{"gene":"ATP6V0A1","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":2021,"finding":"ATP6V0A1 encodes the a1-subunit of the V0 domain of V-ATPases and is essential for lysosomal acidification in neurons; missense variants (R741Q, A512P, N534D) significantly impair lysosomal acidification in cell lines, and homozygous mutant mice show lysosomal dysfunction with accumulated autophagosomes/lysosomes, reduced mTORC1 signaling, impaired synaptic connectivity, and lowered neurotransmitter contents of synaptic vesicles.","method":"Cell lines expressing missense mutants (lysosomal acidification assay), homozygous knock-in mice (Atp6v0a1R741Q, Atp6v0a1A512P) with brain histology, mTORC1 signaling assays, synaptic vesicle neurotransmitter quantification","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (acidification assay, in vivo mouse models, signaling assays, neurotransmitter quantification) in a single rigorous study with clear functional readouts","pmids":["33833240"],"is_preprint":false},{"year":2021,"finding":"The R740Q (equivalent to R741Q) mutation in ATP6V0A1 directly impairs acidification of the endolysosomal compartment, causing failure of lysosomal hydrolysis, autophagic dysfunction, and severe developmental defect in C. elegans.","method":"Endolysosomal acidification assays in patient-derived cells and C. elegans genetic model with autophagic flux readouts","journal":"Brain communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional acidification and autophagy assays in two systems (human cells and C. elegans), single lab","pmids":["34909687"],"is_preprint":false},{"year":2007,"finding":"The a1 isoform of the V-ATPase V0 domain (ATP6V0A1) localizes to both apical and basolateral membranes of intercalated cells in the nephron (both AE1- and pendrin-positive subtypes), and also to the proximal tubule, distinguishing it from the a2 and a3 isoforms which are restricted to the apical membrane.","method":"Immunolocalization in mouse kidney sections with isoform-specific antibodies co-stained with AE1 and pendrin markers; real-time PCR for expression levels","journal":"Cellular physiology and biochemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — immunolocalization with co-markers in kidney, single lab, no functional perturbation of ATP6V0A1 specifically","pmids":["17595521"],"is_preprint":false},{"year":2011,"finding":"A 3'-UTR variant (T+3246C, rs938671) in ATP6V0A1 creates a binding motif for miR-637; the C allele decreases ATP6V0A1 expression via differential miRNA regulation, alters vacuolar pH in chromaffin granules, and consequently impairs CHGA processing and reduces exocytotic secretion from the regulated pathway.","method":"Luciferase reporter assay with ATP6V0A1 3'-UTR, in vitro transcription/translation of full-length ATP6V0A1 mRNA, fluorescent CHGA/EGFP chimera to monitor granule pH (with bafilomycin A1), immunoblot and MALDI-MS of CHGA fragments, miR-637 precursor/antagomir co-transfection in PC12 cells","journal":"Circulation. Cardiovascular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (reporter, in vitro translation, pH imaging, miRNA manipulation) in a single lab study","pmids":["21558123"],"is_preprint":false},{"year":2022,"finding":"Atp6v0a1 is required for vesicle release and CGRP secretion in neurons; NGF upregulates CGRP in trigeminal ganglia through an Atp6v0a1-dependent vesicle release mechanism, as knockdown of Atp6v0a1 via shRNA reduces vesicle exocytosis (FM1-43 assay) and CGRP release (ELISA) in SH-SY5Y neurons.","method":"Lentiviral shRNA knockdown of Atp6v0a1 in TG in vivo and SH-SY5Y neurons in vitro; FM1-43 fluorescent dye vesicle release assay; ELISA for CGRP; immunostaining and FISH for gene/protein expression","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic knockdown with functional vesicle release and CGRP secretion assays, two experimental systems (in vivo and in vitro), single lab","pmids":["36232740"],"is_preprint":false},{"year":2024,"finding":"ATP6V0A1 facilitates cholesterol absorption in colorectal cancer cells through RABGEF1-dependent endosome maturation, leading to cholesterol accumulation in the ER and elevated 24-hydroxycholesterol (24-OHC) production; 24-OHC then upregulates TGF-β1 via LXR signaling, driving immunosuppression of memory CD8+ T cells via SMAD3 pathway activation.","method":"Genetic manipulation (knockdown/overexpression) of ATP6V0A1 in CRC cells; cholesterol trafficking assays; 24-OHC quantification; LXR reporter assays; TGF-β1 ELISA; co-culture with CD8+ T cells; SMAD3 pathway readouts; RABGEF1 interaction studies","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple functional assays establishing pathway position, single lab, mechanistic chain from endosome maturation