{"gene":"OSTM1","run_date":"2026-06-10T05:19:53","timeline":{"discoveries":[{"year":2006,"finding":"OSTM1 (Ostm1) forms a molecular complex with ClC-7, co-localizing in late endosomes and lysosomes and in the ruffled border of bone-resorbing osteoclasts, functioning as a β-subunit of ClC-7. ClC-7 is required for Ostm1 to reach lysosomes, where the highly glycosylated Ostm1 luminal domain is cleaved. In Ostm1-deficient (grey-lethal) mice, ClC-7 protein levels fall below 10% of normal, indicating Ostm1 is required for ClC-7 protein stability.","method":"Co-immunoprecipitation, subcellular co-localization (immunofluorescence/fractionation), protein level analysis in grey-lethal mice","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, direct localization with functional consequence, protein stability data; replicated and foundational study","pmids":["16525474"],"is_preprint":false},{"year":2020,"finding":"Cryo-EM structures of CLC-7 alone and in complex with OSTM1 at up to 2.8 Å resolution show that the luminal surface of CLC-7 is entirely covered by a dimer of heavily glycosylated and disulfide-bonded OSTM1, which protects CLC-7 from the degradative lysosomal lumen. OSTM1 binding causes only minor conformational changes in the ion-conduction pathway of CLC-7, potentially contributing to its regulatory role.","method":"Cryo-electron microscopy (cryo-EM) structural determination","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution cryo-EM structure with functional interpretation, independent of prior co-IP data","pmids":["32749217"],"is_preprint":false},{"year":2020,"finding":"Cryo-EM structure of human CLC-7/Ostm1 complex reveals that Ostm1 functions as a lid positioned above CLC-7, interacting extensively with CLC-7 within the membrane. Structural analyses and electrophysiology studies indicate that the domain interaction interfaces between the amino terminus, TMD, and CBS domains of CLC-7 affect the slow gating kinetics of CLC-7/Ostm1.","method":"Cryo-EM structural determination combined with electrophysiology","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure plus electrophysiology in a single study, orthogonal methods","pmids":["32851177"],"is_preprint":false},{"year":2013,"finding":"Slow voltage-dependent activation of ClC-7/Ostm1 operates via common gating (acting on both subunits of the dimer simultaneously, not protopore gates). The CBS domain-containing C-terminus is required for currents and slow gating; when ClC-7 was truncated after the last intramembrane helix, currents were abolished but restored by co-expression of the C-terminus alone or fused to the Ostm1 C-terminus.","method":"Electrophysiology with ClC-7 mutants and trans-complementation of truncated constructs in heterologous expression","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of gating using mutagenesis and electrophysiology, multiple mutant combinations tested","pmids":["23983121"],"is_preprint":false},{"year":2014,"finding":"Using ion transport-deficient ClC-7 knock-in mice (Clcn7td/td), it was established that both protein-protein interactions (presence of ClC-7/Ostm1 complex) and ion transport activity are mechanistically separable contributors to different ClC-7-related disease phenotypes: osteopetrosis requires both, whereas hair pigmentation requires only protein presence (not transport activity), and neurodegeneration is exacerbated by Cl− conductance.","method":"In vivo knock-in mouse models with defined transport-deficient mutations, phenotypic analysis","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with defined knock-in alleles, multiple phenotypes dissected in vivo","pmids":["24820037"],"is_preprint":false},{"year":2006,"finding":"MITF transcription factor directly binds a single M-box in the Ostm1 promoter, as shown by EMSA with anti-MITF supershift and abolition of binding by M-box mutation, and by chromatin immunoprecipitation. MITF co-regulates Ostm1 expression during osteoclastogenesis in concert with Clcn7.","method":"EMSA, ChIP, reporter gene assay, microarray","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — EMSA with supershift and mutagenesis plus ChIP, single lab","pmids":["17105730"],"is_preprint":false},{"year":2008,"finding":"OSTM1 is required for Wnt/β-catenin canonical signaling: overexpression of OSTM1 in F9 cells increased Wnt3a-responsive