{"gene":"RRAGD","run_date":"2026-06-10T07:46:28","timeline":{"discoveries":[{"year":2021,"finding":"Heterozygous missense variants in RRAGD (encoding RagD GTPase) cause constitutive activation of mTOR signaling in vitro, leading to an autosomal dominant condition (ADKH-RRAGD) characterized by kidney tubulopathy, hypomagnesemia, hypokalemia, salt wasting, nephrocalcinosis, and dilated cardiomyopathy. RagD expression was detected along the mammalian nephron including the thick ascending limb and distal convoluted tubule.","method":"Whole-exome/genome sequencing of patient cohort; in vitro functional analyses of RRAGD variants (mTOR signaling assays); immunolocalization along the nephron","journal":"Journal of the American Society of Nephrology : JASN","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple independent patient families, in vitro functional validation of variants, replicated across multiple labs in subsequent studies","pmids":["34607910"],"is_preprint":false},{"year":2023,"finding":"RRAGD auto-activating disease mutations cause constitutive phosphorylation of TFEB and TFE3 by mTORC1 (non-canonical pathway) without affecting canonical mTORC1 substrates such as S6K, even in the absence of Folliculin (the GAP responsible for RagC/D activation). This leads to inhibition of TFEB and TFE3 nuclear translocation and transcriptional activity, impairing the response to lysosomal and mitochondrial injury.","method":"HeLa and HK-2 cell lines, human iPSC-derived cardiomyocytes, and patient-derived primary fibroblasts; phosphorylation assays; nuclear translocation assays; FOLLICULIN-knockout contexts","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal cell models including patient-derived cells, mutagenesis in disease-relevant context, mechanistic dissection of canonical vs. non-canonical mTORC1 signaling","pmids":["37188688"],"is_preprint":false},{"year":2018,"finding":"TFEB promotes endocytic assembly of an mTORC1-containing nutrient-sensing complex through formation of endosomes carrying RRAGD, the amino acid transporter SLC38A9, and activated AKT. These TFEB-induced signaling endosomes en route to lysosomes dissociate TSC2 and re-tether/activate mTORC1 on endolysosomal membranes.","method":"Live-cell imaging, co-immunoprecipitation, overexpression/knockdown experiments in HEK293T and CAD cells, endocytosis rate measurements","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (imaging, Co-IP, functional assays) in single lab","pmids":["30145926"],"is_preprint":false},{"year":2021,"finding":"Loss of FLCN in human renal tubular epithelial cells activates TFE3 and upregulates RRAGD expression (as an E-box target of TFE3) without modifying mTORC1 activity, identifying RRAGD as a transcriptional target of TFE3 in renal cells.","method":"FLCN knockout in RPTEC/TERT1 cells; transcriptomic analysis; integrated proteomics; functional validation","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined molecular readout, integrated omics + functional follow-up, single lab","pmids":["33459596"],"is_preprint":false},{"year":2023,"finding":"RRAGD expression is induced by IL-4 signaling through STAT6 in follicular lymphoma cells; RRAGD is required for mTOR activation in lymphoma cells, and IL4-enhanced BCR signaling-induced mTOR activation depends on this axis. CREBBP mutations attenuate IL4-induced RRAGD expression, while activating STAT6 mutations augment it.","method":"RNA-seq on primary human FL samples; ex vivo IL4 stimulation; RRAGD knockdown with mTOR activity readout; CREBBP and STAT6 mutant functional analysis","journal":"Leukemia","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — primary human samples plus functional knockdown experiments, multiple orthogonal methods, single lab","pmids":["39910284"],"is_preprint":false},{"year":2024,"finding":"Overexpression of disease-associated RRAGD mutants (p.S76L and p.P119R) in zebrafish embryos caused decreased ventricular fractional shortening, ejection fraction, and pericardial swelling, recapitulating cardiomyopathy. These phenotypes were reversible by treatment with rapamycin (mTOR inhibitor), establishing that RRAGD-variant-induced cardiac dysfunction is mTOR-dependent.","method":"Zebrafish embryo cRNA injection model; cardiac functional measurements (fractional shortening, ejection fraction); rapamycin rescue experiment","journal":"American journal of physiology. Heart and circulatory physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo vertebrate model with pharmacological rescue, multiple cardiac functional readouts, single lab","pmids":["39331021"],"is_preprint":false},{"year":2025,"finding":"Novel RRAGD variants p.(Ser77Phe) and p.(Ile100Arg) cause constitutive activation of non-canonical mTORC1 signaling as shown by in vitro assays, further expanding the spectrum of gain-of-function RRAGD mutations causing ADKH. SGLT2 inhibitor dapagliflozin modestly increased serum Mg2+ in patients with p.(Thr97Pro) variant.","method":"In vitro mTORC1 activity assays for novel variants; clinical assessment of therapeutic responses in patients","journal":"Kidney international reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro functional validation of novel variants with defined molecular readout, multi-center case series","pmids":["41141537"],"is_preprint":false},{"year":2025,"finding":"The m6A writer METTL3 recruits the APA factor NUDT21 to the proximal poly(A) site of Rragd mRNA, generating a long 3'UTR isoform with m6A modifications. Nudt21 deficiency causes Rragd 3'UTR shortening, increases Rragd expression, and leads to overactivation of mTOR signaling and T cell hyperactivation.","method":"NUDT21 deletion in T cells; RNA-seq/poly(A) site profiling; METTL3-NUDT21 co-immunoprecipitation; m6A mapping; functional T cell assays","journal":"Science advances","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO with defined molecular mechanism, Co-IP, multiple orthogonal methods, single lab","pmids":["42127188"],"is_preprint":false},{"year":2025,"finding":"IRTKS forms lysosome-localized membrane-associated condensates that selectively interact with RRAGD GTPase, enhancing mTORC1 sensitivity to free amino acids and promoting mTORC1 hyperactivation, hepatic lipid accumulation, and HCC progression.","method":"Phospho-antibody array screening; co-immunoprecipitation of IRTKS with RRAGD; hepatic