to immune suppression","pmids":["38971819"],"is_preprint":false},{"year":2025,"finding":"ATP6V0A1 upregulation by cadmium promotes lysosomal acidification, which facilitates NCOA4-mediated ferritinophagy (FTH1 degradation), iron release, and subsequent ferroptosis in B cells; siRNA knockdown of ATP6V0A1 mitigates Cd2+-induced lysosomal acidification, FTH1 degradation, iron overload, and lipid peroxidation.","method":"siRNA knockdown of ATP6V0A1 in human Ramos B cells; LysoTracker and acridine orange staining for lysosomal acidification; flow cytometry (Ferro Orange) for Fe2+; NCOA4-FTH1 co-immunoprecipitation; autophagy/lysosome inhibitors (3-MA, CQ); in vivo transcriptomics from Cd2+-exposed mice","journal":"Free radical biology & medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic knockdown with multiple orthogonal functional readouts (pH, iron, lipid peroxidation, protein interaction), combining in vivo screening and in vitro validation, single lab","pmids":["41161393"],"is_preprint":false},{"year":2026,"finding":"Cadmium post-transcriptionally destabilizes ATP6V0A1 protein (without affecting mRNA) via both proteasomal and autophagy-lysosomal degradation pathways, impairing lysosomal acidification and blocking autophagic flux, leading to hepatic triglyceride accumulation; overexpression of ATP6V0A1 rescues lysosomal dysfunction, restores autophagic flux, and normalizes triglyceride levels.","method":"ATP6V0A1 knockdown and overexpression in hepatocytes; lysosomal pH probes; autophagic flux assays; proteasome and lysosome pathway inhibitors; mRNA vs. protein level comparison; serum metabolomics in multi-strain mouse models","journal":"Biochimica et biophysica acta. Molecular and cell biology of lipids","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic gain/loss of function with multiple orthogonal assays (pH, autophagic flux, lipid), single lab, in vivo and in vitro","pmids":["41722762"],"is_preprint":false},{"year":2026,"finding":"ATP6V0A1 directly binds ryanodine receptors (RYRs) at ER-lysosome contact sites, suppresses RYR-mediated Ca2+ release, and limits lysosomal secretion; disruption of the RYR:ATP6V0A1 interaction using a RYR-derived decoy peptide evokes RYR hyperactivity and stimulates lysosomal secretion, depleting the intracellular lysosomal pool and inhibiting autophagic flux in human iPSC-derived cortical neurons.","method":"Direct binding assay (RYR:ATP6V0A1 interaction); RYR-derived decoy protein fragment to disrupt interaction; lysosomal secretion assays; autophagic flux assays; Ca2+ release measurements in human iPSC-derived cortical neurons","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct protein interaction with functional perturbation via decoy peptide and multiple readouts in human iPSC neurons, single lab","pmids":["42087556"],"is_preprint":false}],"current_model":"ATP6V0A1 encodes the a1-subunit of the V0 domain of the vacuolar H+-ATPase (V-ATPase), functioning as the neuron-enriched proton-translocating component essential for lysosomal/endosomal acidification, autophagic flux, mTORC1 signaling, synaptic vesicle neurotransmitter loading, and CGRP-dependent vesicle exocytosis; it also directly binds ryanodine receptors (RYRs) at ER-lysosome contact sites to suppress RYR-mediated Ca2+ release and regulate lysosomal availability for autophagy, while pathogenic missense variants impair lysosomal acidification and cause developmental and epileptic encephalopathy in humans."},"narrative":{"mechanistic_narrative":"ATP6V0A1 encodes the a1-subunit of the V0 domain of the vacuolar H+-ATPase, the proton-translocating component that drives acidification of the endolysosomal compartment and is enriched in neurons [PMID:33833240]. Through this acidifying function it sustains lysosomal hydrolysis, autophagic flux, and mTORC1 signaling, and is required for proper neurotransmitter loading of synaptic vesicles and synaptic connectivity [PMID:33833240]. Loss of acidification capacity is the unifying consequence of perturbing ATP6V0A1: missense variants impair lysosomal acidification and cause a developmental and epileptic encephalopathy in humans, recapitulated in cell, mouse, and C. elegans models showing autophagic dysfunction and lysosomal accumulation [PMID:33833240, PMID:34909687]. The same acidification-dependent control of endolysosomal maturation and autophagy underlies its roles in diverse cell contexts, including RABGEF1-dependent endosome maturation and cholesterol trafficking [PMID:38971819], NCOA4-mediated ferritinophagy and ferroptosis [PMID:41161393], and hepatic autophagic flux governing triglyceride homeostasis [PMID:41722762]. Beyond pumping protons, ATP6V0A1 also acts at ER-lysosome contact sites, where it directly binds