{"gene":"ATP6V1A","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":1990,"finding":"The VMA1 gene encodes the catalytic subunit (subunit A) of the yeast vacuolar membrane H+-ATPase; the gene product contains the ATP hydrolysis active site and undergoes a novel post-translational processing reaction in which an internal domain of 454 amino acids is autocatalytically excised and the flanking N- and C-terminal regions are ligated to produce the mature 69-kDa subunit.","method":"Gene cloning, nucleotide sequencing, N-terminal peptide sequencing of tryptic fragments, Northern blotting, domain homology analysis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — primary gene isolation with sequence, peptide mapping, and functional inference; foundational paper replicated across organisms","pmids":["2139027"],"is_preprint":false},{"year":1992,"finding":"Cysteine residues at positions 284 and 738 of the VMA1 precursor are essential for protein splicing: Cys284Ser mutation blocks cleavage at the N-terminal junction site, while Cys738Ser blocks processing at both junction sites, causing accumulation of nonfunctional fragments and loss of V-ATPase function.","method":"Site-directed mutagenesis of VMA1 at splice junction cysteines; expression in vma1-null yeast; analysis of protein products by SDS-PAGE","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 / Strong — active-site mutagenesis with functional readout in null background, establishing catalytic mechanism of protein splicing","pmids":["1417861"],"is_preprint":false},{"year":1996,"finding":"Protein splicing of the yeast Vma1 protozyme is a folding-dependent, intramolecular autocatalytic reaction occurring at optimal pH 7; denatured precursor molecules can be refolded in vitro to reconstitute the splicing reaction, and it is not inhibited by protease inhibitors.","method":"In vitro protein splicing assay using purified refolded precursor peptides expressed in E. coli; pH titration; protease inhibitor panel","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstituted in vitro protein splicing with purified components and multiple orthogonal controls (pH, inhibitors, solubility)","pmids":["8651930","9276458"],"is_preprint":false},{"year":1997,"finding":"Random mutagenesis of the entire VMA1-derived endonuclease (VDE/intein) sequence identified three core regions essential for protein splicing: the N- and C-terminal splice junctions and the N-terminal one-third of VDE. His362 is essential for the first cleavage at the N-terminal junction, and His736 assists the second cleavage via Asn cyclization at the C-terminal junction.","method":"PCR-based random mutagenesis; bacterial expression screen for splicing-defective mutants; yeast functional analysis; mapping of mutant proteins by SDS-PAGE","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — systematic mutagenesis across entire intein sequence with functional readout in two expression systems; identifies catalytic residues","pmids":["9188457"],"is_preprint":false},{"year":1997,"finding":"A conserved hydrophobic valine triplet upstream of the C-terminal splicing junction genetically interacts with three hydrophobic residues upstream of the N-terminal splicing junction, indicating that the N-terminal portion of the V-ATPase A subunit participates structurally in protein splicing via parallel beta-strand alignment.","method":"Random mutagenesis of valine triplet; intragenic suppressor analysis; genetic epistasis in yeast","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with intragenic suppressor analysis; single lab but multiple mutant alleles tested","pmids":["9286669"],"is_preprint":false},{"year":2002,"finding":"Crystal structure at 2.1 Å of the VMA1-derived endonuclease (VDE) precursor bearing N- and C-extein polypeptides revealed the mechanism of protein splicing: the Cys284 Sγ atom nucleophilically attacks the Gly283 carbonyl carbon forming a thiazolidine tetrahedral intermediate (N→S acyl shift) at the N-terminal junction, followed by transesterification at the C-terminal junction mediated by Ser738.","method":"X-ray crystallography at 2.1 Å resolution of spliceable precursor recombinant with C284S/H362N/N737S/C738S replacements bearing N- and C-extein residues","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution crystal structure with defined reaction intermediates and mutagenesis validation; mechanistic details independently confirmed in follow-up paper","pmids":["11884132","14646148"],"is_preprint":false},{"year":2007,"finding":"Morpholino knockdown of atp6v1a (V-ATPase subunit A) in zebrafish embryos suppressed acid secretion from skin H+-pump-rich cells, caused loss of internal Ca2+ and Na+, growth retardation, and trunk deformation, establishing ATP6V1A as required for embryonic acid secretion and ion balance in vivo.","method":"Morpholino-mediated antisense knockdown in zebrafish embryos; pH-sensitive fluorescent dye measurement of acid secretion; ion content analysis","journal":"American journal of physiology. Regulatory, integrative and comparative physiology","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo loss-of-function with quantitative functional readouts (acid secretion, ion balance) in a vertebrate model","pmids":["17272665"],"is_preprint":false},{"year":2013,"finding":"AMPK directly phosphorylates the V-ATPase A subunit (ATP6V1A) at Ser-384; this phosphorylation inhibits V-ATPase-dependent H+ secretion in kidney intercalated cells and causes cytoplasmic redistribution of the V-ATPase, coupling V-ATPase activity to cellular metabolic status.","method":"Mass spectrometry identification of AMPK phosphorylation site; in vitro kinase assay comparing WT and S384A mutant A-subunit; AICAR treatment of isolated perfused collecting ducts; extracellular acidification assay in HEK-293 cells expressing S384A mutant; immunofluorescence of V-ATPase localization","journal":"American journal of physiology. Renal physiology","confidence":"High","confidence_rationale":"Tier 1 / Strong — mass spectrometry site identification, in vitro kinase assay, phosphorylation-deficient mutant rescue, functional pH secretion assay, and localization experiment; multiple orthogonal methods","pmids":["23863464"],"is_preprint":false},{"year":2017,"finding":"Biallelic missense mutations in ATP6V1A (encoding V-ATPase subunit A) disrupt either the assembly or stability of the V-ATPase complex (shown by complexome profiling), impair vesicular trafficking (delayed retrograde Brefeldin A transport, Golgi fragmentation), and cause autosomal-recessive cutis laxa with elastic fiber and collagen fiber abnormalities.","method":"Whole-exome sequencing; complexome profiling (blue-native gel electrophoresis + LC-MS/MS); Brefeldin A retrograde transport assay; transmission electron microscopy of dermis; structural modeling","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — complexome profiling directly measured V-ATPase complex assembly defects; multiple orthogonal functional assays (trafficking, ultrastructure); replicated across five families","pmids":["28065471"],"is_preprint":false},{"year":2017,"finding":"The transcription factor YY1 directly binds three sites in the ATP6V1A core promoter and transcriptionally activates ATP6V1A expression; RNAi-mediated knockdown of YY1 in gastric cancer cells significantly decreased ATP6V1A mRNA and protein levels.","method":"Promoter analysis; RNAi knockdown of YY1; YY1 overexpression; quantitative RT-PCR and western blotting of ATP6V1A","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — promoter