Affinage

RRAGD

Ras-related GTP-binding protein D · UniProt Q9NQL2

Length
400 aa
Mass
45.6 kDa
Annotated
2026-06-10
36 papers in source corpus 18 papers cited in narrative 18 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

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).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2018 Medium

    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

    PMID:30145926

    Open questions at the time
    • Stoichiometry and obligate partner (RagC) of the endosomal RagD complex not defined
    • Direct biochemical demonstration of mTORC1 re-tethering by RagD not shown
  2. 2021 High

    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

    PMID:34607910

    Open questions at the time
    • Mechanism connecting tubular mTOR activation to magnesium/potassium handling not resolved
    • Which mTORC1 substrate drives the renal phenotype not specified at this stage
  3. 2021 Medium

    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

    PMID:33459596

    Open questions at the time
    • 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
  4. 2023 High

    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

    PMID:37188688

    Open questions at the time
    • Structural basis for substrate selectivity (TFEB/TFE3 vs. S6K) not determined
    • How nucleotide state of mutant RagD enforces this selectivity unresolved
  5. 2023 Medium

    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

    PMID:37772772

    Open questions at the time
    • Direct effect on RagD nucleotide loading not assayed
    • Generality beyond pancreatic cancer context untested
  6. 2023 Medium

    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

    PMID:39910284

    Open questions at the time
    • Direct STAT6 binding at the RRAGD locus not mapped
    • Whether canonical or non-canonical mTORC1 output mediates the lymphoma effect unclear
  7. 2024 Medium

    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

    PMID:39331021

    Open questions at the time
    • Cell-autonomous cardiomyocyte mechanism vs. systemic effect not separated
    • Whether TFEB/TFE3 inactivation drives the cardiac phenotype not tested in vivo
  8. 2025 Medium

    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

    PMID:41141537

    Open questions at the time
    • Mechanism of SGLT2-inhibitor benefit on Mg2+ handling not established
    • Genotype-phenotype correlation across variants incomplete
  9. 2025 Medium

    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

    PMID:42127188

    Open questions at the time
    • Whether 3'UTR length alters RagD nucleotide state or only abundance unclear
    • Relevance to RRAGD regulation in non-immune tissues untested
  10. 2025 Medium

    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

    PMID:41575860

    Open questions at the time
    • Whether IRTKS binding alters RagD GTPase cycle not biochemically resolved
    • Reciprocal validation of the interaction in physiological tissue limited
  11. 2025 Medium

    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

    PMID:39835593

    Open questions at the time
    • Direct effect on RagD GAP loading not measured
    • Selectivity for TFEB over TFE3 in this context not addressed
  12. 2026 Low

    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

    PMID:33434687 PMID:35720506 PMID:38471617 PMID:39214417 PMID:40651979 PMID:40817797 PMID:41076529

    Open questions at the time
    • 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

Open questions

Synthesis pass · forward-looking unresolved questions
  • The structural and biochemical basis by which RagD nucleotide state dictates selective mTORC1 phosphorylation of MiT/TFE factors versus canonical substrates remains unresolved.
  • 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

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003924 GTPase activity 2 GO:0098772 molecular function regulator activity 2
Localization
GO:0005764 lysosome 2 GO:0005768 endosome 1
Partners
FLCNFNIP1FNIP2IRTKSRRAGCSLC38A9
Complex memberships
Rag GTPase heterodimer (RagC/RagD)

