proteasome inhibitor rescue, double-knockdown epistasis, and Hippo target immunoblot\",\n      \"pmids\": [\"42245125\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct ubiquitination of SNX9 by RAB40C not demonstrated biochemically\", \"Mechanistic link to Hippo effectors indirect\", \"Limited methodological detail\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RAB40C selects among its diverse substrates, and whether its membrane targeting (lipid droplet vs recycling compartment) spatially partitions degradative versus stabilizing E3 ligase activities, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of the RAB40C CRL5 complex with substrates\", \"Determinants of K48- vs K63-linkage and proteasomal vs lysosomal routing unknown\", \"Physiological (non-cancer) roles largely uncharacterized in the corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [3, 6, 7]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [6, 7, 8]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [7, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005811\", \"supporting_discovery_ids\": [2, 4]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [3, 6, 7]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [1, 8, 9]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [7, 8, 9]}\n    ],\n    \"complexes\": [\"CRL5 (Cullin5 ubiquitin E3 ligase)\"],\n    \"partners\": [\"CUL5\", \"VPS9D1/Varp\", \"ANKRD28\", \"RACK1\", \"SNX9\", \"DAB2IP\", \"TRIM21\", \"TIP47\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}