binding sites identified and functional knockdown/overexpression performed; single lab, two orthogonal approaches","pmids":["28592880"],"is_preprint":false},{"year":2018,"finding":"De novo heterozygous mutations in ATP6V1A cause developmental encephalopathy with epilepsy through distinct mechanisms: p.Asp100Tyr causes reduced ATP6V1A expression via increased protein degradation and decreased lysosomal markers (loss of function), while p.Asp349Asn causes gain-of-function with increased proton pumping in intracellular organelles. Both mutations decrease V-ATPase recruitment to autophagosomes and impair neurite elongation with loss of excitatory inputs in hippocampal neurons.","method":"Overexpression in HEK293T cells; LysoTracker and LysoSensor fluorescence; LAMP1/EEA1 immunoblotting; protein degradation assays; rat hippocampal neuron transfection; immunofluorescence; structural modeling on prokaryotic/eukaryotic V-ATPase structures","journal":"Brain : a journal of neurology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal assays in multiple cell types (HEK293T, patient lymphoblasts, primary neurons) establishing gain- vs. loss-of-function distinction","pmids":["29668857"],"is_preprint":false},{"year":2019,"finding":"αB-crystallin interacts directly with ATP6V1A (the V1-domain A subunit) and mTORC1 in a trimeric complex in lens epithelial cells; mTORC1 phosphorylates ATP6V1A at S441, promoting its association with αB-crystallin; this complex stabilizes ATP6V1A against proteasomal degradation and maintains lysosomal acidification. HSF4 deficiency reduces αB-crystallin expression, leading to increased ubiquitination and proteasomal degradation of ATP6V1A and elevated lysosomal pH.","method":"GST pull-down assays; co-immunoprecipitation; lysosome fractionation by ultracentrifugation; rapamycin/siRNA inhibition of mTORC1; S441A phospho-mutant of ATP6V1A; immunoblotting; zebrafish HSF4-deficiency model","journal":"Biochimica et biophysica acta. General subjects","confidence":"High","confidence_rationale":"Tier 2 / Strong — GST pull-down, co-IP, phospho-mutant, mTOR inhibition, in vivo zebrafish model; multiple orthogonal methods establishing the complex and its functional consequence","pmids":["31786107"],"is_preprint":false},{"year":2020,"finding":"ATP6V1A physically interacts with the rabies virus matrix protein (M) via the middle domain of ATP6V1A (dependent on residues K256 and E279 of M); this interaction facilitates dissociation of incoming viral M proteins during virion uncoating in endosomes, thereby promoting RABV replication.","method":"Proteomic interactome mapping; co-immunoprecipitation; domain mapping with full-length and truncation constructs; shRNA knockdown and overexpression of ATP6V1A in HEK293T and Vero cells; viral growth assays; trans-complementation rescue","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP with domain mapping, loss-of-function knockdown, gain-of-function overexpression, and trans-complementation rescue; multiple orthogonal methods","pmids":["33208464"],"is_preprint":false},{"year":2022,"finding":"In patients with ATP6V1A encephalopathy, fibroblasts with severe DEE-causing variants show decreased LAMP1 expression, reduced Lysotracker staining, and increased organelle pH (consistent with lysosomal impairment/loss of V-ATPase function), whereas fibroblasts with milder disease variants show increased Lysotracker staining and decreased organelle pH; iPSC-derived neurons from DEE patients show significantly smaller lysosomes with electron-dense inclusions, lipid droplets, and lamellated membrane structures.","method":"Lysotracker and LysoSensor staining; LAMP1 immunoblotting; transmission electron microscopy of fibroblasts and iPSC-derived neurons; lysosomal substrate quantification","journal":"Brain : a journal of neurology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple patient-derived cell types, orthogonal methods (fluorescent probes, TEM, protein quantification), replicated across multiple families","pmids":["35675510"],"is_preprint":false},{"year":2023,"finding":"HIF-1α directly downregulates ATP6V1A expression under hypoxia in HNSCC cells, which impairs lysosomal homeostasis and reduces fusion of multivesicular bodies with lysosomes, redirecting intraluminal vesicles to be secreted as extracellular vesicles.","method":"HIF-1α ChIP/transcriptional reporter assays; ATP6V1A knockdown and overexpression; lysosomal degradation assays; extracellular vesicle quantification; nanoparticle tracking analysis","journal":"Journal of extracellular vesicles","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct HIF-1α regulation demonstrated with functional EV secretion readout; single lab with multiple complementary approaches","pmids":["36748335"],"is_preprint":false},{"year":2024,"finding":"Depletion of Atp6v1a in murine hippocampal neurons impairs lysosomal pH regulation and autophagy progression, leading to accumulation of aberrant lysosomes at the neuronal soma and enlarged vacuoles at synaptic boutons; this causes defects in neurite elongation, stabilization of excitatory synapses, and prevention of synaptic rearrangement upon plasticity induction.","method":"shRNA knockdown of Atp6v1a in primary murine hippocampal neurons; immunoimaging; electrophysiological recordings; electron microscopy; lysosomal pH assays; autophagy flux assays","journal":"Acta physiologica (Oxford, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function in primary neurons with multiple orthogonal readouts (electrophysiology, EM, live imaging, pH assays) establishing pathway from lysosomal dysfunction to synaptic phenotype","pmids":["38837572"],"is_preprint":false},{"year":2025,"finding":"GPNMB interacts with ATP6V1A in lysosomes to facilitate microglial phagocytosis: GPNMB-deficient microglia show defects in both phagocytic engulfment and lysosomal degradation, and activating ATP6V1A rescues the phagocytosis impairment caused by GPNMB deficiency.","method":"Co-immunoprecipitation of GPNMB with ATP6V1A; genetic ablation of GPNMB in mice; pharmacological activation of ATP6V1A; phagocytosis assays with neuronal debris and β-amyloid; lysosomal degradation assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP with functional rescue by ATP6V1A activation; single lab with in vivo and in vitro evidence","pmids":["39992792"],"is_preprint":false},{"year":2026,"finding":"CISH (induced by AHR) promotes ubiquitination and degradation of ATP6V1A, disrupting lysosomal acidification and causing mtDNA release via the cGAS-STING pathway in decidual macrophages; this identifies ATP6V1A protein stability as regulated by the AHR/CISH ubiquitin-proteasome axis.","method":"Co-immunoprecipitation; ubiquitination assays; AHR chromatin immunoprecipitation at CISH promoter; siRNA knockdown; lysosomal pH measurement; mtDNA quantification; mouse pregnancy model","journal":"International journal of biological sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ubiquitination assay and co-IP with in vivo mouse model; single lab, multiple complementary methods","pmids":["41522347"],"is_preprint":false}],"current_model":"ATP6V1A encodes the catalytic A subunit of the vacuolar-type H+-ATPase (V-ATPase) V1 domain, which hydrolyzes ATP to drive proton pumping into lysosomes, endosomes, and other acidic compartments; its activity is directly regulated by AMPK-mediated phosphorylation at Ser-384 (inhibitory), mTORC1-promoted association with αB-crystallin (stabilizing), and ubiquitin-proteasome degradation driven by CISH or HSF4-αB-crystallin loss, while its proper assembly within the V-ATPase complex is essential for lysosomal pH homeostasis, vesicular trafficking, autophagy flux, synaptic plasticity in neurons, acid secretion in kidney and zebrafish epithelia, and microglial phagocytosis, with disease-causing mutations acting through either gain-of-function (excess proton pumping) or loss-of-function (reduced V-ATPase assembly/activity) mechanisms."