{"gene":"ROGDI","run_date":"2026-06-10T06:43:37","timeline":{"discoveries":[{"year":2012,"finding":"Wild-type ROGDI localizes to the nuclear envelope; in cells of KTS-affected individuals homozygous for a nonsense mutation (p.Arg157*), ROGDI protein is not detectable, establishing loss of protein as the molecular consequence of this mutation.","method":"Immunofluorescence/immunodetection in patient-derived cells","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct localization experiment in patient cells, single lab, single method","pmids":["22482807"],"is_preprint":false},{"year":2017,"finding":"Crystal structure of human ROGDI was determined at atomic resolution, revealing a novel elongated curved structure comprising an α domain with a leucine-zipper-like four-helix bundle (N-terminal H1 helix paired antiparallel with C-terminal H6 helix) and a β-sheet domain. Disruption of the four-helix bundle by KTS-associated mutations results in significant destabilization of the structure, and the α domain is proposed to provide a platform for protein-protein interactions.","method":"X-ray crystallography with biochemical stability assays and mutagenesis","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — atomic-resolution crystal structure combined with biochemical mutagenesis data, single lab but multiple orthogonal methods","pmids":["28638151"],"is_preprint":false},{"year":2017,"finding":"Rogdi localizes to presynaptic sites in rat hippocampal neurons, colocalizing with presynaptic scaffolding protein Bassoon and synaptic vesicle markers Synaptophysin, Synapsin-1, VAMP2/Synaptobrevin, and Mover. Recombinant GFP-Rogdi expressed in cultured neurons was efficiently targeted to presynaptic sites, demonstrating that Rogdi harbors intrinsic presynaptic targeting signals.","method":"Immunofluorescence of endogenous Rogdi in rat hippocampal neurons and brain sections; live imaging of GFP-Rogdi in cultured neurons","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct localization with functional tagging, single lab, two complementary approaches","pmids":["29150638"],"is_preprint":false},{"year":2017,"finding":"Drosophila Rogdi acts as a sleep-promoting factor through supporting GABAergic transmission primarily via metabotropic GABA receptors upstream of wake-promoting dopaminergic pathways. Rogdi mutant flies show insomnia-like behavior rescued by sustaining GABAergic transmission or blocking dopaminergic pathways; transgenic rescue mapped the requirement to GABAergic neurons.","method":"Drosophila genetics: loss-of-function mutants, transgenic rescue, pharmacological manipulation (GABA receptor agonists), behavioral assays (sleep analysis)","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with pharmacological validation and cell-type-specific transgenic rescue, single lab","pmids":["28900300"],"is_preprint":false},{"year":2016,"finding":"Downregulation of ROGDI in cervical cancer cells led to decreased expression of CDK1, CDK2, cyclin A, and cyclin B, resulting in G2/M phase transition block and increased γ-H2AX activation, indicating ROGDI regulates cell cycle progression and DNA damage response.","method":"siRNA knockdown, flow cytometry cell cycle analysis, clonogenic survival assay, Western blot for CDKs/cyclins and γ-H2AX","journal":"Cancer biology & therapy","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — knockdown with multiple molecular readouts (cell cycle, DNA damage marker, survival), single lab","pmids":["27636029"],"is_preprint":false},{"year":2025,"finding":"ROGDI is a novel subunit of the mammalian Rabconnectin-3 complex (the functional equivalent of yeast RAVE) and acts as the Rav2 homolog. ROGDI shares extensive structural homology with yeast Rav2 and can functionally replace Rav2 in yeast. ROGDI binds to the N-terminal domains of both Rabconnectin-3α and Rabconnectin-3β, co-immunoprecipitates with Rabconnectin-3 subunits from mammalian cell lysates, and co-localizes with Rabconnectin-3α in acidic perinuclear lysosomes by immunofluorescence. ROGDI is present in immunopurified lysosomes of mammalian cells. Molecular modeling suggests ROGDI bridges the two Rabconnectin-3 subunits, placing it as a regulator of V-ATPase reassembly and organelle