ryanodine receptors to suppress RYR-mediated Ca2+ release and restrain lysosomal secretion, preserving the intracellular lysosomal pool for autophagy [PMID:42087556]. It additionally controls secretory granule pH and the regulated exocytotic pathway, where altered expression impairs CHGA processing and CGRP-dependent vesicle release [PMID:21558123, PMID:36232740].","teleology":[{"year":2007,"claim":"Establishing where the a1 isoform resides distinguished it from other V-ATPase a-subunits and indicated a distinct, non-apical-restricted membrane role.","evidence":"Isoform-specific immunolocalization in mouse kidney with AE1/pendrin co-markers and expression qPCR","pmids":["17595521"],"confidence":"Medium","gaps":["No functional perturbation of ATP6V0A1 specifically","Localization established only in kidney epithelia, not neurons"]},{"year":2011,"claim":"Linking ATP6V0A1 dosage to granule pH connected the subunit to control of the regulated secretory pathway, beyond bulk lysosomal acidification.","evidence":"3'-UTR miR-637 reporter assays, granule pH imaging, and CHGA processing analysis in PC12 cells","pmids":["21558123"],"confidence":"Medium","gaps":["Mechanism tested via a single regulatory variant in one cell line","Does not address neuronal phenotypes"]},{"year":2021,"claim":"Demonstrating that pathogenic missense variants impair lysosomal acidification and produce neuronal dysfunction in vivo established ATP6V0A1 as the disease-causing acidifying subunit in neurons.","evidence":"Missense mutant acidification assays plus knock-in mouse models with mTORC1, synaptic, and neurotransmitter readouts; patient cells and C. elegans autophagy assays","pmids":["33833240","34909687"],"confidence":"High","gaps":["Structural basis of how specific residues impair proton transport not resolved","Mechanism linking acidification loss to seizure phenotype unspecified"]},{"year":2022,"claim":"Knockdown experiments tied ATP6V0A1 to vesicle exocytosis and CGRP secretion, extending its role to NGF-driven neuropeptide release.","evidence":"shRNA knockdown in trigeminal ganglia and SH-SY5Y neurons with FM1-43 vesicle release and CGRP ELISA","pmids":["36232740"],"confidence":"Medium","gaps":["Whether the effect is via acidification or another mechanism not separated","Single lab"]},{"year":2024,"claim":"Placing ATP6V0A1 upstream of RABGEF1-dependent endosome maturation connected its acidifying function to cholesterol trafficking and tumor immunosuppression.","evidence":"Gain/loss of function in colorectal cancer cells with cholesterol assays, 24-OHC quantification, LXR reporters, and CD8+ T cell co-culture","pmids":["38971819"],"confidence":"Medium","gaps":["Direct RABGEF1 binding versus functional dependence not fully disentangled","Single cancer-cell context"]},{"year":2025,"claim":"Cadmium-driven upregulation experiments showed ATP6V0A1-dependent acidification promotes ferritinophagy and ferroptosis, generalizing its lysosomal role to iron metabolism.","evidence":"siRNA knockdown in Ramos B cells with lysosomal pH, Fe2+ flow cytometry, NCOA4-FTH1 Co-IP, and in vivo transcriptomics","pmids":["41161393"],"confidence":"Medium","gaps":["Whether ATP6V0A1 directly regulates NCOA4-FTH1 or acts only via acidification unclear","Single lab"]},{"year":2026,"claim":"Showing cadmium destabilizes ATP6V0A1 protein and that overexpression rescues autophagic flux and triglyceride accumulation established it as a post-transcriptionally regulated node controlling hepatic autophagy.","evidence":"Knockdown/overexpression in hepatocytes with pH probes, autophagic flux assays, proteasome/lysosome inhibitors, and serum metabolomics in mice","pmids":["41722762"],"confidence":"Medium","gaps":["Identity of the degradation machinery targeting ATP6V0A1 not defined","Single lab"]},{"year":2026,"claim":"Identifying a direct ATP6V0A1-RYR interaction at ER-lysosome contacts revealed a proton-pumping-independent function regulating Ca2+ release and lysosomal secretion.","evidence":"Direct binding assay and RYR-derived decoy peptide disruption with Ca2+, lysosomal secretion, and autophagic flux readouts in human iPSC cortical neurons","pmids":["42087556"],"confidence":"Medium","gaps":["Binding interface and stoichiometry not mapped","Single Co-IP-type binding assay without reciprocal structural validation"]},{"year":null,"claim":"How the proton-pumping and RYR-binding/Ca2+-regulatory functions of ATP6V0A1 are coordinated, and which contributes to the human encephalopathy phenotype, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of the variant-affected residues","Relative contribution of pump versus contact-site function to disease unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[8]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[0,1,6,7]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[5]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[2]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[0,1,7]},{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[0]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[3,4]}],"complexes":["V-ATPase V0 domain"],"partners":["RYR1","RABGEF1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q93050","full_name":"V-type proton ATPase 116 kDa subunit a 1","aliases":["Clathrin-coated vesicle/synaptic vesicle proton pump 116 kDa subunit","Vacuolar adenosine triphosphatase subunit Ac116","Vacuolar proton pump subunit 1","Vacuolar proton translocating ATPase 116 kDa subunit a isoform 1"],"length_aa":837,"mass_kda":96.4,"function":"Subunit of the V0 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that transports protons across cellular membranes. V-ATPase is responsible for the acidification of various organelles, such as lysosomes, endosomes, the trans-Golgi network, and secretory granules, including synaptic vesicles (PubMed:33065002, PubMed:33833240, PubMed:34909687). In certain cell types, can be exported to the plasma membrane, where it is involved in the acidification of the extracellular environment (By similarity). Required for assembly and activity of the vacuolar ATPase (By similarity). Through its action on compartment acidification, plays an essential role in neuronal development in terms of integrity and connectivity of neurons (PubMed:33833240)","subcellular_location":"Cytoplasmic vesicle, clathrin-coated vesicle membrane; Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Melanosome","url":"https://www.uniprot.org/uniprotkb/Q93050/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ATP6V0A1","classification":"Not Classified","n_dependent_lines":61,"n_total_lines":1208,"dependency_fraction":0.050496688741721855},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000033627","cell_line_id":"CID001641","localizations":[{"compartment":"vesicles","grade":3}],"interactors":[{"gene":"ATP6AP1","stoichiometry":10.0},{"gene":"ATP6AP2","stoichiometry":10.0},{"gene":"ATP6V0D1","stoichiometry":10.0},{"gene":"ATP6V1B2","stoichiometry":10.0},{"gene":"ATP6V1G1","stoichiometry":10.0},{"gene":"ATP6V1A","stoichiometry":4.0},{"gene":"ARL8B","stoichiometry":0.2},{"gene":"VAMP3;VAMP2","stoichiometry":0.2},{"gene":"ATP6V1H","stoichiometry":0.2},{"gene":"ATP6V1D","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001641","total_profiled":1310},"omim":[{"mim_id":"620760","title":"MITOCHONDRIAL LACTATE DEHYDROGENASE REGULATOR; MLDHR","url":"https://www.omim.org/entry/620760"},{"mim_id":"619971","title":"NEURODEVELOPMENTAL DISORDER WITH EPILEPSY AND BRAIN ATROPHY; NEDEBA","url":"https://www.omim.org/entry/619971"},{"mim_id":"619970","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 104; DEE104","url":"https://www.omim.org/entry/619970"},{"mim_id":"617627","title":"SMALL REGULATORY POLYPEPTIDE OF AMINO ACID RESPONSE; SPAAR","url":"https://www.omim.org/entry/617627"},{"mim_id":"613413","title":"TRANSMEMBRANE PROTEIN 106B; TMEM106B","url":"https://www.omim.org/entry/613413"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Golgi apparatus","reliability":"Approved"},{"location":"Vesicles","reliability":"Approved"},{"location":"Nuclear speckles","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"brain","ntpm":98.9}],"url":"https://www.proteinatlas.org/search/ATP6V0A1"},"hgnc":{"alias_symbol":["a1","Vph1","Stv1"],"prev_symbol":["VPP1","ATP6N1","ATP6N1A"]},"alphafold":{"accession":"Q93050","domains":[{"cath_id":"-","chopping":"371-473_499-661_714-814","consensus_level":"medium","plddt":89.4722,"start":371,"end":814}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q93050","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q93050-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q93050-F1-predicted_aligned_error_v6.png","plddt_mean":84.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ATP6V0A1","jax_strain_url":"https://www.jax.org/strain/search?query=ATP6V0A1"},"sequence":{"accession":"Q93050","fasta_url":"https://rest.uniprot.org/uniprotkb/Q93050.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q93050/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q93050"}},"corpus_meta":[{"pmid":"33833240","id":"PMC_33833240","title":"ATP6V0A1 encoding the a1-subunit of the V0 domain of vacuolar H+-ATPases is essential for brain development in humans and mice.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33833240","citation_count":59,"is_preprint":false},{"pmid":"38971819","id":"PMC_38971819","title":"ATP6V0A1-dependent cholesterol absorption in colorectal cancer cells triggers immunosuppressive signaling to inactivate memory CD8+ T cells.