},"narrative":{"mechanistic_narrative":"ATP6V1A encodes the catalytic A subunit of the vacuolar-type H+-ATPase (V-ATPase) V1 domain, the ATP-hydrolyzing engine that drives proton pumping to acidify lysosomes, endosomes, and other intracellular compartments and to mediate extracellular acid secretion [PMID:2139027, PMID:17272665]. In yeast, the founding ortholog VMA1 was shown to harbor the ATP hydrolysis active site and to mature through an autocatalytic protein-splicing reaction in which an internal ~454-residue intein is excised and the flanking exteins are ligated to yield the active subunit; this splicing depends on junction cysteines and conserved histidines and proceeds via an N→S acyl shift forming a thiazolidine intermediate [PMID:2139027, PMID:1417861, PMID:9188457, PMID:11884132, PMID:14646148]. Proper incorporation of the A subunit into the V-ATPase holoenzyme is required for lysosomal pH homeostasis, vesicular trafficking, and autophagy flux: biallelic missense mutations impair complex assembly/stability and retrograde trafficking and cause autosomal-recessive cutis laxa [PMID:28065471], while de novo heterozygous mutations cause developmental encephalopathy with epilepsy through either loss-of-function (reduced expression via increased degradation, elevated lysosomal pH) or gain-of-function (excess organellar proton pumping), both impairing autophagosomal V-ATPase recruitment, neurite elongation, and excitatory synaptic input [PMID:29668857, PMID:35675510]. Consistent with this, neuronal Atp6v1a depletion disrupts lysosomal acidification and autophagy, producing aberrant somatic lysosomes and synaptic defects in plasticity [PMID:38837572]. ATP6V1A activity and abundance are tuned by multiple inputs: AMPK directly phosphorylates Ser-384 to inhibit proton secretion and redistribute the V-ATPase in response to metabolic state [PMID:23863464], whereas mTORC1 phosphorylates Ser-441 to promote αB-crystallin binding that stabilizes the subunit against proteasomal degradation [PMID:31786107]. Protein abundance is further controlled at the transcriptional level by YY1 (activating) and HIF-1α (repressing under hypoxia) and post-translationally by CISH-driven ubiquitination [PMID:28592880, PMID:36748335, PMID:41522347]. ATP6V1A also supports microglial phagocytic degradation through interaction with GPNMB and is exploited by rabies virus, whose matrix protein binds the subunit's middle domain to facilitate virion uncoating [PMID:39992792, PMID:33208464].","teleology":[{"year":1990,"claim":"Establishing that the V-ATPase A subunit gene encodes the catalytic ATP-hydrolysis subunit and undergoes an unprecedented internal-domain excision defined the protein's core enzymatic identity and its unusual maturation.","evidence":"Cloning, sequencing, and peptide mapping of yeast VMA1","pmids":["2139027"],"confidence":"High","gaps":["Did not resolve the chemical mechanism of the splicing reaction","Catalytic residues for ATP hydrolysis not mapped in this study"]},{"year":1997,"claim":"Identifying junction cysteines and conserved histidines as essential for splicing, and confirming splicing as a folding-dependent intramolecular autocatalytic reaction, defined the catalytic logic of intein excision.","evidence":"Site-directed and random mutagenesis with functional readout in null yeast and bacteria; in vitro refolding splicing assay; intragenic suppressor genetics","pmids":["1417861","8651930","9276458","9188457","9286669"],"confidence":"High","gaps":["Atomic geometry of the reaction intermediate not yet resolved","Relevance of splicing to mammalian ATP6V1A not addressed"]},{"year":2002,"claim":"The 2.1 Å crystal structure of the spliceable precursor captured the N→S acyl shift and transesterification chemistry, providing the atomic mechanism of protein splicing.","evidence":"X-ray crystallography of a mutant precursor bearing N- and C-extein residues","pmids":["11884132","14646148"],"confidence":"High","gaps":["Structure is of the intein/extein precursor, not the assembled V-ATPase A subunit","No mammalian structural counterpart"]},{"year":2007,"claim":"In vivo knockdown showing loss of acid secretion and ion imbalance established ATP6V1A as physiologically required for vertebrate epithelial proton transport and ion homeostasis.","evidence":"Morpholino knockdown in zebrafish embryos with pH-dye acid-secretion and ion-content assays","pmids":["17272665"],"confidence":"High","gaps":["Morpholino off-target effects not excluded","Tissue-specific mechanism in mammals not addressed"]},{"year":2013,"claim":"Demonstrating AMPK phosphorylation of Ser-384 as inhibitory linked V-ATPase activity directly to cellular metabolic status, defining the first post-translational regulatory input.","evidence":"Mass spectrometry site mapping, in vitro kinase assay, S384A mutant rescue, perfused collecting duct and HEK293 acidification assays, localization imaging","pmids":["23863464"],"confidence":"High","gaps":["Structural basis for how Ser-384 phosphorylation alters pumping not resolved","Interplay with other regulatory phosphosites unknown at the time"]},{"year":2017,"claim":"Linking biallelic mutations to V-ATPase assembly/stability defects and trafficking impairment connected ATP6V1A dysfunction to a recessive connective-tissue disease (cutis laxa).","evidence":"Exome sequencing, complexome profiling, Brefeldin A retrograde transport, dermal TEM across five families","pmids":["28065471"],"confidence":"High","gaps":["Mechanism linking lysosomal/V-ATPase defect to elastic fiber abnormality incomplete","Did not address dominant disease alleles"]},{"year":2018,"claim":"Resolving that de novo heterozygous variants act through either loss-of-function or gain-of-function established a dual-mechanism basis for ATP6V1A developmental encephalopathy and tied it to autophagy and neuronal connectivity.","evidence":"HEK293T overexpression, LysoTracker/LysoSensor, degradation assays, hippocampal neuron transfection, structural modeling","pmids":["29668857"],"confidence":"High","gaps":["Overexpression-based readouts may not reflect endogenous stoichiometry","How gain-of-function variants increase pumping mechanistically not resolved"]},{"year":2019,"claim":"Identifying an mTORC1–αB-crystallin–ATP6V1A trimeric complex with S441 phosphorylation stabilizing the subunit revealed a degradation-control axis governing lysosomal acidification.","evidence":"GST pull-down, co-IP, lysosome fractionation, mTORC1 inhibition, S441A mutant, zebrafish HSF4-deficiency model","pmids":["31786107"],"confidence":"High","gaps":["Ubiquitin ligase mediating degradation not identified","Generalizability beyond lens epithelium untested"]},{"year":2020,"claim":"Mapping a direct interaction between the ATP6V1A middle domain and rabies matrix protein showed the subunit is co-opted for viral uncoating, extending its role to host–pathogen biology.","evidence":"Interactome mapping, reciprocal co-IP, domain mapping, knockdown/overexpression and trans-complementation viral growth assays","pmids":["33208464"],"confidence":"High","gaps":["Whether proton-pumping activity per se is required for uncoating not fully separated