acidification.","method":"Yeast functional complementation, co-immunoprecipitation from mammalian cell lysates, lysosome immunopurification, immunofluorescence microscopy, molecular modeling","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (yeast complementation, Co-IP, organelle fractionation, localization, structural homology modeling) in a single rigorous study establishing a definitive mechanism","pmids":["40049412"],"is_preprint":false},{"year":2024,"finding":"Rogdi knockout mice lack cyclic dental acidification during enamel maturation, and transcriptomic analysis of postnatal day 5 incisors showed downregulated enamel matrix proteins (Enam, Amelx, Ambn) and expression changes in Wdr72, Slc9a3r2, and Atp6v0c — proteins that interact through the acidifying V-ATPase complex — suggesting ROGDI is required for V-ATPase-dependent tooth acidification.","method":"Rogdi knockout mouse model, scanning electron microscopy, RNA sequencing of postnatal incisors, behavioral and seizure testing","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo KO model with transcriptomic and ultrastructural readouts, single lab, multiple phenotypic and molecular endpoints","pmids":["38172607"],"is_preprint":false},{"year":2024,"finding":"In yeast aging, the level of Rav2 (the yeast ortholog of ROGDI/Rabconnectin-3 subunit) declines in aged cells, and Rav2 overexpression delays V-ATPase disassembly with age, preserving vacuolar pH homeostasis. Deletion of Rav1 (yeast ortholog of Rabconnectin-3α) shortens replicative lifespan, placing the RAVE complex upstream of V-ATPase assembly and lysosomal acidification in aging.","method":"Yeast replicative aging assays, vacuolar pH measurement, V-ATPase subunit fractionation, genetic deletion and overexpression","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 2 / Weak — yeast ortholog (Rav2) study, preprint, single lab; relevant to ROGDI mechanism but indirect via ortholog","pmids":[],"is_preprint":true}],"current_model":"ROGDI is a structural homolog of yeast Rav2 and functions as a novel subunit of the mammalian Rabconnectin-3 complex, where it bridges Rabconnectin-3α and Rabconnectin-3β at lysosomes to promote V-ATPase reassembly and organelle acidification; structurally, it forms an elongated α-helical/leucine-zipper-like four-helix bundle required for protein–protein interactions, and loss of function (via KTS-associated mutations) destabilizes this structure, abolishes tooth acidification, disrupts neuronal presynaptic function and GABAergic/dopaminergic signaling, and causes cell cycle dysregulation."},"narrative":{"mechanistic_narrative":"ROGDI is a regulator of V-ATPase-dependent organelle acidification that operates as a novel subunit of the mammalian Rabconnectin-3 complex, the functional equivalent of the yeast RAVE complex [PMID:40049412]. Acting as the structural and functional homolog of yeast Rav2, ROGDI can replace Rav2 in yeast and bridges the N-terminal domains of both Rabconnectin-3α and Rabconnectin-3β, co-immunoprecipitating with these subunits and co-localizing with Rabconnectin-3α in acidic perinuclear lysosomes [PMID:40049412]. Structurally, ROGDI is an elongated curved protein whose α domain forms a leucine-zipper-like four-helix bundle (N-terminal H1 paired antiparallel with C-terminal H6) that provides a platform for these protein–protein interactions; KTS-associated mutations disrupt this bundle and destabilize the protein [PMID:28638151]. ROGDI is required in vivo for V-ATPase-dependent tooth acidification, as Rogdi knockout mice lack cyclic dental acidification during enamel maturation and show altered expression of V-ATPase-associated factors and enamel matrix proteins [PMID:38172607]. In neurons, ROGDI localizes to presynaptic sites alongside scaffolding and synaptic vesicle proteins and harbors intrinsic presynaptic targeting signals [PMID:29150638], and in Drosophila it promotes sleep by supporting GABAergic transmission upstream of wake-promoting dopaminergic pathways [PMID:28900300]. Biallelic loss-of-function mutations in ROGDI cause Kohlschütter-Tönz syndrome, with a nonsense mutation (p.Arg157*) abolishing detectable protein [PMID:22482807]. A distinct role in cell cycle progression and the DNA damage response has