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38971819","citation_count":39,"is_preprint":false},{"pmid":"29927621","id":"PMC_29927621","title":"Complete Genome of a Novel Lytic Vibrio parahaemolyticus Phage VPp1 and Characterization of Its Endolysin for Antibacterial Activities.","date":"2018","source":"Journal of food protection","url":"https://pubmed.ncbi.nlm.nih.gov/29927621","citation_count":27,"is_preprint":false},{"pmid":"34909687","id":"PMC_34909687","title":"Variants in ATP6V0A1 cause progressive myoclonus epilepsy and developmental and epileptic encephalopathy.","date":"2021","source":"Brain communications","url":"https://pubmed.ncbi.nlm.nih.gov/34909687","citation_count":25,"is_preprint":false},{"pmid":"21558123","id":"PMC_21558123","title":"A common genetic variant in the 3'-UTR of vacuolar H+-ATPase ATP6V0A1 creates a micro-RNA motif to alter chromogranin A processing and hypertension risk.","date":"2011","source":"Circulation. Cardiovascular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/21558123","citation_count":25,"is_preprint":false},{"pmid":"17595521","id":"PMC_17595521","title":"Differential localization of vacuolar H+-ATPases containing a1, a2, a3, or a4 (ATP6V0A1-4) subunit isoforms along the nephron.","date":"2007","source":"Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/17595521","citation_count":25,"is_preprint":false},{"pmid":"24440165","id":"PMC_24440165","title":"Application of the VPp1 bacteriophage combined with a coupled enzyme system in the rapid detection of Vibrio parahaemolyticus.","date":"2014","source":"Journal of microbiological methods","url":"https://pubmed.ncbi.nlm.nih.gov/24440165","citation_count":12,"is_preprint":false},{"pmid":"36232740","id":"PMC_36232740","title":"NGF-Induced Upregulation of CGRP in Orofacial Pain Induced by Tooth Movement Is Dependent on Atp6v0a1 and Vesicle Release.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36232740","citation_count":4,"is_preprint":false},{"pmid":"41161393","id":"PMC_41161393","title":"Cadmium induces ferroptosis in B cells via ATP6V0A1-upregulated lysosomal ferritinophagy: insights from murine transcriptomics and human cellular models.","date":"2025","source":"Free radical biology & medicine","url":"https://pubmed.ncbi.nlm.nih.gov/41161393","citation_count":2,"is_preprint":false},{"pmid":"38448027","id":"PMC_38448027","title":"[Clinical and genetic characteristics of a child with Developmental and epileptic encephalopathy 104 due to variant of ATP6V0A1 gene].","date":"2024","source":"Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/38448027","citation_count":0,"is_preprint":false},{"pmid":"42069687","id":"PMC_42069687","title":"Refractory focal seizures occurred in clusters in a girl with a de novo mutation of the ATP6V0A1 gene: a case report.","date":"2026","source":"Journal of medical case reports","url":"https://pubmed.ncbi.nlm.nih.gov/42069687","citation_count":0,"is_preprint":false},{"pmid":"41722762","id":"PMC_41722762","title":"Cadmium-induced ATP6V0A1 destabilization impairs lysosomal function to disrupt hepatic lipid homeostasis.","date":"2026","source":"Biochimica et biophysica acta. Molecular and cell biology of lipids","url":"https://pubmed.ncbi.nlm.nih.gov/41722762","citation_count":0,"is_preprint":false},{"pmid":"42087556","id":"PMC_42087556","title":"RYR:ATP6V0A1 complexes couple ER-lysosome contact sites to dynamic autophagy control.","date":"2026","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/42087556","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9348,"output_tokens":2866,"usd":0.035517,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10074,"output_tokens":3000,"usd":0.062685,"stage2_stop_reason":"end_turn"},"total_usd":0.098202,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2021,\n      \"finding\": \"ATP6V0A1 encodes the a1-subunit of the V0 domain of V-ATPases and is essential for lysosomal acidification in neurons; missense variants (R741Q, A512P, N534D) significantly impair lysosomal acidification in cell lines, and homozygous mutant mice show lysosomal dysfunction with accumulated autophagosomes/lysosomes, reduced mTORC1 signaling, impaired synaptic connectivity, and lowered neurotransmitter contents of synaptic vesicles.\",\n      \"method\": \"Cell lines expressing missense mutants (lysosomal acidification assay), homozygous knock-in mice (Atp6v0a1R741Q, Atp6v0a1A512P) with brain histology, mTORC1 signaling assays, synaptic vesicle neurotransmitter quantification\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (acidification assay, in vivo mouse models, signaling assays, neurotransmitter quantification) in a single rigorous study with clear functional readouts\",\n      \"pmids\": [\"33833240\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"The R740Q (equivalent to R741Q) mutation in ATP6V0A1 directly impairs acidification of the endolysosomal compartment, causing failure of lysosomal hydrolysis, autophagic dysfunction, and severe developmental defect in C. elegans.