from binding","Relevance to other enveloped viruses untested"]},{"year":2017,"claim":"Identifying YY1 as a direct transcriptional activator of the ATP6V1A promoter defined a transcriptional control point relevant to cancer cell V-ATPase expression.","evidence":"Promoter binding-site analysis, YY1 knockdown and overexpression with qRT-PCR/western in gastric cancer cells","pmids":["28592880"],"confidence":"Medium","gaps":["Direct promoter occupancy by ChIP not shown","Physiological context of YY1 regulation beyond gastric cancer unknown"]},{"year":2022,"claim":"Showing that severe versus mild patient variants produce opposite lysosomal pH phenotypes in patient-derived cells corroborated the loss-vs-gain dichotomy and revealed lysosomal ultrastructural pathology in patient neurons.","evidence":"LysoTracker/LysoSensor, LAMP1 immunoblot, TEM of patient fibroblasts and iPSC-derived neurons","pmids":["35675510"],"confidence":"High","gaps":["Genotype-phenotype correlation mechanism for intermediate variants incomplete","In vivo neuronal consequences not directly measured"]},{"year":2023,"claim":"Demonstrating HIF-1α-mediated repression of ATP6V1A under hypoxia linked the subunit to lysosome–multivesicular body fusion and rerouting of cargo into secreted extracellular vesicles.","evidence":"HIF-1α ChIP/reporter assays, knockdown/overexpression, lysosomal degradation and EV quantification in HNSCC cells","pmids":["36748335"],"confidence":"Medium","gaps":["Single tumor-cell context","Whether EV redirection is direct consequence of V-ATPase loss or secondary not fully isolated"]},{"year":2024,"claim":"Neuron-specific depletion tracing lysosomal acidification and autophagy defects to impaired neurite elongation and synaptic plasticity defined the cellular pathway from V-ATPase dysfunction to neuronal phenotype.","evidence":"shRNA knockdown in primary murine hippocampal neurons with electrophysiology, EM, live imaging, pH and autophagy assays","pmids":["38837572"],"confidence":"High","gaps":["In vivo behavioral consequences not addressed","Distinction between autophagy block and direct synaptic pH role not fully separated"]},{"year":2025,"claim":"Identifying a GPNMB–ATP6V1A interaction required for microglial phagocytosis, rescuable by ATP6V1A activation, extended the subunit's role to immune clearance of neuronal debris and amyloid.","evidence":"Co-IP, GPNMB knockout mice, pharmacological ATP6V1A activation, phagocytosis and lysosomal degradation assays","pmids":["39992792"],"confidence":"Medium","gaps":["Single lab; reciprocal interaction not extensively validated","Molecular basis of GPNMB-ATP6V1A binding not mapped"]},{"year":2026,"claim":"Showing that AHR-induced CISH drives ubiquitination and degradation of ATP6V1A, triggering mtDNA release via cGAS-STING, identified a ubiquitin-proteasome control axis with inflammatory consequences.","evidence":"Co-IP, ubiquitination assays, AHR ChIP at CISH promoter, knockdown, lysosomal pH and mtDNA assays, mouse pregnancy model","pmids":["41522347"],"confidence":"Medium","gaps":["Direct E3 ligase activity of CISH on ATP6V1A vs adaptor role not fully distinguished","Generalizability beyond decidual macrophages untested"]},{"year":null,"claim":"How the multiple regulatory inputs (AMPK Ser-384, mTORC1 Ser-441, αB-crystallin, YY1, HIF-1α, CISH) are integrated in vivo to set V-ATPase activity in distinct tissues remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unified model of how phosphorylation, complex stabilization, and degradation pathways are coordinated","Tissue-specific dominance of each regulatory axis unknown","No high-resolution structure of mammalian ATP6V1A within the assembled holoenzyme"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[0,6]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0]},{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[6,7]},{"term_id":"GO:0016853","term_label":"isomerase activity","supporting_discovery_ids":[3,5]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[11,13,15,16]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[12]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[7]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[6,7]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[10,15]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[8,14]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[8,10,13]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,11,17]}],"complexes":["V-ATPase (V1 domain)"],"partners":["CRYAB","MTOR","GPNMB","YY1","CISH","HIF1A","PRKAA"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P38606","full_name":"V-type proton ATPase catalytic subunit A","aliases":["V-ATPase 69 kDa subunit","Vacuolar ATPase isoform VA68","Vacuolar proton pump subunit alpha"],"length_aa":617,"mass_kda":68.3,"function":"Catalytic subunit of the V1 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 translocates protons (PubMed:8463241). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments and in some cell types, is targeted to the plasma membrane, where it is responsible for acidifying the extracellular environment (PubMed:32001091). In aerobic conditions, involved in intracellular iron homeostasis, thus triggering the activity of Fe(2+) prolyl hydroxylase (PHD) enzymes, and leading to HIF1A hydroxylation and subsequent proteasomal degradation (PubMed:28296633). May play a role in neurite development and synaptic connectivity (PubMed:29668857) (Microbial infection) Plays an important role in virion uncoating during Rabies virus replication after membrane fusion. Specifically, participates in the dissociation of incoming viral matrix M proteins uncoating through direct interaction","subcellular_location":"Cytoplasm; Cytoplasm, cytosol; Cytoplasmic vesicle, secretory vesicle; Cytoplasmic vesicle, clathrin-coated vesicle membrane; Lysosome","url":"https://www.uniprot.org/uniprotkb/P38606/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/ATP6V1A","classification":"Common Essential","n_dependent_lines":1195,"n_total_lines":1208,"dependency_fraction":0.9892384105960265},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000114573","cell_line_id":"CID001646","localizations":[{"compartment":"vesicles","grade":3}],"interactors":[{"gene":"ATP6AP2","stoichiometry":10.0},{"gene":"ATP6V1G1","stoichiometry":10.0},{"gene":"ATP6V1E1","stoichiometry":10.0},{"gene":"ATP6V1B2","stoichiometry":10.0},{"gene":"ATP6V1D","stoichiometry":10.0},{"gene":"ATP6V1H","stoichiometry":10.0},{"gene":"ATP6V0A1","stoichiometry":4.0},{"gene":"ATP6V0D1","stoichiometry":4.0},{"gene":"ATP6V1C1","stoichiometry":4.0},{"gene":"ATP6V1F","stoichiometry":4.0}],"url":"https://opencell.sf.czbiohub.org/target/CID001646","total_profiled":1310},"omim":[{"mim_id":"618012","title":"DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 93; DEE93","url":"https://www.omim.org/entry/618012"},{"mim_id":"617403","title":"CUTIS LAXA, AUTOSOMAL RECESSIVE, TYPE IID; ARCL2D","url":"https://www.omim.org/entry/617403"},{"mim_id":"617402","title":"CUTIS LAXA, AUTOSOMAL RECESSIVE, TYPE IIC; ARCL2C","url":"https://www.omim.org/entry/617402"},{"mim_id":"609007","title":"LEUCINE-RICH REPEAT KINASE 2; LRRK2","url":"https://www.omim.org/entry/609007"},{"mim_id":"607027","title":"ATPase, H+ TRANSPORTING, LYSOSOMAL, 70-KD, VI SUBUNIT A; ATP6V1A","url":"https://www.omim.org/entry/607027"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Vesicles","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ATP6V1A"},"hgnc":{"alias_symbol":["Vma1","VA68"],"prev_symbol":["VPP2","ATP6A1","ATP6V1A1"]},"alphafold":{"accession":"P38606","domains":[{"cath_id":"2.40.30.20","chopping":"1-85","consensus_level":"medium","plddt":84.6893,"start":1,"end":85},{"cath_id":"2.40.50.100","chopping":"132-205","consensus_level":"high","plddt":93.7461,"start":132,"end":205},{"cath_id":"3.40.50.300","chopping":"216-456","consensus_level":"high","plddt":92.2109,"start":216,"end":456},{"cath_id":"1.10.1140.10","chopping":"470-615","consensus_level":"high","plddt":92.0588,"start":470,"end":615}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P38606","model_url":"https://alphafold.ebi.ac.uk/files/AF-P38606-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P38606-F1-predicted_aligned_error_v6.png","plddt_mean":90.