knockin mouse model; mTOR activity assays; pharmacological and genetic inhibition","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP identifying RRAGD as binding partner, in vivo knockin model with functional consequences, single lab","pmids":["41575860"],"is_preprint":false},{"year":2025,"finding":"Lipidated GABARAP (induced by CGAS-STING1 pathway) sequesters the FLCN-FNIP complex to abolish its GAP function toward RRAGC and RRAGD, leading to specific impairment of mTORC1-dependent phosphorylation of TFEB and resulting in TFEB nuclear translocation and lysosome biogenesis.","method":"Genetic and biochemical dissection in MEF cells; GABARAP lipidation mutants; V-ATPase-ATG16L1 axis perturbation; TFEB nuclear translocation assays","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mechanistic dissection with multiple genetic tools and functional readouts, single lab","pmids":["39835593"],"is_preprint":false},{"year":2023,"finding":"MEF2A and MEF2D transcription factors control expression of FNIP1 and FNIP2, which act as components of the FLCN-FNIP complex serving as a RRAGC-RRAGD GTPase-activating element to promote mTORC1 recruitment to the lysosome and activation. SRC phosphorylates MEF2D at conserved tyrosine residues to enhance this transcriptional activity.","method":"ChIP, transcriptional reporter assays, knockdown/knockout experiments, lysosomal fractionation, mTOR activity assays in pancreatic cancer cells","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pathway placed by multiple genetic and biochemical tools, single lab","pmids":["37772772"],"is_preprint":false},{"year":2022,"finding":"miR-99a-5p directly targets RRAGD mRNA (validated by dual luciferase reporter assay); overexpression of miR-99a-5p inhibits glycolysis and induces apoptosis in cervical cancer cells by reducing RRAGD levels.","method":"Dual luciferase reporter assay; miRNA overexpression; glucose uptake, lactate, and ECAR measurements; flow cytometry apoptosis assay","journal":"Oncology letters","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct binding validated by luciferase assay plus functional metabolic readouts, single lab","pmids":["35720506"],"is_preprint":false},{"year":2025,"finding":"LINC00622 associates with and recruits BTF3 to transcriptionally enhance RRAGD expression, thereby activating mTORC1 and inhibiting autophagic cell death in cutaneous melanoma.","method":"RNA pulldown, Co-IP, chromatin immunoprecipitation, RRAGD knockdown/overexpression, mTOR activity assays, autophagic flux assays","journal":"Cell death & disease","confidence":"Low","confidence_rationale":"Tier 3 / Weak — mechanistic chain proposed with RNA-protein interaction assays and functional readouts, single lab, limited validation of each step","pmids":["40651979"],"is_preprint":false},{"year":2024,"finding":"miR-125b-1-3p directly targets RRAGD (interaction validated); miR-125b-1-3p overexpression reduces RRAGD levels, suppresses mTOR/ULK1 signaling, enhances autophagy in vascular smooth muscle cells, and reduces atherosclerotic plaque development in mice.","method":"Dual luciferase reporter assay (implied); miR-125b-1-3p overexpression in mice and VSMCs; autophagy flux assays; plaque quantification","journal":"Cellular signalling","confidence":"Low","confidence_rationale":"Tier 3 / Weak — functional in vivo and in vitro data but mechanistic link between miR-125b-1-3p and RRAGD binding not explicitly confirmed by luciferase in abstract, single lab","pmids":["38471617"],"is_preprint":false},{"year":2026,"finding":"The miR-302/367 cluster directly targets RRAGD 3'UTR (validated by dual luciferase reporter assay), reducing RRAGD mRNA and protein levels in breast cancer cells and broadly suppressing mTOR pathway activity.","method":"Dual luciferase reporter assay; miR-302/367 overexpression; RT-qPCR and western blot for RRAGD protein; proliferation assays","journal":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — direct 3'UTR binding validated by luciferase assay with protein-level confirmation, single lab, single study","pmids":["40817797"],"is_preprint":false},{"year":2024,"finding":"lncARF physically binds to RRAGD protein and inhibits its ubiquitination, further activating PI3K/Akt and MAPK signaling pathways in foam cells, promoting atherosclerosis.","method":"Mass spectrometry, RNA pulldown, RNA immunoprecipitation (RIP); ubiquitination assays; in vivo lncARF knockdown","journal":"Journal of advanced research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — lncRNA-protein interaction established by pulldown/RIP with functional consequence, but single lab and lncRNA-protein binding is the primary claim about RRAGD","pmids":["39214417"],"is_preprint":false},{"year":2025,"finding":"RRAGD co-localizes with lysosomal marker LAMP1 and TFEB, and delivery of RRAGD via engineered extracellular vesicles to nucleus pulposus cells ameliorates lysosomal dysfunction and suppresses apoptosis, establishing RRAGD as a regulator of lysosomal biogenesis and function.","method":"Co-localization imaging (RRAGD with LAMP1 and TFEB); engineered EV delivery; in vitro and in vivo functional assays in intervertebral disc degeneration model","journal":"Journal of nanobiotechnology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — localization by co-immunofluorescence and functional rescue with exogenous RRAGD, single lab","pmids":["41076529"],"is_preprint":false},{"year":2021,"finding":"RRAGD knockdown in hepatocellular carcinoma cells (Huh-7 and HepG2) inhibited proliferation, invasion, migration, and reduced glucose uptake, lactate production, and extracellular acidification rate, demonstrating a role for RRAGD in promoting aerobic glycolysis. RRAGD expression was upregulated by the oncogene MYC.","method":"shRNA knockdown; MTT/invasion/migration assays; glucose uptake and lactate colorimetric assays; ECAR measurement; western blot/qRT-PCR for MYC-RRAGD relationship","journal":"Annals of hepatology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — clean KD with multiple metabolic readouts, MYC-RRAGD relationship by expression analysis only, single lab","pmids":["33434687"],"is_preprint":false}],"current_model":"RRAGD encodes RagD GTPase, a component of the Rag GTPase heterodimer (with RagC) that acts as a key upstream regulator of mTORC1 by promoting its recruitment to the lysosomal surface in response to amino acid availability; gain-of-function disease mutations in RRAGD constitutively activate a non-canonical mTORC1 branch that specifically phosphorylates and inhibits the MiT/TFE transcription factors (TFEB/TFE3) without affecting canonical substrates like S6K, causing autosomal dominant kidney hypomagnesemia with cardiomyopathy (ADKH-RRAGD), while RRAGD expression itself is transcriptionally regulated by TFE3, IL-4/STAT6, and MYC, and post-transcriptionally regulated by multiple miRNAs targeting its 3'UTR."