β-catenin accumulation and Lef/Tcf-sensitive transcription, while knockdown attenuated Wnt3a signaling. Wild-type OSTM1 stimulated the Wnt-dependent association of β-catenin with Lef1, whereas an osteopetrosis-associated C-terminal deletion mutant inhibited this interaction and Lef/Tcf transcription even with constitutively active β-catenin, but not with a β-catenin/Lef chimera.","method":"Overexpression and knockdown in F9 cells, reporter gene assays, co-immunoprecipitation of β-catenin/Lef1","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — co-IP and reporter assays, single lab, two orthogonal functional readouts","pmids":["18296023"],"is_preprint":false},{"year":2008,"finding":"The gl (Ostm1-null) osteopetrotic defect is non-cell autonomous: conditional Ostm1 transgene targeted only to committed osteoclasts did not rescue the bone phenotype, but expression driven by PU.1 (broader hematopoietic cells) rescued osteoclast function as well as B- and T-lymphoid lineage phenotypes, establishing an essential role for Ostm1 in multiple hematopoietic cell types beyond osteoclasts.","method":"Conditional transgenic mouse rescue experiments, flow cytometric analysis of hematopoietic lineages","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis via cell-type-specific transgenic rescue, single lab","pmids":["18790735"],"is_preprint":false},{"year":2014,"finding":"In Ostm1-null mice, severe neurodegeneration is accompanied by accumulation of autophagosomes causing axonal swelling, downregulation of mTOR signaling, and storage of carbohydrates, lipids, and ubiquitinated proteins in neurons. Cell-type-specific transgenic rescue showed that Ostm1 has a primary and autonomous role in neuronal homeostasis independent of the hematopoietic lineage.","method":"Conditional transgenic mouse rescue, immunohistochemistry, autophagosome and mTOR pathway markers, cell-type specific targeting","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cell-autonomous rescue in defined CNS subpopulations, multiple cellular markers, single lab","pmids":["24719316"],"is_preprint":false},{"year":2015,"finding":"Ostm1 is a type I transmembrane protein (immature 34 kDa) that undergoes post-translational N-glycosylation to ~60 kDa mature form. It localizes to the endoplasmic reticulum, trans-Golgi network, and endosomes/lysosomes. A direct interaction between Ostm1 and kinesin 5B (KIF5B) heavy chains was demonstrated, placing Ostm1 in a cytosolic scaffolding multiprotein complex that acts as a trafficking adaptor for cargo movement from the ER to late endosomal/lysosomal compartments.","method":"Protein screen, co-immunoprecipitation, subcellular fractionation and localization, biochemical analysis of glycosylation","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct co-IP interaction with KIF5B validated, localization and trafficking demonstrated, single lab","pmids":["26598607"],"is_preprint":false},{"year":2018,"finding":"Conditional deletion of the Ostm1 transmembrane domain in osteoclasts alone reproduced the full osteopetrotic phenotype, demonstrating osteoclast-intrinsic deficiency is sufficient. Ostm1 loss of transmembrane domain causes oversized osteoclasts with enhanced multinucleation, elevated intracellular calcium, NFATc1 nuclear re-localization, and upregulation of NFATc1 target genes, establishing Ostm1 as a negative regulator of preosteoclast fusion. Mature osteoclasts show appropriate acidification levels but mislocalized endolysosomes, and TRAP/cathepsin K are sequestered intracellularly rather than secreted.","method":"Conditional mouse knock-in (transmembrane domain deletion), osteoclast culture, calcium imaging, NFATc1 nuclear localization assay, lysosomal trafficking analysis","journal":"Journal of bone and mineral research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional genetic model with multiple orthogonal cellular phenotype readouts, single lab","pmids":["29297601"],"is_preprint":false},{"year":2014,"finding":"A secreted truncated form of OSTM1 (lacking the transmembrane domain) binds to the cell surface of osteoclast precursors and inhibits multinucleated osteoclast formation by reducing cell fusion and survival, acting through downregulation of the BLIMP1-NFATc1 transcriptional axis. In vivo, truncated OSTM1 reduced LPS-induced bone destruction.","method":"Cell