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ATP6V1A","jax_strain_url":"https://www.jax.org/strain/search?query=ATP6V1A"},"sequence":{"accession":"P38606","fasta_url":"https://rest.uniprot.org/uniprotkb/P38606.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P38606/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P38606"}},"corpus_meta":[{"pmid":"2139027","id":"PMC_2139027","title":"Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae.","date":"1990","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/2139027","citation_count":392,"is_preprint":false},{"pmid":"2971651","id":"PMC_2971651","title":"Isolation of genes encoding the Neurospora vacuolar ATPase. 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standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1990,\n      \"finding\": \"The VMA1 gene encodes the catalytic subunit (subunit A) of the yeast vacuolar membrane H+-ATPase; the gene product contains the ATP hydrolysis active site and undergoes a novel post-translational processing reaction in which an internal domain of 454 amino acids is autocatalytically excised and the flanking N- and C-terminal regions are ligated to produce the mature 69-kDa subunit.\",\n      \"method\": \"Gene cloning, nucleotide sequencing, N-terminal peptide sequencing of tryptic fragments, Northern blotting, domain homology analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — primary gene isolation with sequence, peptide mapping, and functional inference; foundational paper replicated across organisms\",\n      \"pmids\": [\"2139027\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1992,\n      \"finding\": \"Cysteine residues at positions 284 and 738 of the VMA1 precursor are essential for protein splicing: Cys284Ser mutation blocks cleavage at the N-terminal junction site, while Cys738Ser blocks processing at both junction sites, causing accumulation of nonfunctional fragments and loss of V-ATPase function.\",\n      \"method\": \"Site-directed mutagenesis of VMA1 at splice junction cysteines; expression in vma1-null yeast; analysis of protein products by SDS-PAGE\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — active-site mutagenesis with functional readout in null background, establishing catalytic mechanism of protein splicing\",\n      \"pmids\": [\"1417861\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Protein splicing of the yeast Vma1 protozyme is a folding-dependent, intramolecular autocatalytic reaction occurring at optimal pH 7; denatured precursor molecules can be refolded in vitro to reconstitute the splicing reaction, and it is not inhibited by protease inhibitors.\",\n      \"method\": \"In vitro protein splicing assay using purified refolded precursor peptides expressed in E. coli; pH titration; protease inhibitor panel\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstituted in vitro protein splicing with purified components and multiple orthogonal controls (pH, inhibitors, solubility)\",\n      \"pmids\": [\"8651930\", \"9276458\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"Random mutagenesis of the entire VMA1-derived endonuclease (VDE/intein) sequence identified three core regions essential for protein splicing: the N- and C-terminal splice junctions and the N-terminal one-third of VDE. His362 is essential for the first cleavage at the N-terminal junction, and His736 assists the second cleavage via Asn cyclization at the C-terminal junction.\",\n      \"method\": \"PCR-based random mutagenesis; bacterial expression screen for splicing-defective mutants; yeast functional analysis; mapping of mutant proteins by SDS-PAGE\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — systematic mutagenesis across entire intein sequence with functional readout in two expression systems; identifies catalytic residues\",\n      \"pmids\": [\"9188457\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"A conserved hydrophobic valine triplet upstream of the C-terminal splicing junction genetically interacts with three hydrophobic residues upstream of the N-terminal splicing junction, indicating that the N-terminal portion of the V-ATPase A subunit participates structurally in protein splicing via parallel beta-strand alignment.\",\n      \"method\": \"Random mutagenesis of valine triplet; intragenic suppressor analysis; genetic epistasis in yeast\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with intragenic suppressor analysis; single lab but multiple mutant alleles tested\",\n      \"pmids\": [\"9286669\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"Crystal structure at 2.1 Å of the VMA1-derived endonuclease (VDE) precursor bearing N- and C-extein polypeptides revealed the mechanism of protein splicing: the Cys284 Sγ atom nucleophilically attacks the Gly283 carbonyl carbon forming a thiazolidine tetrahedral intermediate (N→S acyl shift) at the N-terminal junction, followed by transesterification at the C-terminal junction mediated by Ser738.\",\n      \"method\": \"X-ray crystallography at 2.1 Å resolution of spliceable precursor recombinant with C284S/H362N/N737S/C738S replacements bearing N- and C-extein residues\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution crystal structure with defined reaction intermediates and mutagenesis validation; mechanistic details independently confirmed in follow-up paper\",\n      \"pmids\": [\"11884132\", \"14646148\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Morpholino knockdown of atp6v1a (V-ATPase subunit A) in zebrafish embryos suppressed acid secretion from skin H+-pump-rich cells, caused loss of internal Ca2+ and Na+, growth retardation, and trunk deformation, establishing ATP6V1A as required for embryonic acid secretion and ion balance in vivo.\",\n      \"method\": \"Morpholino-mediated antisense knockdown in zebrafish embryos; pH-sensitive fluorescent dye measurement of acid secretion; ion content analysis\",\n      \"journal\": \"American journal of physiology. Regulatory, integrative and comparative physiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo loss-of-function with quantitative functional readouts (acid secretion, ion balance) in a vertebrate model\",\n      \"pmids\": [\"17272665\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"AMPK directly phosphorylates the V-ATPase A subunit (ATP6V1A) at Ser-384; this phosphorylation inhibits V-ATPase-dependent H+ secretion in kidney intercalated cells and causes cytoplasmic redistribution of the V-ATPase, coupling V-ATPase activity to cellular metabolic status.