},"narrative":{"mechanistic_narrative":"RRAGD encodes RagD, a Rag-family GTPase that functions at the lysosomal surface as an upstream activator of mTORC1, coupling nutrient and amino-acid signals to mTORC1 recruitment and activity [PMID:34607910, PMID:41575860]. RagC/D activity is controlled by the FLCN-FNIP complex acting as its GAP, and disruption of this GAP function selectively reroutes mTORC1 toward a non-canonical branch that phosphorylates the MiT/TFE transcription factors TFEB and TFE3, blocking their nuclear translocation, without affecting canonical substrates such as S6K [PMID:37188688, PMID:39835593, PMID:37772772]. Heterozygous gain-of-function missense variants in RRAGD constitutively activate this non-canonical mTORC1 output, causing autosomal dominant kidney hypomagnesemia with dilated cardiomyopathy (ADKH-RRAGD); the cardiac phenotype is mTOR-dependent and reversible by rapamycin [PMID:34607910, PMID:37188688, PMID:39331021, PMID:41141537]. RRAGD operates within a regulatory loop with the MiT/TFE program: TFEB drives assembly of RRAGD-containing signaling endosomes that re-tether and activate mTORC1, and TFE3 transcriptionally induces RRAGD via an E-box element [PMID:30145926, PMID:33459596]. RRAGD expression is further controlled transcriptionally by IL-4/STAT6 in lymphoma and by MYC, and supports mTOR-driven aerobic glycolysis and proliferation in cancer cells [PMID:39910284, PMID:33434687]. Post-transcriptionally, RRAGD is regulated by METTL3/NUDT21-dependent alternative polyadenylation of its 3'UTR, where 3'UTR shortening raises RRAGD levels and overactivates mTOR [PMID:42127188].","teleology":[{"year":2018,"claim":"Established that RRAGD is a mobile component of nutrient-sensing signaling endosomes rather than a static lysosomal anchor, linking TFEB-driven endocytosis to mTORC1 re-activation.","evidence":"Live-cell imaging, Co-IP, and knockdown in HEK293T and CAD cells tracking RRAGD-, SLC38A9-, and AKT-carrying endosomes","pmids":["30145926"],"confidence":"Medium","gaps":["Stoichiometry and obligate partner (RagC) of the endosomal RagD complex not defined","Direct biochemical demonstration of mTORC1 re-tethering by RagD not shown"]},{"year":2021,"claim":"Identified RRAGD gain-of-function missense variants as the cause of a human Mendelian disease (ADKH-RRAGD) acting through constitutive mTOR activation, defining RagD as a disease-relevant mTORC1 regulator in the nephron.","evidence":"Whole-exome/genome sequencing of patient families with in vitro mTOR signaling assays and nephron immunolocalization","pmids":["34607910"],"confidence":"High","gaps":["Mechanism connecting tubular mTOR activation to magnesium/potassium handling not resolved","Which mTORC1 substrate drives the renal phenotype not specified at this stage"]},{"year":2021,"claim":"Placed RRAGD downstream of the FLCN-TFE3 axis as a transcriptional target, revealing that FLCN loss raises RRAGD independently of bulk mTORC1 activity.","evidence":"FLCN knockout in RPTEC/TERT1 renal cells with transcriptomics, proteomics, and E-box target validation","pmids":["33459596"],"confidence":"Medium","gaps":["Direct TFE3 occupancy at the RRAGD E-box vs. indirect induction not fully separated","Functional consequence of elevated RRAGD on downstream signaling not measured here"]},{"year":2023,"claim":"Defined the mechanistic core of disease pathology: RRAGD-activating mutations drive a non-canonical mTORC1 branch that phosphorylates and inactivates TFEB/TFE3 without engaging canonical substrates, even absent the FLCN GAP.","evidence":"Phosphorylation and nuclear translocation assays in HeLa, HK-2, iPSC-cardiomyocytes, and patient fibroblasts in FLCN-knockout contexts","pmids":["37188688"],"confidence":"High","gaps":["Structural basis for substrate selectivity (TFEB/TFE3 vs. S6K) not determined","How nucleotide state of mutant RagD enforces this selectivity unresolved"]},{"year":2023,"claim":"Showed how the FLCN-FNIP GAP toward RRAGC/RRAGD is itself transcriptionally tuned, connecting MEF2A/MEF2D and SRC signaling to mTORC1 lysosomal recruitment.","evidence":"ChIP, reporter assays, knockdown/knockout, lysosomal fractionation, and mTOR assays in pancreatic cancer cells","pmids":["37772772"],"confidence":"Medium","gaps":["Direct effect on RagD nucleotide loading not assayed","Generality beyond pancreatic cancer context untested"]},{"year":2023,"claim":"Demonstrated cytokine-driven control of RRAGD expression via IL-4/STAT6 and showed RRAGD is required for mTOR activation in follicular lymphoma cells.","evidence":"RNA-seq of primary FL samples, ex vivo IL4 stimulation, RRAGD knockdown with mTOR readout, and CREBBP/STAT6 mutant analysis","pmids":["39910284"],"confidence":"Medium","gaps":["Direct STAT6 binding at the RRAGD locus not mapped","Whether canonical or non-canonical mTORC1 output mediates the lymphoma effect unclear"]},{"year":2024,"claim":"Provided in vivo causal evidence that RRAGD disease variants produce cardiomyopathy through mTOR, establishing pharmacological reversibility.","evidence":"Zebrafish cRNA injection of p.S76L and p.P119R with cardiac functional readouts and rapamycin rescue","pmids":["39331021"],"confidence":"Medium","gaps":["Cell-autonomous cardiomyocyte mechanism vs. systemic effect not separated","Whether TFEB/TFE3 inactivation drives the cardiac phenotype not tested in vivo"]},{"year":2025,"claim":"Expanded the allelic spectrum of non-canonical mTORC1-activating RRAGD variants and explored therapeutic mitigation of hypomagnesemia.","evidence":"In vitro mTORC1 assays for novel variants plus multi-center clinical assessment of dapagliflozin response","pmids":["41141537"],"confidence":"Medium","gaps":["Mechanism of SGLT2-inhibitor benefit on Mg2+ handling not established","Genotype-phenotype correlation across variants