surface binding assay, osteoclast differentiation assay, gene expression analysis, in vivo bone destruction model","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — cell binding and functional osteoclast assays with pathway marker analysis, single lab","pmids":["25359771"],"is_preprint":false},{"year":2013,"finding":"A missense mutation (Y750Q) in the CBS2 domain of ClC-7 largely preserves lysosomal localization and assembly of the ClC-7/Ostm1 complex but drastically accelerates voltage-dependent gating of ClC-7/Ostm1, causing osteopetrosis in cattle. This provides direct evidence that accelerated ClC-7/Ostm1 gating per se is pathogenic, demonstrating a physiological requirement for slow voltage activation.","method":"Autozygosity mapping, genome sequencing, electrophysiology, lysosomal localization assay in cell models","journal":"Disease models & mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — natural mutation characterized by electrophysiology and localization with disease phenotype, single study","pmids":["24159188"],"is_preprint":false},{"year":2022,"finding":"Ostm1 is an essential regulator of T cell ontogeny: Ostm1 ablation caused a cell-autonomous defect in early T cell precursors (ETP, DN subpopulations) in the thymus. Transcriptome analysis identified an Ostm1 crosstalk with a Foxo1-Klf2-S1pr1-Gnai1-Rac1 signaling axis in DN1 T cells. Transgenic rescue of Ostm1 in DN1 cells partially rescued T cell subpopulations from ETP onwards.","method":"Conditional transgenic rescue, flow cytometry of T cell subpopulations, transcriptome analysis","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cell-autonomous rescue with transcriptomic pathway identification, single lab","pmids":["35434560"],"is_preprint":false},{"year":2025,"finding":"SNX10 physically interacts with CLC-7 (co-immunoprecipitation), and loss of SNX10 reduces peripheral LAMP1-positive lysosomes containing CLC-7 and OSTM1. Loss of CLC-7 also depletes peripheral OSTM1-containing lysosomes. All three proteins (SNX10, CLC-7, OSTM1) co-localize in LAMP1-positive lysosomes and regulate lysosome trafficking to the cell periphery, which controls both fusion arrest and functionality of mature osteoclasts.","method":"Co-immunoprecipitation, immunofluorescence co-localization, knockout cell culture, lysosome distribution analysis","journal":"Journal of bone and mineral research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus localization in KO cells with functional phenotype, single lab","pmids":["41408708"],"is_preprint":false},{"year":2026,"finding":"A cytosolic, non-glycosylated fraction of OSTM1 functions as an E3 ubiquitin ligase that targets phosphodiesterase 3B (PDE3B) for proteasomal degradation. Loss of OSTM1 stabilizes PDE3B, which increases conversion of cAMP to AMP and suppresses the cAMP/PKA/CREB tumor suppressive pathway, thereby promoting B-cell lymphomagenesis.","method":"Whole-genome CRISPR screen, B-cell-specific Ostm1 conditional knockout mouse, E3 ligase activity assay, PDE3B ubiquitination and degradation assays, cAMP/PKA/CREB pathway analysis","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR screen plus mechanistic follow-up with substrate degradation assay and pathway analysis; preprint, not yet peer-reviewed","pmids":["41659680"],"is_preprint":true},{"year":2025,"finding":"La protein is greatly elevated at the surface of osteoclasts upon loss of OSTM1 (or SNX10). Inhibitory antibodies against La suppressed excessive osteoclast fusion and restored resorptive function in OSTM1-deficient osteoclasts, establishing a functional link between OSTM1 loss and dysregulated surface La in osteoclast hyperfusion.","method":"Immunofluorescence surface labeling, inhibitory antibody treatment, osteoclast fusion and resorption assays in OSTM1-KO cells","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab preprint, surface labeling and antibody inhibition, no biochemical interaction data for OSTM1-La","pmids":["bio_10.1101_2025.09.07.674639"],"is_preprint":true}],"current_model":"OSTM1 is a type I transmembrane glycoprotein that functions as the obligate β-subunit of the lysosomal CLC-7 Cl⁻/H⁺ exchanger—covering and protecting CLC-7's luminal face, stabilizing CLC-7 protein, and modulating its slow voltage-dependent gating—while also acting as a cytosolic scaffolding adaptor (via KIF5B) for endolysosomal trafficking, a negative regulator of preosteoclast fusion through the NFATc1 axis, an essential factor in neuronal autophagy homeostasis, a regulator of T cell ontogeny through the Foxo1-Klf2-S1pr1-Gnai1-Rac1 axis, and, in its non-glycosylated cytosolic fraction, an E3 ubiquitin ligase that degrades PDE3B to sustain the cAMP/PKA/CREB tumor-suppressive pathway in B cells."