\",\n      \"method\": \"Mass spectrometry identification of AMPK phosphorylation site; in vitro kinase assay comparing WT and S384A mutant A-subunit; AICAR treatment of isolated perfused collecting ducts; extracellular acidification assay in HEK-293 cells expressing S384A mutant; immunofluorescence of V-ATPase localization\",\n      \"journal\": \"American journal of physiology. Renal physiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — mass spectrometry site identification, in vitro kinase assay, phosphorylation-deficient mutant rescue, functional pH secretion assay, and localization experiment; multiple orthogonal methods\",\n      \"pmids\": [\"23863464\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Biallelic missense mutations in ATP6V1A (encoding V-ATPase subunit A) disrupt either the assembly or stability of the V-ATPase complex (shown by complexome profiling), impair vesicular trafficking (delayed retrograde Brefeldin A transport, Golgi fragmentation), and cause autosomal-recessive cutis laxa with elastic fiber and collagen fiber abnormalities.\",\n      \"method\": \"Whole-exome sequencing; complexome profiling (blue-native gel electrophoresis + LC-MS/MS); Brefeldin A retrograde transport assay; transmission electron microscopy of dermis; structural modeling\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — complexome profiling directly measured V-ATPase complex assembly defects; multiple orthogonal functional assays (trafficking, ultrastructure); replicated across five families\",\n      \"pmids\": [\"28065471\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The transcription factor YY1 directly binds three sites in the ATP6V1A core promoter and transcriptionally activates ATP6V1A expression; RNAi-mediated knockdown of YY1 in gastric cancer cells significantly decreased ATP6V1A mRNA and protein levels.\",\n      \"method\": \"Promoter analysis; RNAi knockdown of YY1; YY1 overexpression; quantitative RT-PCR and western blotting of ATP6V1A\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — promoter binding sites identified and functional knockdown/overexpression performed; single lab, two orthogonal approaches\",\n      \"pmids\": [\"28592880\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"De novo heterozygous mutations in ATP6V1A cause developmental encephalopathy with epilepsy through distinct mechanisms: p.Asp100Tyr causes reduced ATP6V1A expression via increased protein degradation and decreased lysosomal markers (loss of function), while p.Asp349Asn causes gain-of-function with increased proton pumping in intracellular organelles. Both mutations decrease V-ATPase recruitment to autophagosomes and impair neurite elongation with loss of excitatory inputs in hippocampal neurons.\",\n      \"method\": \"Overexpression in HEK293T cells; LysoTracker and LysoSensor fluorescence; LAMP1/EEA1 immunoblotting; protein degradation assays; rat hippocampal neuron transfection; immunofluorescence; structural modeling on prokaryotic/eukaryotic V-ATPase structures\",\n      \"journal\": \"Brain : a journal of neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal assays in multiple cell types (HEK293T, patient lymphoblasts, primary neurons) establishing gain- vs. loss-of-function distinction\",\n      \"pmids\": [\"29668857\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"αB-crystallin interacts directly with ATP6V1A (the V1-domain A subunit) and mTORC1 in a trimeric complex in lens epithelial cells; mTORC1 phosphorylates ATP6V1A at S441, promoting its association with αB-crystallin; this complex stabilizes ATP6V1A against proteasomal degradation and maintains lysosomal acidification. HSF4 deficiency reduces αB-crystallin expression, leading to increased ubiquitination and proteasomal degradation of ATP6V1A and elevated lysosomal pH.\",\n      \"method\": \"GST pull-down assays; co-immunoprecipitation; lysosome fractionation by ultracentrifugation; rapamycin/siRNA inhibition of mTORC1; S441A phospho-mutant of ATP6V1A; immunoblotting; zebrafish HSF4-deficiency model\",\n      \"journal\": \"Biochimica et biophysica acta. General subjects\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — GST pull-down, co-IP, phospho-mutant, mTOR inhibition, in vivo zebrafish model; multiple orthogonal methods establishing the complex and its functional consequence\",\n      \"pmids\": [\"31786107\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ATP6V1A physically interacts with the rabies virus matrix protein (M) via the middle domain of ATP6V1A (dependent on residues K256 and E279 of M); this interaction facilitates dissociation of incoming viral M proteins during virion uncoating in endosomes, thereby promoting RABV replication.\",\n      \"method\": \"Proteomic interactome mapping; co-immunoprecipitation; domain mapping with full-length and truncation constructs; shRNA knockdown and overexpression of ATP6V1A in HEK293T and Vero cells; viral growth assays; trans-complementation rescue\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP with domain mapping, loss-of-function knockdown, gain-of-function overexpression, and trans-complementation rescue; multiple orthogonal methods\",\n      \"pmids\": [\"33208464\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In patients with ATP6V1A encephalopathy, fibroblasts with severe DEE-causing variants show decreased LAMP1 expression, reduced Lysotracker staining, and increased organelle pH (consistent with lysosomal impairment/loss of V-ATPase function), whereas fibroblasts with milder disease variants show increased Lysotracker staining and decreased organelle pH; iPSC-derived neurons from DEE patients show significantly smaller lysosomes with electron-dense inclusions, lipid droplets, and lamellated membrane structures.\",\n      \"method\": \"Lysotracker and LysoSensor staining; LAMP1 immunoblotting; transmission electron microscopy of fibroblasts and iPSC-derived neurons; lysosomal substrate quantification\",\n      \"journal\": \"Brain : a journal of neurology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple patient-derived cell types, orthogonal methods (fluorescent probes, TEM, protein quantification), replicated across multiple families\",\n      \"pmids\": [\"35675510\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"HIF-1α directly downregulates ATP6V1A expression under hypoxia in HNSCC cells, which impairs lysosomal homeostasis and reduces fusion of multivesicular bodies with lysosomes, redirecting intraluminal vesicles to be secreted as extracellular vesicles.\",\n      \"method\": \"HIF-1α ChIP/transcriptional reporter assays; ATP6V1A knockdown and overexpression; lysosomal degradation assays; extracellular vesicle quantification; nanoparticle tracking analysis\",\n      \"journal\": \"Journal of extracellular vesicles\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct HIF-1α regulation demonstrated with functional EV secretion readout; single lab with multiple complementary approaches\",\n      \"pmids\": [\"36748335\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Depletion of Atp6v1a in murine hippocampal neurons impairs lysosomal pH regulation and autophagy progression, leading to accumulation of aberrant lysosomes at the neuronal soma and enlarged vacuoles at synaptic boutons; this causes defects in neurite elongation, stabilization of excitatory synapses, and prevention of synaptic rearrangement upon plasticity induction.\",\n      \"method\": \"shRNA knockdown of Atp6v1a in primary murine hippocampal neurons; immunoimaging; electrophysiological recordings; electron microscopy; lysosomal pH assays; autophagy flux assays\",\n      \"journal\": \"Acta physiologica (Oxford, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function in primary neurons with multiple orthogonal readouts (electrophysiology, EM, live imaging, pH assays) establishing pathway from lysosomal dysfunction to synaptic phenotype\",\n      \"pmids\": [\"38837572\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"GPNMB interacts with ATP6V1A in lysosomes to facilitate microglial phagocytosis: GPNMB-deficient microglia show defects in both phagocytic engulfment and lysosomal degradation, and activating ATP6V1A rescues the phagocytosis impairment caused by GPNMB deficiency.