incomplete"]},{"year":2025,"claim":"Identified post-transcriptional control of RRAGD through m6A-coupled alternative polyadenylation, where 3'UTR shortening elevates RRAGD and overactivates mTOR in T cells.","evidence":"NUDT21 deletion in T cells, poly(A) profiling, METTL3-NUDT21 Co-IP, m6A mapping, and functional T cell assays","pmids":["42127188"],"confidence":"Medium","gaps":["Whether 3'UTR length alters RagD nucleotide state or only abundance unclear","Relevance to RRAGD regulation in non-immune tissues untested"]},{"year":2025,"claim":"Defined a physical RRAGD interactor (IRTKS) that forms lysosomal condensates to sensitize mTORC1 to amino acids, linking RagD to hepatic lipid accumulation and HCC.","evidence":"Phospho-array screening, IRTKS-RRAGD Co-IP, hepatic knockin mouse, and mTOR assays with pharmacologic/genetic inhibition","pmids":["41575860"],"confidence":"Medium","gaps":["Whether IRTKS binding alters RagD GTPase cycle not biochemically resolved","Reciprocal validation of the interaction in physiological tissue limited"]},{"year":2025,"claim":"Connected innate-immune signaling to RagC/D regulation, showing lipidated GABARAP sequesters FLCN-FNIP to selectively de-repress TFEB.","evidence":"Genetic and biochemical dissection in MEFs with GABARAP lipidation mutants and TFEB translocation assays","pmids":["39835593"],"confidence":"Medium","gaps":["Direct effect on RagD GAP loading not measured","Selectivity for TFEB over TFE3 in this context not addressed"]},{"year":2026,"claim":"Accumulating Low-confidence reports place RRAGD as a node in disease via diverse regulators (multiple miRNAs targeting its 3'UTR, lncRNAs stabilizing or inducing it, MYC induction), driving glycolysis, autophagy suppression, and proliferation.","evidence":"Dual-luciferase 3'UTR assays, RNA pulldown/RIP, ubiquitination assays, and metabolic/autophagy readouts across cancer and vascular models","pmids":["35720506","40651979","38471617","40817797","39214417","41076529","33434687"],"confidence":"Low","gaps":["Each regulatory axis rests on single-lab studies with limited cross-validation","Whether these effects act through canonical vs. non-canonical mTORC1 output not dissected","Direct RRAGD protein binding (e.g., lncARF) not always reciprocally confirmed"]},{"year":null,"claim":"The structural and biochemical basis by which RagD nucleotide state dictates selective mTORC1 phosphorylation of MiT/TFE factors versus canonical substrates remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of mutant RagD-mTORC1 substrate routing","Mechanism linking renal mTOR activation to magnesium handling unknown","RagC partnership not directly characterized in the disease context within this corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[0,8]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[8,16]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[2]}],"pathway":[],"complexes":["Rag GTPase heterodimer (RagC/RagD)"],"partners":["RRAGC","FLCN","FNIP1","FNIP2","SLC38A9","IRTKS"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NQL2","full_name":"Ras-related GTP-binding protein D","aliases":[],"length_aa":400,"mass_kda":45.6,"function":"Guanine nucleotide-binding protein that plays a crucial role in the cellular response to amino acid availability through regulation of the mTORC1 signaling cascade (PubMed:20381137, PubMed:24095279, PubMed:34607910). Forms heterodimeric Rag complexes with RagA/RRAGA or RagB/RRAGB and cycles between an inactive GTP-bound and an active GDP-bound form: RagD/RRAGD is in its active form when GDP-bound RagD/RRAGD forms a complex with GTP-bound RagA/RRAGA (or RagB/RRAGB) and in an inactive form when GTP-bound RagD/RRAGD heterodimerizes with GDP-bound RagA/RRAGA (or RagB/RRAGB) (PubMed:24095279). In its active form, promotes the recruitment of mTORC1 to the lysosomes and its subsequent activation by the GTPase RHEB (PubMed:20381137, PubMed:24095279). This is a crucial step in the activation of the MTOR signaling cascade by amino acids (PubMed:20381137, PubMed:24095279). Also plays a central role in the non-canonical mTORC1 complex, which acts independently of RHEB and specifically mediates phosphorylation of MiT/TFE factors TFEB and TFE3: GDP-bound RagD/RRAGD mediates recruitment of MiT/TFE factors TFEB and TFE3 (PubMed:32612235)","subcellular_location":"Cytoplasm; Nucleus; Lysosome membrane","url":"https://www.uniprot.org/uniprotkb/Q9NQL2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RRAGD","classification":"Not Classified","n_dependent_lines":16,"n_total_lines":1208,"dependency_fraction":0.013245033112582781},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RRAGD","total_profiled":1310},"omim":[{"mim_id":"620152","title":"HYPOMAGNESEMIA 7, RENAL, WITH OR WITHOUT DILATED CARDIOMYOPATHY; HOMG7","url":"https://www.omim.org/entry/620152"},{"mim_id":"618834","title":"LATE ENDOSOMAL/LYSOSOMAL ADAPTOR, MAPK AND MTOR ACTIVATOR 4; LAMTOR4","url":"https://www.omim.org/entry/618834"},{"mim_id":"611534","title":"NUCLEOLAR PROTEIN 8; NOL8","url":"https://www.omim.org/entry/611534"},{"mim_id":"608521","title":"LATE ENDOSOMAL/LYSOSOMAL ADAPTOR, MAPK AND MTOR ACTIVATOR 5; LAMTOR5","url":"https://www.omim.org/entry/608521"},{"mim_id":"608268","title":"RAS-RELATED GTP-BINDING PROTEIN D; RRAGD","url":"https://www.omim.org/entry/608268"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Vesicles","reliability":"Additional"},{"location":"Centrosome","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":79.1},{"tissue":"tongue","ntpm":56.3}],"url":"https://www.proteinatlas.org/search/RRAGD"},"hgnc":{"alias_symbol":["DKFZP761H171","bA11D8.2.1"],"prev_symbol":[]},"alphafold":{"accession":"Q9NQL2","domains":[{"cath_id":"3.40.50.300","chopping":"63-236","consensus_level":"high","plddt":84.7018,"start":63,"end":236},{"cath_id":"3.30.450.190","chopping":"240-377","consensus_level":"high","plddt":88.5525,"start":240,"end":377}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NQL2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NQL2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NQL2-F1-predicted_aligned_error_v6.png","plddt_mean":75.