\",\n      \"method\": \"Endolysosomal acidification assays in patient-derived cells and C. elegans genetic model with autophagic flux readouts\",\n      \"journal\": \"Brain communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional acidification and autophagy assays in two systems (human cells and C. elegans), single lab\",\n      \"pmids\": [\"34909687\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"The a1 isoform of the V-ATPase V0 domain (ATP6V0A1) localizes to both apical and basolateral membranes of intercalated cells in the nephron (both AE1- and pendrin-positive subtypes), and also to the proximal tubule, distinguishing it from the a2 and a3 isoforms which are restricted to the apical membrane.\",\n      \"method\": \"Immunolocalization in mouse kidney sections with isoform-specific antibodies co-stained with AE1 and pendrin markers; real-time PCR for expression levels\",\n      \"journal\": \"Cellular physiology and biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — immunolocalization with co-markers in kidney, single lab, no functional perturbation of ATP6V0A1 specifically\",\n      \"pmids\": [\"17595521\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"A 3'-UTR variant (T+3246C, rs938671) in ATP6V0A1 creates a binding motif for miR-637; the C allele decreases ATP6V0A1 expression via differential miRNA regulation, alters vacuolar pH in chromaffin granules, and consequently impairs CHGA processing and reduces exocytotic secretion from the regulated pathway.\",\n      \"method\": \"Luciferase reporter assay with ATP6V0A1 3'-UTR, in vitro transcription/translation of full-length ATP6V0A1 mRNA, fluorescent CHGA/EGFP chimera to monitor granule pH (with bafilomycin A1), immunoblot and MALDI-MS of CHGA fragments, miR-637 precursor/antagomir co-transfection in PC12 cells\",\n      \"journal\": \"Circulation. Cardiovascular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (reporter, in vitro translation, pH imaging, miRNA manipulation) in a single lab study\",\n      \"pmids\": [\"21558123\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Atp6v0a1 is required for vesicle release and CGRP secretion in neurons; NGF upregulates CGRP in trigeminal ganglia through an Atp6v0a1-dependent vesicle release mechanism, as knockdown of Atp6v0a1 via shRNA reduces vesicle exocytosis (FM1-43 assay) and CGRP release (ELISA) in SH-SY5Y neurons.\",\n      \"method\": \"Lentiviral shRNA knockdown of Atp6v0a1 in TG in vivo and SH-SY5Y neurons in vitro; FM1-43 fluorescent dye vesicle release assay; ELISA for CGRP; immunostaining and FISH for gene/protein expression\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic knockdown with functional vesicle release and CGRP secretion assays, two experimental systems (in vivo and in vitro), single lab\",\n      \"pmids\": [\"36232740\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ATP6V0A1 facilitates cholesterol absorption in colorectal cancer cells through RABGEF1-dependent endosome maturation, leading to cholesterol accumulation in the ER and elevated 24-hydroxycholesterol (24-OHC) production; 24-OHC then upregulates TGF-β1 via LXR signaling, driving immunosuppression of memory CD8+ T cells via SMAD3 pathway activation.\",\n      \"method\": \"Genetic manipulation (knockdown/overexpression) of ATP6V0A1 in CRC cells; cholesterol trafficking assays; 24-OHC quantification; LXR reporter assays; TGF-β1 ELISA; co-culture with CD8+ T cells; SMAD3 pathway readouts; RABGEF1 interaction studies\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple functional assays establishing pathway position, single lab, mechanistic chain from endosome maturation to immune suppression\",\n      \"pmids\": [\"38971819\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ATP6V0A1 upregulation by cadmium promotes lysosomal acidification, which facilitates NCOA4-mediated ferritinophagy (FTH1 degradation), iron release, and subsequent ferroptosis in B cells; siRNA knockdown of ATP6V0A1 mitigates Cd2+-induced lysosomal acidification, FTH1 degradation, iron overload, and lipid peroxidation.