been reported in cervical cancer cells, where ROGDI depletion reduces CDK/cyclin expression and arrests cells at G2/M [PMID:27636029].","teleology":[{"year":2012,"claim":"Established that ROGDI loss is the molecular cause of a recessive disease, linking the gene to a defined human phenotype before its biochemical function was known.","evidence":"Immunofluorescence/immunodetection in cells of KTS-affected individuals homozygous for p.Arg157*","pmids":["22482807"],"confidence":"Medium","gaps":["Nuclear envelope localization not reconciled with later lysosomal/presynaptic findings","No molecular function assigned","Single method in patient cells"]},{"year":2016,"claim":"Tested whether ROGDI influences proliferation, revealing a role in cell cycle progression and the DNA damage response distinct from its later-defined acidification function.","evidence":"siRNA knockdown in cervical cancer cells with flow cytometry, clonogenic assay, and Western blot for CDKs/cyclins and γ-H2AX","pmids":["27636029"],"confidence":"Medium","gaps":["Mechanism connecting ROGDI to CDK/cyclin expression unknown","Single cell-line context","Relationship to V-ATPase role unexplained"]},{"year":2017,"claim":"Determined the atomic structure of ROGDI, defining a leucine-zipper-like four-helix bundle as a protein-interaction platform and showing how disease mutations destabilize it.","evidence":"X-ray crystallography with biochemical stability assays and mutagenesis of KTS-associated variants","pmids":["28638151"],"confidence":"High","gaps":["Interaction partners bound by the platform not identified in this study","No structure of a ROGDI-containing complex"]},{"year":2017,"claim":"Located ROGDI to presynaptic terminals and demonstrated intrinsic targeting, framing a neuronal role consistent with the seizure phenotype of KTS.","evidence":"Immunofluorescence of endogenous Rogdi and live imaging of GFP-Rogdi in rat hippocampal neurons","pmids":["29150638"],"confidence":"Medium","gaps":["Presynaptic molecular function undefined","Targeting signal sequence not mapped","No interacting presynaptic partner shown biochemically"]},{"year":2017,"claim":"Placed Rogdi in a defined neural circuit by showing it promotes sleep through GABAergic transmission upstream of dopaminergic wake pathways.","evidence":"Drosophila loss-of-function, cell-type-specific transgenic rescue, pharmacological GABA manipulation, and sleep behavioral assays","pmids":["28900300"],"confidence":"Medium","gaps":["Molecular link between Rogdi and GABAergic signaling not established","Mammalian relevance of sleep phenotype untested"]},{"year":2024,"claim":"Connected ROGDI to V-ATPase-dependent acidification in vivo, explaining the dental phenotype of KTS through failed enamel acidification.","evidence":"Rogdi knockout mouse with SEM, RNA-seq of postnatal incisors, and seizure testing","pmids":["38172607"],"confidence":"Medium","gaps":["Direct V-ATPase interaction not demonstrated in this study","Transcriptomic changes are correlative","Tissue-specificity of acidification defect unexplored"]},{"year":2025,"claim":"Defined the biochemical function of ROGDI as the Rav2 homolog and a bridging subunit of the Rabconnectin-3/RAVE complex regulating V-ATPase reassembly and lysosomal acidification.","evidence":"Yeast functional complementation, Co-IP from mammalian lysates, lysosome immunopurification, immunofluorescence, and molecular modeling","pmids":["40049412"],"confidence":"High","gaps":["No experimental structure of the assembled ROGDI–Rabconnectin-3 complex","Bridging model is from modeling, not direct structure","Mechanism of V-ATPase reassembly regulation not kinetically characterized"]},{"year":2024,"claim":"Provided ortholog-based support that the RAVE/Rabconnectin-3 module sustains V-ATPase assembly and vacuolar pH during aging.","evidence":"Yeast replicative aging assays, vacuolar pH measurement, V-ATPase fractionation, and Rav1/Rav2 genetic manipulation (preprint)","pmids":[],"confidence":"Low","gaps":["Yeast ortholog study, not direct ROGDI evidence","Preprint, not peer-reviewed","Aging relevance of mammalian ROGDI untested"]},{"year":null,"claim":"How ROGDI's lysosomal V-ATPase function mechanistically connects to its reported presynaptic, GABAergic, and