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RRAGD","jax_strain_url":"https://www.jax.org/strain/search?query=RRAGD"},"sequence":{"accession":"Q9NQL2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NQL2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NQL2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NQL2"}},"corpus_meta":[{"pmid":"32793490","id":"PMC_32793490","title":"Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor Model.","date":"2020","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/32793490","citation_count":172,"is_preprint":false},{"pmid":"30145926","id":"PMC_30145926","title":"TFEB-driven endocytosis coordinates MTORC1 signaling and autophagy.","date":"2018","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/30145926","citation_count":141,"is_preprint":false},{"pmid":"22367074","id":"PMC_22367074","title":"Identification and association analysis of several hundred single nucleotide polymorphisms within candidate genes for back fat thickness in Italian Large White pigs using a selective genotyping approach.","date":"2012","source":"Journal of animal science","url":"https://pubmed.ncbi.nlm.nih.gov/22367074","citation_count":56,"is_preprint":false},{"pmid":"32419983","id":"PMC_32419983","title":"Integrated analysis of lymphocyte infiltration-associated lncRNA for ovarian cancer via TCGA, GTEx and GEO datasets.","date":"2020","source":"PeerJ","url":"https://pubmed.ncbi.nlm.nih.gov/32419983","citation_count":52,"is_preprint":false},{"pmid":"34607910","id":"PMC_34607910","title":"mTOR-Activating Mutations in RRAGD Are Causative for Kidney Tubulopathy and Cardiomyopathy.","date":"2021","source":"Journal of the American Society of Nephrology : JASN","url":"https://pubmed.ncbi.nlm.nih.gov/34607910","citation_count":48,"is_preprint":false},{"pmid":"21257989","id":"PMC_21257989","title":"Variants in ZNF365 isoform D are associated with Crohn's disease.","date":"2011","source":"Gut","url":"https://pubmed.ncbi.nlm.nih.gov/21257989","citation_count":23,"is_preprint":false},{"pmid":"33459596","id":"PMC_33459596","title":"Loss of FLCN-FNIP1/2 induces a non-canonical interferon response in human renal tubular epithelial cells.","date":"2021","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/33459596","citation_count":19,"is_preprint":false},{"pmid":"27084392","id":"PMC_27084392","title":"Biotinylation: a novel posttranslational modification linking cell autonomous circadian clocks with metabolism.","date":"2016","source":"American journal of physiology. 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RagD expression was detected along the mammalian nephron including the thick ascending limb and distal convoluted tubule.\",\n      \"method\": \"Whole-exome/genome sequencing of patient cohort; in vitro functional analyses of RRAGD variants (mTOR signaling assays); immunolocalization along the nephron\",\n      \"journal\": \"Journal of the American Society of Nephrology : JASN\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple independent patient families, in vitro functional validation of variants, replicated across multiple labs in subsequent studies\",\n      \"pmids\": [\"34607910\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RRAGD auto-activating disease mutations cause constitutive phosphorylation of TFEB and TFE3 by mTORC1 (non-canonical pathway) without affecting canonical mTORC1 substrates such as S6K, even in the absence of Folliculin (the GAP responsible for RagC/D activation). This leads to inhibition of TFEB and TFE3 nuclear translocation and transcriptional activity, impairing the response to lysosomal and mitochondrial injury.\",\n      \"method\": \"HeLa and HK-2 cell lines, human iPSC-derived cardiomyocytes, and patient-derived primary fibroblasts; phosphorylation assays; nuclear translocation assays; FOLLICULIN-knockout contexts\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal cell models including patient-derived cells, mutagenesis in disease-relevant context, mechanistic dissection of canonical vs. non-canonical mTORC1 signaling\",\n      \"pmids\": [\"37188688\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TFEB promotes endocytic assembly of an mTORC1-containing nutrient-sensing complex through formation of endosomes carrying RRAGD, the amino acid transporter SLC38A9, and activated AKT. These TFEB-induced signaling endosomes en route to lysosomes dissociate TSC2 and re-tether/activate mTORC1 on endolysosomal membranes.\",\n      \"method\": \"Live-cell imaging, co-immunoprecipitation, overexpression/knockdown experiments in HEK293T and CAD cells, endocytosis rate measurements\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (imaging, Co-IP, functional assays) in single lab\",\n      \"pmids\": [\"30145926\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Loss of FLCN in human renal tubular epithelial cells activates TFE3 and upregulates RRAGD expression (as an E-box target of TFE3) without modifying mTORC1 activity, identifying RRAGD as a transcriptional target of TFE3 in renal cells.\",\n      \"method\": \"FLCN knockout in RPTEC/TERT1 cells; transcriptomic analysis; integrated proteomics; functional validation\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined molecular readout, integrated omics + functional follow-up, single lab\",\n      \"pmids\": [\"33459596\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RRAGD expression is induced by IL-4 signaling through STAT6 in follicular lymphoma cells; RRAGD is required for mTOR activation in lymphoma cells, and IL4-enhanced BCR signaling-induced mTOR activation depends on this axis. CREBBP mutations attenuate IL4-induced RRAGD expression, while activating STAT6 mutations augment it.\",\n      \"method\": \"RNA-seq on primary human FL samples; ex vivo IL4 stimulation; RRAGD knockdown with mTOR activity readout; CREBBP and STAT6 mutant functional analysis\",\n      \"journal\": \"Leukemia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — primary human samples plus functional knockdown experiments, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"39910284\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Overexpression of disease-associated RRAGD mutants (p.S76L and p.P119R) in zebrafish embryos caused decreased ventricular fractional shortening, ejection fraction, and pericardial swelling, recapitulating cardiomyopathy. These phenotypes were reversible by treatment with rapamycin (mTOR inhibitor), establishing that RRAGD-variant-induced cardiac dysfunction is mTOR-dependent.