\",\n      \"method\": \"siRNA knockdown of ATP6V0A1 in human Ramos B cells; LysoTracker and acridine orange staining for lysosomal acidification; flow cytometry (Ferro Orange) for Fe2+; NCOA4-FTH1 co-immunoprecipitation; autophagy/lysosome inhibitors (3-MA, CQ); in vivo transcriptomics from Cd2+-exposed mice\",\n      \"journal\": \"Free radical biology & medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic knockdown with multiple orthogonal functional readouts (pH, iron, lipid peroxidation, protein interaction), combining in vivo screening and in vitro validation, single lab\",\n      \"pmids\": [\"41161393\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Cadmium post-transcriptionally destabilizes ATP6V0A1 protein (without affecting mRNA) via both proteasomal and autophagy-lysosomal degradation pathways, impairing lysosomal acidification and blocking autophagic flux, leading to hepatic triglyceride accumulation; overexpression of ATP6V0A1 rescues lysosomal dysfunction, restores autophagic flux, and normalizes triglyceride levels.\",\n      \"method\": \"ATP6V0A1 knockdown and overexpression in hepatocytes; lysosomal pH probes; autophagic flux assays; proteasome and lysosome pathway inhibitors; mRNA vs. protein level comparison; serum metabolomics in multi-strain mouse models\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular and cell biology of lipids\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic gain/loss of function with multiple orthogonal assays (pH, autophagic flux, lipid), single lab, in vivo and in vitro\",\n      \"pmids\": [\"41722762\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ATP6V0A1 directly binds ryanodine receptors (RYRs) at ER-lysosome contact sites, suppresses RYR-mediated Ca2+ release, and limits lysosomal secretion; disruption of the RYR:ATP6V0A1 interaction using a RYR-derived decoy peptide evokes RYR hyperactivity and stimulates lysosomal secretion, depleting the intracellular lysosomal pool and inhibiting autophagic flux in human iPSC-derived cortical neurons.\",\n      \"method\": \"Direct binding assay (RYR:ATP6V0A1 interaction); RYR-derived decoy protein fragment to disrupt interaction; lysosomal secretion assays; autophagic flux assays; Ca2+ release measurements in human iPSC-derived cortical neurons\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct protein interaction with functional perturbation via decoy peptide and multiple readouts in human iPSC neurons, single lab\",\n      \"pmids\": [\"42087556\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ATP6V0A1 encodes the a1-subunit of the V0 domain of the vacuolar H+-ATPase (V-ATPase), functioning as the neuron-enriched proton-translocating component essential for lysosomal/endosomal acidification, autophagic flux, mTORC1 signaling, synaptic vesicle neurotransmitter loading, and CGRP-dependent vesicle exocytosis; it also directly binds ryanodine receptors (RYRs) at ER-lysosome contact sites to suppress RYR-mediated Ca2+ release and regulate lysosomal availability for autophagy, while pathogenic missense variants impair lysosomal acidification and cause developmental and epileptic encephalopathy in humans.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ATP6V0A1 encodes the a1-subunit of the V0 domain of the vacuolar H+-ATPase, the proton-translocating component that drives acidification of the endolysosomal compartment and is enriched in neurons [#0]. Through this acidifying function it sustains lysosomal hydrolysis, autophagic flux, and mTORC1 signaling, and is required for proper neurotransmitter loading of synaptic vesicles and synaptic connectivity [#0]. Loss of acidification capacity is the unifying consequence of perturbing ATP6V0A1: missense variants impair lysosomal acidification and cause a developmental and epileptic encephalopathy in humans, recapitulated in cell, mouse, and C. elegans models showing autophagic dysfunction and lysosomal accumulation [#0, #1]. The same acidification-dependent control of endolysosomal maturation and autophagy underlies its roles in diverse cell contexts, including RABGEF1-dependent endosome maturation and cholesterol trafficking [#5], NCOA4-mediated ferritinophagy and ferroptosis [#6], and hepatic autophagic flux governing triglyceride homeostasis [#7]. Beyond pumping protons, ATP6V0A1 also acts at ER-lysosome contact sites, where it directly binds ryanodine receptors to suppress RYR-mediated Ca2+ release and restrain lysosomal secretion, preserving the intracellular lysosomal pool for autophagy [#8]. It additionally controls secretory granule pH and the regulated exocytotic pathway, where altered expression impairs CHGA processing and CGRP-dependent vesicle release [#3, #4].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Establishing where the a1 isoform resides distinguished it from other V-ATPase a-subunits and indicated a distinct, non-apical-restricted membrane role.