cell-cycle roles remains unresolved.","evidence":"No single study integrates the acidification, neuronal, and proliferative phenotypes","pmids":[],"confidence":"Low","gaps":["Unified mechanism across tissues lacking","Whether neuronal and cell-cycle phenotypes are downstream of acidification defects untested","No structure of ROGDI bound to Rabconnectin-3 subunits"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[5]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[5]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[2]},{"term_id":"GO:0005635","term_label":"nuclear envelope","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[5,6]}],"complexes":["Rabconnectin-3 complex (RAVE)"],"partners":["DMXL2","WDR7"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9GZN7","full_name":"Protein rogdi homolog","aliases":[],"length_aa":287,"mass_kda":32.3,"function":"","subcellular_location":"Nucleus envelope; Presynapse; Cell projection, axon; Perikaryon; Cell projection, dendrite; Cytoplasmic vesicle, secretory vesicle, synaptic vesicle","url":"https://www.uniprot.org/uniprotkb/Q9GZN7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ROGDI","classification":"Not Classified","n_dependent_lines":4,"n_total_lines":1208,"dependency_fraction":0.0033112582781456954},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ATP6V1B2","stoichiometry":0.2},{"gene":"ATP6V1E1","stoichiometry":0.2},{"gene":"ATP6V1F","stoichiometry":0.2},{"gene":"ATP6V1G1","stoichiometry":0.2},{"gene":"ATP6V1H","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/ROGDI","total_profiled":1310},"omim":[{"mim_id":"615905","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 25 WITH AMELOGENESIS IMPERFECTA; DEE25","url":"https://www.omim.org/entry/615905"},{"mim_id":"614574","title":"ROGDI ATYPICAL LEUCINE ZIPPER; ROGDI","url":"https://www.omim.org/entry/614574"},{"mim_id":"608305","title":"SOLUTE CARRIER FAMILY 13 (SODIUM-DEPENDENT CITRATE TRANSPORTER), MEMBER 5; SLC13A5","url":"https://www.omim.org/entry/608305"},{"mim_id":"226750","title":"KOHLSCHUTTER-TONZ SYNDROME; KTZS","url":"https://www.omim.org/entry/226750"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ROGDI"},"hgnc":{"alias_symbol":["FLJ22386","ROGD1","RAV2"],"prev_symbol":[]},"alphafold":{"accession":"Q9GZN7","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9GZN7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9GZN7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9GZN7-F1-predicted_aligned_error_v6.png","plddt_mean":89.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ROGDI","jax_strain_url":"https://www.jax.org/strain/search?query=ROGDI"},"sequence":{"accession":"Q9GZN7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9GZN7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9GZN7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9GZN7"}},"corpus_meta":[{"pmid":"20084269","id":"PMC_20084269","title":"Two plant viral suppressors of silencing require the ethylene-inducible host transcription factor RAV2 to block RNA 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Part A","url":"https://pubmed.ncbi.nlm.nih.gov/34939736","citation_count":9,"is_preprint":false},{"pmid":"27636029","id":"PMC_27636029","title":"Downregulation of a novel human gene, ROGDI, increases radiosensitivity in cervical cancer cells.","date":"2016","source":"Cancer biology & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/27636029","citation_count":9,"is_preprint":false},{"pmid":"31159208","id":"PMC_31159208","title":"Mutations in Both the Surface and Transmembrane Envelope Glycoproteins of the RAV-2 Subgroup B Avian Sarcoma and Leukosis Virus Are Required to Escape the Antiviral Effect of a Secreted Form of the TvbS3 Receptor †.","date":"2019","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/31159208","citation_count":9,"is_preprint":false},{"pmid":"28322011","id":"PMC_28322011","title":"FcRav2, a gene with a ROGDI domain involved in Fusarium head blight and crown rot on durum wheat caused by Fusarium culmorum.","date":"2017","source":"Molecular plant pathology","url":"https://pubmed.ncbi.nlm.nih.gov/28322011","citation_count":7,"is_preprint":false},{"pmid":"38172607","id":"PMC_38172607","title":"The Rogdi knockout mouse is a model for Kohlschütter-Tönz syndrome.","date":"2024","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/38172607","citation_count":5,"is_preprint":false},{"pmid":"40049412","id":"PMC_40049412","title":"The ROGDI protein mutated in Kohlschutter-Tonz syndrome is a novel subunit of the Rabconnectin-3 complex implicated in V-ATPase assembly.