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2021 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. Whole-exome/genome sequencing of patient cohort; in vitro functional analyses of RRAGD variants (mTOR signaling assays); immunolocalization along the nephron Journal of the American Society of Nephrology : JASN High 34607910
2023 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. HeLa and HK-2 cell lines, human iPSC-derived cardiomyocytes, and patient-derived primary fibroblasts; phosphorylation assays; nuclear translocation assays; FOLLICULIN-knockout contexts Nature communications High 37188688
2018 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. Live-cell imaging, co-immunoprecipitation, overexpression/knockdown experiments in HEK293T and CAD cells, endocytosis rate measurements Autophagy Medium 30145926
2021 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. FLCN knockout in RPTEC/TERT1 cells; transcriptomic analysis; integrated proteomics; functional validation eLife Medium 33459596
2023 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. RNA-seq on primary human FL samples; ex vivo IL4 stimulation; RRAGD knockdown with mTOR activity readout; CREBBP and STAT6 mutant functional analysis Leukemia Medium 39910284
2024 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. Zebrafish embryo cRNA injection model; cardiac functional measurements (fractional shortening, ejection fraction); rapamycin rescue experiment American journal of physiology. Heart and circulatory physiology Medium 39331021
2025 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. In vitro mTORC1 activity assays for novel variants; clinical assessment of therapeutic responses in patients Kidney international reports Medium 41141537
2025 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. NUDT21 deletion in T cells; RNA-seq/poly(A) site profiling; METTL3-NUDT21 co-immunoprecipitation; m6A mapping; functional T cell assays Science advances Medium 42127188
2025 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. Phospho-antibody array screening; co-immunoprecipitation of IRTKS with RRAGD; hepatic knockin mouse model; mTOR activity assays; pharmacological and genetic inhibition Cell reports Medium 41575860
2025 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. Genetic and biochemical dissection in MEF cells; GABARAP lipidation mutants; V-ATPase-ATG16L1 axis perturbation; TFEB nuclear translocation assays Autophagy Medium 39835593
2023 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. ChIP, transcriptional reporter assays, knockdown/knockout experiments, lysosomal fractionation, mTOR activity assays in pancreatic cancer cells Autophagy Medium 37772772
2022 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. Dual luciferase reporter assay; miRNA overexpression; glucose uptake, lactate, and ECAR measurements; flow cytometry apoptosis assay Oncology letters Medium 35720506
2025 LINC00622 associates with and recruits BTF3 to transcriptionally enhance RRAGD expression, thereby activating mTORC1 and inhibiting autophagic cell death in cutaneous melanoma. RNA pulldown, Co-IP, chromatin immunoprecipitation, RRAGD knockdown/overexpression, mTOR activity assays, autophagic flux assays Cell death & disease Low 40651979
2024 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. Dual luciferase reporter assay (implied); miR-125b-1-3p overexpression in mice and VSMCs; autophagy flux assays; plaque quantification Cellular signalling Low 38471617
2026 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. Dual luciferase reporter assay; miR-302/367 overexpression; RT-qPCR and western blot for RRAGD protein; proliferation assays FASEB journal : official publication of the Federation of American Societies for Experimental Biology Low 40817797
2024 lncARF physically binds to RRAGD protein and inhibits its ubiquitination, further activating PI3K/Akt and MAPK signaling pathways in foam cells, promoting atherosclerosis. Mass spectrometry, RNA pulldown, RNA immunoprecipitation (RIP); ubiquitination assays; in vivo lncARF knockdown Journal of advanced research Low 39214417
2025 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. Co-localization imaging (RRAGD with LAMP1 and TFEB); engineered EV delivery; in vitro and in vivo functional assays in intervertebral disc degeneration model Journal of nanobiotechnology Low 41076529
2021 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. shRNA knockdown; MTT/invasion/migration assays; glucose uptake and lactate colorimetric assays; ECAR measurement; western blot/qRT-PCR for MYC-RRAGD relationship Annals of hepatology Low 33434687