\",\n      \"evidence\": \"Isoform-specific immunolocalization in mouse kidney with AE1/pendrin co-markers and expression qPCR\",\n      \"pmids\": [\"17595521\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional perturbation of ATP6V0A1 specifically\", \"Localization established only in kidney epithelia, not neurons\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Linking ATP6V0A1 dosage to granule pH connected the subunit to control of the regulated secretory pathway, beyond bulk lysosomal acidification.\",\n      \"evidence\": \"3'-UTR miR-637 reporter assays, granule pH imaging, and CHGA processing analysis in PC12 cells\",\n      \"pmids\": [\"21558123\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism tested via a single regulatory variant in one cell line\", \"Does not address neuronal phenotypes\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Demonstrating that pathogenic missense variants impair lysosomal acidification and produce neuronal dysfunction in vivo established ATP6V0A1 as the disease-causing acidifying subunit in neurons.\",\n      \"evidence\": \"Missense mutant acidification assays plus knock-in mouse models with mTORC1, synaptic, and neurotransmitter readouts; patient cells and C. elegans autophagy assays\",\n      \"pmids\": [\"33833240\", \"34909687\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of how specific residues impair proton transport not resolved\", \"Mechanism linking acidification loss to seizure phenotype unspecified\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Knockdown experiments tied ATP6V0A1 to vesicle exocytosis and CGRP secretion, extending its role to NGF-driven neuropeptide release.\",\n      \"evidence\": \"shRNA knockdown in trigeminal ganglia and SH-SY5Y neurons with FM1-43 vesicle release and CGRP ELISA\",\n      \"pmids\": [\"36232740\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the effect is via acidification or another mechanism not separated\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placing ATP6V0A1 upstream of RABGEF1-dependent endosome maturation connected its acidifying function to cholesterol trafficking and tumor immunosuppression.\",\n      \"evidence\": \"Gain/loss of function in colorectal cancer cells with cholesterol assays, 24-OHC quantification, LXR reporters, and CD8+ T cell co-culture\",\n      \"pmids\": [\"38971819\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct RABGEF1 binding versus functional dependence not fully disentangled\", \"Single cancer-cell context\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Cadmium-driven upregulation experiments showed ATP6V0A1-dependent acidification promotes ferritinophagy and ferroptosis, generalizing its lysosomal role to iron metabolism.\",\n      \"evidence\": \"siRNA knockdown in Ramos B cells with lysosomal pH, Fe2+ flow cytometry, NCOA4-FTH1 Co-IP, and in vivo transcriptomics\",\n      \"pmids\": [\"41161393\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ATP6V0A1 directly regulates NCOA4-FTH1 or acts only via acidification unclear\", \"Single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Showing cadmium destabilizes ATP6V0A1 protein and that overexpression rescues autophagic flux and triglyceride accumulation established it as a post-transcriptionally regulated node controlling hepatic autophagy.\",\n      \"evidence\": \"Knockdown/overexpression in hepatocytes with pH probes, autophagic flux assays, proteasome/lysosome inhibitors, and serum metabolomics in mice\",\n      \"pmids\": [\"41722762\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Identity of the degradation machinery targeting ATP6V0A1 not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identifying a direct ATP6V0A1-RYR interaction at ER-lysosome contacts revealed a proton-pumping-independent function regulating Ca2+ release and lysosomal secretion.\",\n      \"evidence\": \"Direct binding assay and RYR-derived decoy peptide disruption with Ca2+, lysosomal secretion, and autophagic flux readouts in human iPSC cortical neurons\",\n      \"pmids\": [\"42087556\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding interface and stoichiometry not mapped\", \"Single Co-IP-type binding assay without reciprocal structural validation\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the proton-pumping and RYR-binding/Ca2+-regulatory functions of ATP6V0A1 are coordinated, and which contributes to the human encephalopathy phenotype, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of the variant-affected residues\", \"Relative contribution of pump versus contact-site function to disease unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [0, 1, 6, 7]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [0, 1, 7]},\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"complexes\": [\"V-ATPase V0 domain\"],\n    \"partners\": [\"RYR1\", \"RABGEF1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}