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40049412","citation_count":4,"is_preprint":false},{"pmid":"25284547","id":"PMC_25284547","title":"Kohlschütter-Tönz syndrome in siblings without ROGDI mutation.","date":"2014","source":"Oral health and dental management","url":"https://pubmed.ncbi.nlm.nih.gov/25284547","citation_count":4,"is_preprint":false},{"pmid":"37974187","id":"PMC_37974187","title":"Perampanel effectiveness in treating ROGDI-related Kohlschütter-Tönz syndrome: first reported case in China and literature review.","date":"2023","source":"BMC medical genomics","url":"https://pubmed.ncbi.nlm.nih.gov/37974187","citation_count":3,"is_preprint":false},{"pmid":"39445602","id":"PMC_39445602","title":"Nephrocalcinosis, distal renal tubular acidosis and skeletal abnormality in two siblings with ROGDI -related Kohlschütter-Tönz syndrome.","date":"2024","source":"Clinical dysmorphology","url":"https://pubmed.ncbi.nlm.nih.gov/39445602","citation_count":2,"is_preprint":false},{"pmid":"39993789","id":"PMC_39993789","title":"Transcript Long-Read Sequencing Unveils the Molecular Complexity of a Novel ROGDI Splicing Variant in a Tunisian Family With Kohlschütter-Tönz Syndrome.","date":"2025","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39993789","citation_count":1,"is_preprint":false},{"pmid":"41153423","id":"PMC_41153423","title":"ROGDI-Related Disorder Resulting from Disruption of Complex Interactive Neuro-Dental Developmental Networks: A Review and Description of the First Missense Variant.","date":"2025","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/41153423","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.11.18.25340532","title":"Common and rare variant genetic contributions in African Americans with autism","date":"2025-11-19","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.18.25340532","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.07.23.604825","title":"V-ATPase Disassembly at the Yeast Lysosome-Like Vacuole Is a Phenotypic Driver of Lysosome Dysfunction in Replicative Aging","date":"2024-07-25","source":"bioRxiv","url":"https://doi.org/10.1101/2024.07.23.604825","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12924,"output_tokens":2220,"usd":0.036036,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9374,"output_tokens":3038,"usd":0.06141,"stage2_stop_reason":"end_turn"},"total_usd":0.097446,"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\": 2012,\n      \"finding\": \"Wild-type ROGDI localizes to the nuclear envelope; in cells of KTS-affected individuals homozygous for a nonsense mutation (p.Arg157*), ROGDI protein is not detectable, establishing loss of protein as the molecular consequence of this mutation.\",\n      \"method\": \"Immunofluorescence/immunodetection in patient-derived cells\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct localization experiment in patient cells, single lab, single method\",\n      \"pmids\": [\"22482807\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structure of human ROGDI was determined at atomic resolution, revealing a novel elongated curved structure comprising an α domain with a leucine-zipper-like four-helix bundle (N-terminal H1 helix paired antiparallel with C-terminal H6 helix) and a β-sheet domain. Disruption of the four-helix bundle by KTS-associated mutations results in significant destabilization of the structure, and the α domain is proposed to provide a platform for protein-protein interactions.\",\n      \"method\": \"X-ray crystallography with biochemical stability assays and mutagenesis\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — atomic-resolution crystal structure combined with biochemical mutagenesis data, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"28638151\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Rogdi localizes to presynaptic sites in rat hippocampal neurons, colocalizing with presynaptic scaffolding protein Bassoon and synaptic vesicle markers Synaptophysin, Synapsin-1, VAMP2/Synaptobrevin, and Mover. Recombinant GFP-Rogdi expressed in cultured neurons was efficiently targeted to presynaptic sites, demonstrating that Rogdi harbors intrinsic presynaptic targeting signals.