Source papers

Stage 0 corpus · 36 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2020 Multi-Omics Characterization of the 4T1 Murine Mammary Gland Tumor Model. Frontiers in oncology 172 32793490
2018 TFEB-driven endocytosis coordinates MTORC1 signaling and autophagy. Autophagy 141 30145926
2012 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. Journal of animal science 56 22367074
2020 Integrated analysis of lymphocyte infiltration-associated lncRNA for ovarian cancer via TCGA, GTEx and GEO datasets. PeerJ 52 32419983
2021 mTOR-Activating Mutations in RRAGD Are Causative for Kidney Tubulopathy and Cardiomyopathy. Journal of the American Society of Nephrology : JASN 48 34607910
2011 Variants in ZNF365 isoform D are associated with Crohn's disease. Gut 23 21257989
2021 Loss of FLCN-FNIP1/2 induces a non-canonical interferon response in human renal tubular epithelial cells. eLife 19 33459596
2016 Biotinylation: a novel posttranslational modification linking cell autonomous circadian clocks with metabolism. American journal of physiology. Heart and circulatory physiology 18 27084392
2023 RagD auto-activating mutations impair MiT/TFE activity in kidney tubulopathy and cardiomyopathy syndrome. Nature communications 16 37188688
2022 miR-99a-5p inhibits glycolysis and induces cell apoptosis in cervical cancer by targeting RRAGD. Oncology letters 16 35720506
2023 Direct regulation of FNIP1 and FNIP2 by MEF2 sustains MTORC1 activation and tumor progression in pancreatic cancer. Autophagy 13 37772772
2011 Genome-wide approach to identify novel candidate genes for beta blocker response in heart failure using an experimental model. Discovery medicine 11 21524389
2021 Ras related GTP binding D promotes aerobic glycolysis of hepatocellular carcinoma. Annals of hepatology 10 33434687
2024 microRNA-125b-1-3p mediates autophagy via the RRAGD/mTOR/ULK1 signaling pathway and mitigates atherosclerosis progression. Cellular signalling 9 38471617
2022 Identification of autophagy-related biomarker and analysis of immune infiltrates in oral carcinoma. Journal of clinical laboratory analysis 9 35421271
2024 Diagnostic yield of exome and genome sequencing after non-diagnostic multi-gene panels in patients with single-system diseases. Orphanet journal of rare diseases 5 38790019
2024 RRAGD-Associated Autosomal Dominant Kidney Hypomagnesemia with Cardiomyopathy: A Review on the Clinical Manifestations and Therapeutic Options. Kidney & blood pressure research 5 38901414
2024 Novel long noncoding lncARF mediated hyperhomocysteinemia-induced atherosclerosis via autophagy inhibition in foam cells. Journal of advanced research 5 39214417
2023 LncTUG1 contributes to the progression of hepatocellular carcinoma via the miR-144-3p/RRAGD axis and mTOR/S6K pathway. Scientific reports 5 37160972
2025 Transcriptome Remodeling and Adaptive Preservation of Muscle Protein Content in Hibernating Black Bears. Ecology and evolution 4 40584666
2025 STAT6 mutations compensate for CREBBP mutations and hyperactivate IL4/STAT6/RRAGD/mTOR signaling in follicular lymphoma. Leukemia 3 39910284
2025 The Effect of Valine on the Synthesis of α-Casein in MAC-T Cells and the Expression and Phosphorylation of Genes Related to the mTOR Signaling Pathway. International journal of molecular sciences 3 40243924
2024 RRAGD variants cause cardiac dysfunction in a zebrafish model. American journal of physiology. Heart and circulatory physiology 3 39331021
2022 Identification of miRNA-mRNA-TF regulatory networks in peripheral blood mononuclear cells of type 1 diabetes. BMC endocrine disorders 3 35534828
2022 An approach combining bioinformatics and machine learning to identify eight autophagy-related biomarkers and construct molecular mechanisms underlying COVID-19 and major depressive disorders. European review for medical and pharmacological sciences 3 36394763
2025 Transcriptome remodeling and adaptive preservation of muscle protein content in hibernating black bears. bioRxiv : the preprint server for biology 2 40166218
2025 Customized extracellular vesicles targeting lysosomal biogenesis deliver therapeutic cargo for intervertebral disc degeneration treatment. Journal of nanobiotechnology 2 41076529
2026 Lysosome-localized IRTKS condensates promote mTORC1 activity leading to MASLD and HCC. Cell reports 1 41575860
2025 LINC00622 transcriptionally promotes RRAGD to repress mTORC1-modulated autophagic cell death by associating with BTF3 in cutaneous melanoma. Cell death & disease 1 40651979
2025 Suppression of mTOR Signaling by miR-302/367 Cluster in Breast Cancer Cells. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 1 40817797
2025 Novel RRAGD Variants in Autosomal Dominant Kidney Hypomagnesemia and Therapeutic Perspectives. Kidney international reports 1 41141537
2024 Exploration of the Regulatory Network of Programmed Cell Death Genes in Rheumatoid Arthritis Based on Blood-Derived circRNA Transcriptome Information and Single-Cell Multi-omics Data. Biochemical genetics 1 39656402
2026 Autophagic molecular network in IS pathogenesis: A multi-omics Mendelian randomization study. Medicine 0 41578456
2026 m6A RNA modification guides alternative polyadenylation to maintain T cell quiescence. Science advances 0 42127188
2025 Induction of lysosome biogenesis is a novel function of the CGAS-STING1 pathway. Autophagy 0 39835593
2025 Regenerative growth in Eriocheir sinensis is driven by Slc7a5-TORC1-regulated cell signaling. Developmental biology 0 40505941

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