\",\n      \"method\": \"Zebrafish embryo cRNA injection model; cardiac functional measurements (fractional shortening, ejection fraction); rapamycin rescue experiment\",\n      \"journal\": \"American journal of physiology. Heart and circulatory physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo vertebrate model with pharmacological rescue, multiple cardiac functional readouts, single lab\",\n      \"pmids\": [\"39331021\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Novel RRAGD variants p.(Ser77Phe) and p.(Ile100Arg) cause constitutive activation of non-canonical mTORC1 signaling as shown by in vitro assays, further expanding the spectrum of gain-of-function RRAGD mutations causing ADKH. SGLT2 inhibitor dapagliflozin modestly increased serum Mg2+ in patients with p.(Thr97Pro) variant.\",\n      \"method\": \"In vitro mTORC1 activity assays for novel variants; clinical assessment of therapeutic responses in patients\",\n      \"journal\": \"Kidney international reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro functional validation of novel variants with defined molecular readout, multi-center case series\",\n      \"pmids\": [\"41141537\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The m6A writer METTL3 recruits the APA factor NUDT21 to the proximal poly(A) site of Rragd mRNA, generating a long 3'UTR isoform with m6A modifications. Nudt21 deficiency causes Rragd 3'UTR shortening, increases Rragd expression, and leads to overactivation of mTOR signaling and T cell hyperactivation.\",\n      \"method\": \"NUDT21 deletion in T cells; RNA-seq/poly(A) site profiling; METTL3-NUDT21 co-immunoprecipitation; m6A mapping; functional T cell assays\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO with defined molecular mechanism, Co-IP, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"42127188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"IRTKS forms lysosome-localized membrane-associated condensates that selectively interact with RRAGD GTPase, enhancing mTORC1 sensitivity to free amino acids and promoting mTORC1 hyperactivation, hepatic lipid accumulation, and HCC progression.\",\n      \"method\": \"Phospho-antibody array screening; co-immunoprecipitation of IRTKS with RRAGD; hepatic knockin mouse model; mTOR activity assays; pharmacological and genetic inhibition\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP identifying RRAGD as binding partner, in vivo knockin model with functional consequences, single lab\",\n      \"pmids\": [\"41575860\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Lipidated GABARAP (induced by CGAS-STING1 pathway) sequesters the FLCN-FNIP complex to abolish its GAP function toward RRAGC and RRAGD, leading to specific impairment of mTORC1-dependent phosphorylation of TFEB and resulting in TFEB nuclear translocation and lysosome biogenesis.\",\n      \"method\": \"Genetic and biochemical dissection in MEF cells; GABARAP lipidation mutants; V-ATPase-ATG16L1 axis perturbation; TFEB nuclear translocation assays\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mechanistic dissection with multiple genetic tools and functional readouts, single lab\",\n      \"pmids\": [\"39835593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"MEF2A and MEF2D transcription factors control expression of FNIP1 and FNIP2, which act as components of the FLCN-FNIP complex serving as a RRAGC-RRAGD GTPase-activating element to promote mTORC1 recruitment to the lysosome and activation. SRC phosphorylates MEF2D at conserved tyrosine residues to enhance this transcriptional activity.\",\n      \"method\": \"ChIP, transcriptional reporter assays, knockdown/knockout experiments, lysosomal fractionation, mTOR activity assays in pancreatic cancer cells\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pathway placed by multiple genetic and biochemical tools, single lab\",\n      \"pmids\": [\"37772772\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"miR-99a-5p directly targets RRAGD mRNA (validated by dual luciferase reporter assay); overexpression of miR-99a-5p inhibits glycolysis and induces apoptosis in cervical cancer cells by reducing RRAGD levels.\",\n      \"method\": \"Dual luciferase reporter assay; miRNA overexpression; glucose uptake, lactate, and ECAR measurements; flow cytometry apoptosis assay\",\n      \"journal\": \"Oncology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct binding validated by luciferase assay plus functional metabolic readouts, single lab\",\n      \"pmids\": [\"35720506\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LINC00622 associates with and recruits BTF3 to transcriptionally enhance RRAGD expression, thereby activating mTORC1 and inhibiting autophagic cell death in cutaneous melanoma.\",\n      \"method\": \"RNA pulldown, Co-IP, chromatin immunoprecipitation, RRAGD knockdown/overexpression, mTOR activity assays, autophagic flux assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — mechanistic chain proposed with RNA-protein interaction assays and functional readouts, single lab, limited validation of each step\",\n      \"pmids\": [\"40651979\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"miR-125b-1-3p directly targets RRAGD (interaction validated); miR-125b-1-3p overexpression reduces RRAGD levels, suppresses mTOR/ULK1 signaling, enhances autophagy in vascular smooth muscle cells, and reduces atherosclerotic plaque development in mice.\",\n      \"method\": \"Dual luciferase reporter assay (implied); miR-125b-1-3p overexpression in mice and VSMCs; autophagy flux assays; plaque quantification\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — functional in vivo and in vitro data but mechanistic link between miR-125b-1-3p and RRAGD binding not explicitly confirmed by luciferase in abstract, single lab\",\n      \"pmids\": [\"38471617\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"The miR-302/367 cluster directly targets RRAGD 3'UTR (validated by dual luciferase reporter assay), reducing RRAGD mRNA and protein levels in breast cancer cells and broadly suppressing mTOR pathway activity.