\",\n      \"method\": \"Immunofluorescence of endogenous Rogdi in rat hippocampal neurons and brain sections; live imaging of GFP-Rogdi in cultured neurons\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct localization with functional tagging, single lab, two complementary approaches\",\n      \"pmids\": [\"29150638\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Drosophila Rogdi acts as a sleep-promoting factor through supporting GABAergic transmission primarily via metabotropic GABA receptors upstream of wake-promoting dopaminergic pathways. Rogdi mutant flies show insomnia-like behavior rescued by sustaining GABAergic transmission or blocking dopaminergic pathways; transgenic rescue mapped the requirement to GABAergic neurons.\",\n      \"method\": \"Drosophila genetics: loss-of-function mutants, transgenic rescue, pharmacological manipulation (GABA receptor agonists), behavioral assays (sleep analysis)\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with pharmacological validation and cell-type-specific transgenic rescue, single lab\",\n      \"pmids\": [\"28900300\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Downregulation of ROGDI in cervical cancer cells led to decreased expression of CDK1, CDK2, cyclin A, and cyclin B, resulting in G2/M phase transition block and increased γ-H2AX activation, indicating ROGDI regulates cell cycle progression and DNA damage response.\",\n      \"method\": \"siRNA knockdown, flow cytometry cell cycle analysis, clonogenic survival assay, Western blot for CDKs/cyclins and γ-H2AX\",\n      \"journal\": \"Cancer biology & therapy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — knockdown with multiple molecular readouts (cell cycle, DNA damage marker, survival), single lab\",\n      \"pmids\": [\"27636029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ROGDI is a novel subunit of the mammalian Rabconnectin-3 complex (the functional equivalent of yeast RAVE) and acts as the Rav2 homolog. ROGDI shares extensive structural homology with yeast Rav2 and can functionally replace Rav2 in yeast. ROGDI binds to the N-terminal domains of both Rabconnectin-3α and Rabconnectin-3β, co-immunoprecipitates with Rabconnectin-3 subunits from mammalian cell lysates, and co-localizes with Rabconnectin-3α in acidic perinuclear lysosomes by immunofluorescence. ROGDI is present in immunopurified lysosomes of mammalian cells. Molecular modeling suggests ROGDI bridges the two Rabconnectin-3 subunits, placing it as a regulator of V-ATPase reassembly and organelle acidification.\",\n      \"method\": \"Yeast functional complementation, co-immunoprecipitation from mammalian cell lysates, lysosome immunopurification, immunofluorescence microscopy, molecular modeling\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (yeast complementation, Co-IP, organelle fractionation, localization, structural homology modeling) in a single rigorous study establishing a definitive mechanism\",\n      \"pmids\": [\"40049412\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Rogdi knockout mice lack cyclic dental acidification during enamel maturation, and transcriptomic analysis of postnatal day 5 incisors showed downregulated enamel matrix proteins (Enam, Amelx, Ambn) and expression changes in Wdr72, Slc9a3r2, and Atp6v0c — proteins that interact through the acidifying V-ATPase complex — suggesting ROGDI is required for V-ATPase-dependent tooth acidification.\",\n      \"method\": \"Rogdi knockout mouse model, scanning electron microscopy, RNA sequencing of postnatal incisors, behavioral and seizure testing\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo KO model with transcriptomic and ultrastructural readouts, single lab, multiple phenotypic and molecular endpoints\",\n      \"pmids\": [\"38172607\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In yeast aging, the level of Rav2 (the yeast ortholog of ROGDI/Rabconnectin-3 subunit) declines in aged cells, and Rav2 overexpression delays V-ATPase disassembly with age, preserving vacuolar pH homeostasis. Deletion of Rav1 (yeast ortholog of Rabconnectin-3α) shortens replicative lifespan, placing the RAVE complex upstream of V-ATPase assembly and lysosomal acidification in aging.