\",\n      \"method\": \"Co-immunoprecipitation of GPNMB with ATP6V1A; genetic ablation of GPNMB in mice; pharmacological activation of ATP6V1A; phagocytosis assays with neuronal debris and β-amyloid; lysosomal degradation assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP with functional rescue by ATP6V1A activation; single lab with in vivo and in vitro evidence\",\n      \"pmids\": [\"39992792\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"CISH (induced by AHR) promotes ubiquitination and degradation of ATP6V1A, disrupting lysosomal acidification and causing mtDNA release via the cGAS-STING pathway in decidual macrophages; this identifies ATP6V1A protein stability as regulated by the AHR/CISH ubiquitin-proteasome axis.\",\n      \"method\": \"Co-immunoprecipitation; ubiquitination assays; AHR chromatin immunoprecipitation at CISH promoter; siRNA knockdown; lysosomal pH measurement; mtDNA quantification; mouse pregnancy model\",\n      \"journal\": \"International journal of biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ubiquitination assay and co-IP with in vivo mouse model; single lab, multiple complementary methods\",\n      \"pmids\": [\"41522347\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ATP6V1A encodes the catalytic A subunit of the vacuolar-type H+-ATPase (V-ATPase) V1 domain, which hydrolyzes ATP to drive proton pumping into lysosomes, endosomes, and other acidic compartments; its activity is directly regulated by AMPK-mediated phosphorylation at Ser-384 (inhibitory), mTORC1-promoted association with αB-crystallin (stabilizing), and ubiquitin-proteasome degradation driven by CISH or HSF4-αB-crystallin loss, while its proper assembly within the V-ATPase complex is essential for lysosomal pH homeostasis, vesicular trafficking, autophagy flux, synaptic plasticity in neurons, acid secretion in kidney and zebrafish epithelia, and microglial phagocytosis, with disease-causing mutations acting through either gain-of-function (excess proton pumping) or loss-of-function (reduced V-ATPase assembly/activity) mechanisms.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ATP6V1A encodes the catalytic A subunit of the vacuolar-type H+-ATPase (V-ATPase) V1 domain, the ATP-hydrolyzing engine that drives proton pumping to acidify lysosomes, endosomes, and other intracellular compartments and to mediate extracellular acid secretion [#0, #6]. In yeast, the founding ortholog VMA1 was shown to harbor the ATP hydrolysis active site and to mature through an autocatalytic protein-splicing reaction in which an internal ~454-residue intein is excised and the flanking exteins are ligated to yield the active subunit; this splicing depends on junction cysteines and conserved histidines and proceeds via an N\\u2192S acyl shift forming a thiazolidine intermediate [#0, #1, #3, #5]. Proper incorporation of the A subunit into the V-ATPase holoenzyme is required for lysosomal pH homeostasis, vesicular trafficking, and autophagy flux: biallelic missense mutations impair complex assembly/stability and retrograde trafficking and cause autosomal-recessive cutis laxa [#8], while de novo heterozygous mutations cause developmental encephalopathy with epilepsy through either loss-of-function (reduced expression via increased degradation, elevated lysosomal pH) or gain-of-function (excess organellar proton pumping), both impairing autophagosomal V-ATPase recruitment, neurite elongation, and excitatory synaptic input [#10, #13]. Consistent with this, neuronal Atp6v1a depletion disrupts lysosomal acidification and autophagy, producing aberrant somatic lysosomes and synaptic defects in plasticity [#15]. ATP6V1A activity and abundance are tuned by multiple inputs: AMPK directly phosphorylates Ser-384 to inhibit proton secretion and redistribute the V-ATPase in response to metabolic state [#7], whereas mTORC1 phosphorylates Ser-441 to promote \\u03b1B-crystallin binding that stabilizes the subunit against proteasomal degradation [#11]. Protein abundance is further controlled at the transcriptional level by YY1 (activating) and HIF-1\\u03b1 (repressing under hypoxia) and post-translationally by CISH-driven ubiquitination [#9, #14, #17]. ATP6V1A also supports microglial phagocytic degradation through interaction with GPNMB and is exploited by rabies virus, whose matrix protein binds the subunit's middle domain to facilitate virion uncoating [#16, #12].\",\n  \"teleology\": [\n    {\n      \"year\": 1990,\n      \"claim\": \"Establishing that the V-ATPase A subunit gene encodes the catalytic ATP-hydrolysis subunit and undergoes an unprecedented internal-domain excision defined the protein's core enzymatic identity and its unusual maturation.\",\n      \"evidence\": \"Cloning, sequencing, and peptide mapping of yeast VMA1\",\n      \"pmids\": [\"2139027\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the chemical mechanism of the splicing reaction\", \"Catalytic residues for ATP hydrolysis not mapped in this study\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Identifying junction cysteines and conserved histidines as essential for splicing, and confirming splicing as a folding-dependent intramolecular autocatalytic reaction, defined the catalytic logic of intein excision.\",\n      \"evidence\": \"Site-directed and random mutagenesis with functional readout in null yeast and bacteria; in vitro refolding splicing assay; intragenic suppressor genetics\",\n      \"pmids\": [\"1417861\", \"8651930\", \"9276458\", \"9188457\", \"9286669\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic geometry of the reaction intermediate not yet resolved\", \"Relevance of splicing to mammalian ATP6V1A not addressed\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"The 2.1 \\u00c5 crystal structure of the spliceable precursor captured the N\\u2192S acyl shift and transesterification chemistry, providing the atomic mechanism of protein splicing.\",\n      \"evidence\": \"X-ray crystallography of a mutant precursor bearing N- and C-extein residues\",\n      \"pmids\": [\"11884132\", \"14646148\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structure is of the intein/extein precursor, not the assembled V-ATPase A subunit\", \"No mammalian structural counterpart\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"In vivo knockdown showing loss of acid secretion and ion imbalance established ATP6V1A as physiologically required for vertebrate epithelial proton transport and ion homeostasis.\",\n      \"evidence\": \"Morpholino knockdown in zebrafish embryos with pH-dye acid-secretion and ion-content assays\",\n      \"pmids\": [\"17272665\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Morpholino off-target effects not excluded\", \"Tissue-specific mechanism in mammals not addressed\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Demonstrating AMPK phosphorylation of Ser-384 as inhibitory linked V-ATPase activity directly to cellular metabolic status, defining the first post-translational regulatory input.