},"narrative":{"mechanistic_narrative":"OSTM1 is a type I transmembrane glycoprotein that functions as the obligate β-subunit of the lysosomal CLC-7 Cl⁻/H⁺ exchanger, governing endolysosomal ion homeostasis in osteoclasts and neurons [PMID:16525474, PMID:32749217]. It forms a molecular complex with CLC-7 in late endosomes, lysosomes, and the osteoclast ruffled border, where a glycosylated dimer of OSTM1 covers the entire luminal surface of CLC-7 to shield it from lysosomal degradation and stabilize CLC-7 protein levels [PMID:16525474, PMID:32749217]. Beyond stabilization, OSTM1 contributes to the slow common gating of the CLC-7 complex through interactions involving the CLC-7 N-terminus, transmembrane domain, and CBS domains, and physiologically slow voltage activation is itself required—accelerated gating alone is pathogenic [PMID:32851177, PMID:23983121, PMID:24159188]. Protein-protein interaction and ion transport are separable functions: osteopetrosis requires both, hair pigmentation requires only complex presence, and neurodegeneration is exacerbated by Cl⁻ conductance [PMID:24820037]. OSTM1 also acts as a cytosolic scaffolding adaptor that binds KIF5B heavy chains to direct trafficking of cargo toward late endosomal/lysosomal compartments [PMID:26598607], and it positions lysosomes at the cell periphery together with SNX10 and CLC-7 to control osteoclast fusion arrest and resorptive function [PMID:41408708]. Loss of OSTM1 in osteoclasts causes oversized, hyperfused cells with elevated intracellular calcium and NFATc1 nuclear relocalization, establishing OSTM1 as a negative regulator of preosteoclast fusion [PMID:29297601, PMID:25359771]. OSTM1 is independently essential for neuronal autophagy homeostasis, with its loss causing autophagosome accumulation, mTOR downregulation, and storage of undegraded macromolecules [PMID:24719316], and for cell-autonomous T cell ontogeny via a Foxo1-Klf2-S1pr1-Gnai1-Rac1 axis [PMID:35434560]. Mutations disrupting OSTM1 or the CLC-7/OSTM1 complex cause osteopetrosis [PMID:24820037, PMID:24159188].","teleology":[{"year":2006,"claim":"Established the foundational identity of OSTM1 as the β-subunit of CLC-7, answering what molecular partner explains the shared osteopetrotic phenotype of Ostm1 and Clcn7 loss.","evidence":"Reciprocal co-immunoprecipitation, subcellular co-localization, and CLC-7 protein-level analysis in grey-lethal mice","pmids":["16525474"],"confidence":"High","gaps":["Did not resolve the structural basis of the interaction","Did not separate the stabilization role from a gating/regulatory role"]},{"year":2006,"claim":"Identified how OSTM1 expression is transcriptionally coupled to osteoclastogenesis, showing MITF directly drives Ostm1 in concert with Clcn7.","evidence":"EMSA with anti-MITF supershift and M-box mutation, ChIP, and reporter assays during osteoclast differentiation","pmids":["17105730"],"confidence":"Medium","gaps":["Single lab","Does not address post-transcriptional or trafficking regulation of OSTM1"]},{"year":2008,"claim":"Demonstrated that OSTM1 function extends beyond osteoclasts into multiple hematopoietic lineages, reframing the osteopetrotic defect as non-cell-autonomous at the committed-osteoclast stage.","evidence":"Cell-type-specific conditional transgenic rescue (osteoclast-restricted vs PU.1-driven) and flow cytometry of hematopoietic lineages","pmids":["18790735"],"confidence":"Medium","gaps":["Molecular function in lymphoid lineages not defined","Apparent tension with later osteoclast-intrinsic rescue data"]},{"year":2008,"claim":"Linked OSTM1 to Wnt/β-catenin signaling, proposing a function distinct from its lysosomal CLC-7 role.","evidence":"Overexpression/knockdown in F9 cells, Lef/Tcf reporter assays, and β-catenin/Lef1 co-IP","pmids":["18296023"],"confidence":"Medium","gaps":["Single lab and cell line","Mechanistic connection to the lysosomal/CLC-7 function unresolved","No in vivo