\",\n      \"method\": \"Yeast replicative aging assays, vacuolar pH measurement, V-ATPase subunit fractionation, genetic deletion and overexpression\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 2 / Weak — yeast ortholog (Rav2) study, preprint, single lab; relevant to ROGDI mechanism but indirect via ortholog\",\n      \"pmids\": [],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"ROGDI is a structural homolog of yeast Rav2 and functions as a novel subunit of the mammalian Rabconnectin-3 complex, where it bridges Rabconnectin-3α and Rabconnectin-3β at lysosomes to promote V-ATPase reassembly and organelle acidification; structurally, it forms an elongated α-helical/leucine-zipper-like four-helix bundle required for protein–protein interactions, and loss of function (via KTS-associated mutations) destabilizes this structure, abolishes tooth acidification, disrupts neuronal presynaptic function and GABAergic/dopaminergic signaling, and causes cell cycle dysregulation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ROGDI is a regulator of V-ATPase-dependent organelle acidification that operates as a novel subunit of the mammalian Rabconnectin-3 complex, the functional equivalent of the yeast RAVE complex [#5]. Acting as the structural and functional homolog of yeast Rav2, ROGDI can replace Rav2 in yeast and bridges the N-terminal domains of both Rabconnectin-3\\u03b1 and Rabconnectin-3\\u03b2, co-immunoprecipitating with these subunits and co-localizing with Rabconnectin-3\\u03b1 in acidic perinuclear lysosomes [#5]. Structurally, ROGDI is an elongated curved protein whose \\u03b1 domain forms a leucine-zipper-like four-helix bundle (N-terminal H1 paired antiparallel with C-terminal H6) that provides a platform for these protein\\u2013protein interactions; KTS-associated mutations disrupt this bundle and destabilize the protein [#1]. ROGDI is required in vivo for V-ATPase-dependent tooth acidification, as Rogdi knockout mice lack cyclic dental acidification during enamel maturation and show altered expression of V-ATPase-associated factors and enamel matrix proteins [#6]. In neurons, ROGDI localizes to presynaptic sites alongside scaffolding and synaptic vesicle proteins and harbors intrinsic presynaptic targeting signals [#2], and in Drosophila it promotes sleep by supporting GABAergic transmission upstream of wake-promoting dopaminergic pathways [#3]. Biallelic loss-of-function mutations in ROGDI cause Kohlschütter-Tönz syndrome, with a nonsense mutation (p.Arg157*) abolishing detectable protein [#0]. A distinct role in cell cycle progression and the DNA damage response has been reported in cervical cancer cells, where ROGDI depletion reduces CDK/cyclin expression and arrests cells at G2/M [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Established that ROGDI loss is the molecular cause of a recessive disease, linking the gene to a defined human phenotype before its biochemical function was known.\",\n      \"evidence\": \"Immunofluorescence/immunodetection in cells of KTS-affected individuals homozygous for p.Arg157*\",\n      \"pmids\": [\"22482807\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Nuclear envelope localization not reconciled with later lysosomal/presynaptic findings\", \"No molecular function assigned\", \"Single method in patient cells\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Tested whether ROGDI influences proliferation, revealing a role in cell cycle progression and the DNA damage response distinct from its later-defined acidification function.\",\n      \"evidence\": \"siRNA knockdown in cervical cancer cells with flow cytometry, clonogenic assay, and Western blot for CDKs/cyclins and \\u03b3-H2AX\",\n      \"pmids\": [\"27636029\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting ROGDI to CDK/cyclin expression unknown\", \"Single cell-line context\", \"Relationship to V-ATPase role unexplained\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Determined the atomic structure of ROGDI, defining a leucine-zipper-like four-helix bundle as a protein-interaction platform and showing how disease mutations destabilize it.