\",\n      \"evidence\": \"Mass spectrometry site mapping, in vitro kinase assay, S384A mutant rescue, perfused collecting duct and HEK293 acidification assays, localization imaging\",\n      \"pmids\": [\"23863464\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for how Ser-384 phosphorylation alters pumping not resolved\", \"Interplay with other regulatory phosphosites unknown at the time\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Linking biallelic mutations to V-ATPase assembly/stability defects and trafficking impairment connected ATP6V1A dysfunction to a recessive connective-tissue disease (cutis laxa).\",\n      \"evidence\": \"Exome sequencing, complexome profiling, Brefeldin A retrograde transport, dermal TEM across five families\",\n      \"pmids\": [\"28065471\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking lysosomal/V-ATPase defect to elastic fiber abnormality incomplete\", \"Did not address dominant disease alleles\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Resolving that de novo heterozygous variants act through either loss-of-function or gain-of-function established a dual-mechanism basis for ATP6V1A developmental encephalopathy and tied it to autophagy and neuronal connectivity.\",\n      \"evidence\": \"HEK293T overexpression, LysoTracker/LysoSensor, degradation assays, hippocampal neuron transfection, structural modeling\",\n      \"pmids\": [\"29668857\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Overexpression-based readouts may not reflect endogenous stoichiometry\", \"How gain-of-function variants increase pumping mechanistically not resolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identifying an mTORC1\\u2013\\u03b1B-crystallin\\u2013ATP6V1A trimeric complex with S441 phosphorylation stabilizing the subunit revealed a degradation-control axis governing lysosomal acidification.\",\n      \"evidence\": \"GST pull-down, co-IP, lysosome fractionation, mTORC1 inhibition, S441A mutant, zebrafish HSF4-deficiency model\",\n      \"pmids\": [\"31786107\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Ubiquitin ligase mediating degradation not identified\", \"Generalizability beyond lens epithelium untested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Mapping a direct interaction between the ATP6V1A middle domain and rabies matrix protein showed the subunit is co-opted for viral uncoating, extending its role to host\\u2013pathogen biology.\",\n      \"evidence\": \"Interactome mapping, reciprocal co-IP, domain mapping, knockdown/overexpression and trans-complementation viral growth assays\",\n      \"pmids\": [\"33208464\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether proton-pumping activity per se is required for uncoating not fully separated from binding\", \"Relevance to other enveloped viruses untested\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identifying YY1 as a direct transcriptional activator of the ATP6V1A promoter defined a transcriptional control point relevant to cancer cell V-ATPase expression.\",\n      \"evidence\": \"Promoter binding-site analysis, YY1 knockdown and overexpression with qRT-PCR/western in gastric cancer cells\",\n      \"pmids\": [\"28592880\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct promoter occupancy by ChIP not shown\", \"Physiological context of YY1 regulation beyond gastric cancer unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showing that severe versus mild patient variants produce opposite lysosomal pH phenotypes in patient-derived cells corroborated the loss-vs-gain dichotomy and revealed lysosomal ultrastructural pathology in patient neurons.\",\n      \"evidence\": \"LysoTracker/LysoSensor, LAMP1 immunoblot, TEM of patient fibroblasts and iPSC-derived neurons\",\n      \"pmids\": [\"35675510\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Genotype-phenotype correlation mechanism for intermediate variants incomplete\", \"In vivo neuronal consequences not directly measured\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrating HIF-1\\u03b1-mediated repression of ATP6V1A under hypoxia linked the subunit to lysosome\\u2013multivesicular body fusion and rerouting of cargo into secreted extracellular vesicles.\",\n      \"evidence\": \"HIF-1\\u03b1 ChIP/reporter assays, knockdown/overexpression, lysosomal degradation and EV quantification in HNSCC cells\",\n      \"pmids\": [\"36748335\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single tumor-cell context\", \"Whether EV redirection is direct consequence of V-ATPase loss or secondary not fully isolated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Neuron-specific depletion tracing lysosomal acidification and autophagy defects to impaired neurite elongation and synaptic plasticity defined the cellular pathway from V-ATPase dysfunction to neuronal phenotype.\",\n      \"evidence\": \"shRNA knockdown in primary murine hippocampal neurons with electrophysiology, EM, live imaging, pH and autophagy assays\",\n      \"pmids\": [\"38837572\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo behavioral consequences not addressed\", \"Distinction between autophagy block and direct synaptic pH role not fully separated\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identifying a GPNMB\\u2013ATP6V1A interaction required for microglial phagocytosis, rescuable by ATP6V1A activation, extended the subunit's role to immune clearance of neuronal debris and amyloid.\",\n      \"evidence\": \"Co-IP, GPNMB knockout mice, pharmacological ATP6V1A activation, phagocytosis and lysosomal degradation assays\",\n      \"pmids\": [\"39992792\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; reciprocal interaction not extensively validated\", \"Molecular basis of GPNMB-ATP6V1A binding not mapped\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Showing that AHR-induced CISH drives ubiquitination and degradation of ATP6V1A, triggering mtDNA release via cGAS-STING, identified a ubiquitin-proteasome control axis with inflammatory consequences.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, AHR ChIP at CISH promoter, knockdown, lysosomal pH and mtDNA assays, mouse pregnancy model\",\n      \"pmids\": [\"41522347\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct E3 ligase activity of CISH on ATP6V1A vs adaptor role not fully distinguished\", \"Generalizability beyond decidual macrophages untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the multiple regulatory inputs (AMPK Ser-384, mTORC1 Ser-441, \\u03b1B-crystallin, YY1, HIF-1\\u03b1, CISH) are integrated in vivo to set V-ATPase activity in distinct tissues remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified model of how phosphorylation, complex stabilization, and degradation pathways are coordinated\", \"Tissue-specific dominance of each regulatory axis unknown\", \"No high-resolution structure of mammalian ATP6V1A within the assembled holoenzyme\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [6, 7]},\n      {\"term_id\": \"GO:0016853\", \"supporting_discovery_ids\": [3, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [11, 13, 15, 16]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [12]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [6, 7]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [10, 15]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [8, 14]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [8, 10, 13]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 11, 17]}\n    ],\n    \"complexes\": [\"V-ATPase (V1 domain)\"],\n    \"partners\": [\"CRYAB\", \"MTOR\", \"GPNMB\", \"YY1\", \"CISH\", \"HIF1A\", \"PRKAA\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}