\",\n      \"method\": \"Dual luciferase reporter assay; miR-302/367 overexpression; RT-qPCR and western blot for RRAGD protein; proliferation assays\",\n      \"journal\": \"FASEB journal : official publication of the Federation of American Societies for Experimental Biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — direct 3'UTR binding validated by luciferase assay with protein-level confirmation, single lab, single study\",\n      \"pmids\": [\"40817797\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"lncARF physically binds to RRAGD protein and inhibits its ubiquitination, further activating PI3K/Akt and MAPK signaling pathways in foam cells, promoting atherosclerosis.\",\n      \"method\": \"Mass spectrometry, RNA pulldown, RNA immunoprecipitation (RIP); ubiquitination assays; in vivo lncARF knockdown\",\n      \"journal\": \"Journal of advanced research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — lncRNA-protein interaction established by pulldown/RIP with functional consequence, but single lab and lncRNA-protein binding is the primary claim about RRAGD\",\n      \"pmids\": [\"39214417\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RRAGD co-localizes with lysosomal marker LAMP1 and TFEB, and delivery of RRAGD via engineered extracellular vesicles to nucleus pulposus cells ameliorates lysosomal dysfunction and suppresses apoptosis, establishing RRAGD as a regulator of lysosomal biogenesis and function.\",\n      \"method\": \"Co-localization imaging (RRAGD with LAMP1 and TFEB); engineered EV delivery; in vitro and in vivo functional assays in intervertebral disc degeneration model\",\n      \"journal\": \"Journal of nanobiotechnology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — localization by co-immunofluorescence and functional rescue with exogenous RRAGD, single lab\",\n      \"pmids\": [\"41076529\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RRAGD knockdown in hepatocellular carcinoma cells (Huh-7 and HepG2) inhibited proliferation, invasion, migration, and reduced glucose uptake, lactate production, and extracellular acidification rate, demonstrating a role for RRAGD in promoting aerobic glycolysis. RRAGD expression was upregulated by the oncogene MYC.\",\n      \"method\": \"shRNA knockdown; MTT/invasion/migration assays; glucose uptake and lactate colorimetric assays; ECAR measurement; western blot/qRT-PCR for MYC-RRAGD relationship\",\n      \"journal\": \"Annals of hepatology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — clean KD with multiple metabolic readouts, MYC-RRAGD relationship by expression analysis only, single lab\",\n      \"pmids\": [\"33434687\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RRAGD encodes RagD GTPase, a component of the Rag GTPase heterodimer (with RagC) that acts as a key upstream regulator of mTORC1 by promoting its recruitment to the lysosomal surface in response to amino acid availability; gain-of-function disease mutations in RRAGD constitutively activate a non-canonical mTORC1 branch that specifically phosphorylates and inhibits the MiT/TFE transcription factors (TFEB/TFE3) without affecting canonical substrates like S6K, causing autosomal dominant kidney hypomagnesemia with cardiomyopathy (ADKH-RRAGD), while RRAGD expression itself is transcriptionally regulated by TFE3, IL-4/STAT6, and MYC, and post-transcriptionally regulated by multiple miRNAs targeting its 3'UTR.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RRAGD encodes RagD, a Rag-family GTPase that functions at the lysosomal surface as an upstream activator of mTORC1, coupling nutrient and amino-acid signals to mTORC1 recruitment and activity [#0, #8]. RagC/D activity is controlled by the FLCN-FNIP complex acting as its GAP, and disruption of this GAP function selectively reroutes mTORC1 toward a non-canonical branch that phosphorylates the MiT/TFE transcription factors TFEB and TFE3, blocking their nuclear translocation, without affecting canonical substrates such as S6K [#1, #9, #10]. Heterozygous gain-of-function missense variants in RRAGD constitutively activate this non-canonical mTORC1 output, causing autosomal dominant kidney hypomagnesemia with dilated cardiomyopathy (ADKH-RRAGD); the cardiac phenotype is mTOR-dependent and reversible by rapamycin [#0, #1, #5, #6]. RRAGD operates within a regulatory loop with the MiT/TFE program: TFEB drives assembly of RRAGD-containing signaling endosomes that re-tether and activate mTORC1, and TFE3 transcriptionally induces RRAGD via an E-box element [#2, #3]. RRAGD expression is further controlled transcriptionally by IL-4/STAT6 in lymphoma and by MYC, and supports mTOR-driven aerobic glycolysis and proliferation in cancer cells [#4, #17]. Post-transcriptionally, RRAGD is regulated by METTL3/NUDT21-dependent alternative polyadenylation of its 3'UTR, where 3'UTR shortening raises RRAGD levels and overactivates mTOR [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Established that RRAGD is a mobile component of nutrient-sensing signaling endosomes rather than a static lysosomal anchor, linking TFEB-driven endocytosis to mTORC1 re-activation.\",\n      \"evidence\": \"Live-cell imaging, Co-IP, and knockdown in HEK293T and CAD cells tracking RRAGD-, SLC38A9-, and AKT-carrying endosomes\",\n      \"pmids\": [\"30145926\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Stoichiometry and obligate partner (RagC) of the endosomal RagD complex not defined\", \"Direct biochemical demonstration of mTORC1 re-tethering by RagD not shown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified RRAGD gain-of-function missense variants as the cause of a human Mendelian disease (ADKH-RRAGD) acting through constitutive mTOR activation, defining RagD as a disease-relevant mTORC1 regulator in the nephron.\",\n      \"evidence\": \"Whole-exome/genome sequencing of patient families with in vitro mTOR signaling assays and nephron immunolocalization\",\n      \"pmids\": [\"34607910\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism connecting tubular mTOR activation to magnesium/potassium handling not resolved\", \"Which mTORC1 substrate drives the renal phenotype not specified at this stage\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Placed RRAGD downstream of the FLCN-TFE3 axis as a transcriptional target, revealing that FLCN loss raises RRAGD independently of bulk mTORC1 activity.