\",\n      \"evidence\": \"X-ray crystallography with biochemical stability assays and mutagenesis of KTS-associated variants\",\n      \"pmids\": [\"28638151\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Interaction partners bound by the platform not identified in this study\", \"No structure of a ROGDI-containing complex\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Located ROGDI to presynaptic terminals and demonstrated intrinsic targeting, framing a neuronal role consistent with the seizure phenotype of KTS.\",\n      \"evidence\": \"Immunofluorescence of endogenous Rogdi and live imaging of GFP-Rogdi in rat hippocampal neurons\",\n      \"pmids\": [\"29150638\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Presynaptic molecular function undefined\", \"Targeting signal sequence not mapped\", \"No interacting presynaptic partner shown biochemically\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Placed Rogdi in a defined neural circuit by showing it promotes sleep through GABAergic transmission upstream of dopaminergic wake pathways.\",\n      \"evidence\": \"Drosophila loss-of-function, cell-type-specific transgenic rescue, pharmacological GABA manipulation, and sleep behavioral assays\",\n      \"pmids\": [\"28900300\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular link between Rogdi and GABAergic signaling not established\", \"Mammalian relevance of sleep phenotype untested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connected ROGDI to V-ATPase-dependent acidification in vivo, explaining the dental phenotype of KTS through failed enamel acidification.\",\n      \"evidence\": \"Rogdi knockout mouse with SEM, RNA-seq of postnatal incisors, and seizure testing\",\n      \"pmids\": [\"38172607\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct V-ATPase interaction not demonstrated in this study\", \"Transcriptomic changes are correlative\", \"Tissue-specificity of acidification defect unexplored\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined the biochemical function of ROGDI as the Rav2 homolog and a bridging subunit of the Rabconnectin-3/RAVE complex regulating V-ATPase reassembly and lysosomal acidification.\",\n      \"evidence\": \"Yeast functional complementation, Co-IP from mammalian lysates, lysosome immunopurification, immunofluorescence, and molecular modeling\",\n      \"pmids\": [\"40049412\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No experimental structure of the assembled ROGDI\\u2013Rabconnectin-3 complex\", \"Bridging model is from modeling, not direct structure\", \"Mechanism of V-ATPase reassembly regulation not kinetically characterized\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided ortholog-based support that the RAVE/Rabconnectin-3 module sustains V-ATPase assembly and vacuolar pH during aging.\",\n      \"evidence\": \"Yeast replicative aging assays, vacuolar pH measurement, V-ATPase fractionation, and Rav1/Rav2 genetic manipulation (preprint)\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Yeast ortholog study, not direct ROGDI evidence\", \"Preprint, not peer-reviewed\", \"Aging relevance of mammalian ROGDI untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ROGDI's lysosomal V-ATPase function mechanistically connects to its reported presynaptic, GABAergic, and cell-cycle roles remains unresolved.\",\n      \"evidence\": \"No single study integrates the acidification, neuronal, and proliferative phenotypes\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Unified mechanism across tissues lacking\", \"Whether neuronal and cell-cycle phenotypes are downstream of acidification defects untested\", \"No structure of ROGDI bound to Rabconnectin-3 subunits\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005635\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [5, 6]}\n    ],\n    \"complexes\": [\n      \"Rabconnectin-3 complex (RAVE)\"\n    ],\n    \"partners\": [\n      \"DMXL2\",\n      \"WDR7\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":7,"faith_total":7,"faith_pct":100.0}}