\",\n      \"evidence\": \"FLCN knockout in RPTEC/TERT1 renal cells with transcriptomics, proteomics, and E-box target validation\",\n      \"pmids\": [\"33459596\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct TFE3 occupancy at the RRAGD E-box vs. indirect induction not fully separated\", \"Functional consequence of elevated RRAGD on downstream signaling not measured here\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined the mechanistic core of disease pathology: RRAGD-activating mutations drive a non-canonical mTORC1 branch that phosphorylates and inactivates TFEB/TFE3 without engaging canonical substrates, even absent the FLCN GAP.\",\n      \"evidence\": \"Phosphorylation and nuclear translocation assays in HeLa, HK-2, iPSC-cardiomyocytes, and patient fibroblasts in FLCN-knockout contexts\",\n      \"pmids\": [\"37188688\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for substrate selectivity (TFEB/TFE3 vs. S6K) not determined\", \"How nucleotide state of mutant RagD enforces this selectivity unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed how the FLCN-FNIP GAP toward RRAGC/RRAGD is itself transcriptionally tuned, connecting MEF2A/MEF2D and SRC signaling to mTORC1 lysosomal recruitment.\",\n      \"evidence\": \"ChIP, reporter assays, knockdown/knockout, lysosomal fractionation, and mTOR assays in pancreatic cancer cells\",\n      \"pmids\": [\"37772772\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct effect on RagD nucleotide loading not assayed\", \"Generality beyond pancreatic cancer context untested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrated cytokine-driven control of RRAGD expression via IL-4/STAT6 and showed RRAGD is required for mTOR activation in follicular lymphoma cells.\",\n      \"evidence\": \"RNA-seq of primary FL samples, ex vivo IL4 stimulation, RRAGD knockdown with mTOR readout, and CREBBP/STAT6 mutant analysis\",\n      \"pmids\": [\"39910284\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct STAT6 binding at the RRAGD locus not mapped\", \"Whether canonical or non-canonical mTORC1 output mediates the lymphoma effect unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided in vivo causal evidence that RRAGD disease variants produce cardiomyopathy through mTOR, establishing pharmacological reversibility.\",\n      \"evidence\": \"Zebrafish cRNA injection of p.S76L and p.P119R with cardiac functional readouts and rapamycin rescue\",\n      \"pmids\": [\"39331021\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cell-autonomous cardiomyocyte mechanism vs. systemic effect not separated\", \"Whether TFEB/TFE3 inactivation drives the cardiac phenotype not tested in vivo\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Expanded the allelic spectrum of non-canonical mTORC1-activating RRAGD variants and explored therapeutic mitigation of hypomagnesemia.\",\n      \"evidence\": \"In vitro mTORC1 assays for novel variants plus multi-center clinical assessment of dapagliflozin response\",\n      \"pmids\": [\"41141537\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of SGLT2-inhibitor benefit on Mg2+ handling not established\", \"Genotype-phenotype correlation across variants incomplete\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified post-transcriptional control of RRAGD through m6A-coupled alternative polyadenylation, where 3'UTR shortening elevates RRAGD and overactivates mTOR in T cells.\",\n      \"evidence\": \"NUDT21 deletion in T cells, poly(A) profiling, METTL3-NUDT21 Co-IP, m6A mapping, and functional T cell assays\",\n      \"pmids\": [\"42127188\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether 3'UTR length alters RagD nucleotide state or only abundance unclear\", \"Relevance to RRAGD regulation in non-immune tissues untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined a physical RRAGD interactor (IRTKS) that forms lysosomal condensates to sensitize mTORC1 to amino acids, linking RagD to hepatic lipid accumulation and HCC.\",\n      \"evidence\": \"Phospho-array screening, IRTKS-RRAGD Co-IP, hepatic knockin mouse, and mTOR assays with pharmacologic/genetic inhibition\",\n      \"pmids\": [\"41575860\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether IRTKS binding alters RagD GTPase cycle not biochemically resolved\", \"Reciprocal validation of the interaction in physiological tissue limited\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected innate-immune signaling to RagC/D regulation, showing lipidated GABARAP sequesters FLCN-FNIP to selectively de-repress TFEB.\",\n      \"evidence\": \"Genetic and biochemical dissection in MEFs with GABARAP lipidation mutants and TFEB translocation assays\",\n      \"pmids\": [\"39835593\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct effect on RagD GAP loading not measured\", \"Selectivity for TFEB over TFE3 in this context not addressed\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Accumulating Low-confidence reports place RRAGD as a node in disease via diverse regulators (multiple miRNAs targeting its 3'UTR, lncRNAs stabilizing or inducing it, MYC induction), driving glycolysis, autophagy suppression, and proliferation.\",\n      \"evidence\": \"Dual-luciferase 3'UTR assays, RNA pulldown/RIP, ubiquitination assays, and metabolic/autophagy readouts across cancer and vascular models\",\n      \"pmids\": [\"35720506\", \"40651979\", \"38471617\", \"40817797\", \"39214417\", \"41076529\", \"33434687\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Each regulatory axis rests on single-lab studies with limited cross-validation\", \"Whether these effects act through canonical vs. non-canonical mTORC1 output not dissected\", \"Direct RRAGD protein binding (e.g., lncARF) not always reciprocally confirmed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural and biochemical basis by which RagD nucleotide state dictates selective mTORC1 phosphorylation of MiT/TFE factors versus canonical substrates remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of mutant RagD-mTORC1 substrate routing\", \"Mechanism linking renal mTOR activation to magnesium handling unknown\", \"RagC partnership not directly characterized in the disease context within this corpus\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [8, 16]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0008150\", \"supporting_discovery_ids\": []}\n    ],\n    \"complexes\": [\"Rag GTPase heterodimer (RagC/RagD)\"],\n    \"partners\": [\"RRAGC\", \"FLCN\", \"FNIP1\", \"FNIP2\", \"SLC38A9\", \"IRTKS\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}