confirmation"]},{"year":2013,"claim":"Defined the biophysical mechanism of CLC-7/OSTM1 gating, showing slow activation is common gating dependent on the CBS-containing C-terminus.","evidence":"Electrophysiology with CLC-7 mutants and trans-complementation of truncated constructs in heterologous cells","pmids":["23983121"],"confidence":"High","gaps":["Did not establish OSTM1's direct contribution to gating","Physiological role of slow gating not yet demonstrated"]},{"year":2013,"claim":"Provided causal evidence that slow gating is physiologically required, identifying a CBS2 mutation that accelerates gating and causes osteopetrosis despite intact complex assembly.","evidence":"Autozygosity mapping, genome sequencing, electrophysiology, and lysosomal localization in bovine osteopetrosis","pmids":["24159188"],"confidence":"Medium","gaps":["Single natural mutation","Mechanism linking gating speed to bone resorption not detailed"]},{"year":2014,"claim":"Dissected protein-presence versus ion-transport contributions, establishing that distinct CLC-7/OSTM1-related phenotypes have separable molecular requirements.","evidence":"Transport-deficient CLC-7 knock-in mice with multi-phenotype analysis","pmids":["24820037"],"confidence":"High","gaps":["Does not explain why pigmentation tolerates transport loss","Downstream effectors of Cl⁻ conductance in neurodegeneration unknown"]},{"year":2014,"claim":"Revealed a cell-autonomous neuronal role for OSTM1 in autophagy homeostasis independent of the hematopoietic compartment.","evidence":"Cell-type-specific transgenic rescue, autophagosome/mTOR markers, and storage-material histology in Ostm1-null mice","pmids":["24719316"],"confidence":"Medium","gaps":["Whether autophagy defect is downstream of CLC-7 dysfunction unresolved","Single lab"]},{"year":2014,"claim":"Showed a secreted truncated OSTM1 can act extracellularly to inhibit osteoclast fusion, introducing a ligand-like activity for the protein.","evidence":"Cell-surface binding, osteoclast differentiation assays, BLIMP1-NFATc1 expression analysis, and in vivo bone destruction model","pmids":["25359771"],"confidence":"Medium","gaps":["Surface receptor for truncated OSTM1 not identified","Relationship to full-length membrane function unclear"]},{"year":2015,"claim":"Identified a cytosolic scaffolding/trafficking function for OSTM1, showing direct binding to KIF5B that links it to motor-driven cargo transport.","evidence":"Protein screen, co-IP with KIF5B, subcellular fractionation, and glycosylation analysis","pmids":["26598607"],"confidence":"Medium","gaps":["Cargo identity incompletely defined","How trafficking role coordinates with CLC-7 β-subunit role unknown"]},{"year":2018,"claim":"Established osteoclast-intrinsic sufficiency and defined OSTM1 as a negative regulator of preosteoclast fusion acting through calcium and NFATc1.","evidence":"Conditional transmembrane-domain deletion in osteoclasts, calcium imaging, NFATc1 nuclear localization, and endolysosomal trafficking analysis","pmids":["29297601"],"confidence":"Medium","gaps":["Mechanism linking OSTM1 loss to calcium elevation unresolved","Single lab"]},{"year":2020,"claim":"Resolved the structural architecture of the complex, showing an OSTM1 dimer caps and shields the CLC-7 luminal face while the membrane-embedded interface tunes slow gating.","evidence":"Cryo-EM structures of CLC-7 alone and CLC-7/OSTM1 with accompanying electrophysiology","pmids":["32749217","32851177"],"confidence":"High","gaps":["Conformational states underlying gating transitions not fully captured","Structural basis of disease mutations not all mapped"]},{"year":2022,"claim":"Extended OSTM1's essential role to T cell development, identifying a Foxo1-Klf2-S1pr1-Gnai1-Rac1 axis disrupted by its loss.","evidence":"Conditional transgenic rescue, flow cytometry of thymic T cell subsets, and transcriptome analysis","pmids":["35434560"],"confidence":"Medium","gaps":["Direct molecular link between OSTM1 and the signaling axis not defined","Whether lysosomal or scaffolding activity drives the phenotype unclear"]},{"year":2025,"claim":"Placed OSTM1 in a SNX10/CLC-7 lysosome-positioning module controlling osteoclast fusion arrest and resorption.","evidence":"Co-IP, immunofluorescence co-localization, and lysosome distribution analysis in knockout cells","pmids":["41408708"],"confidence":"Medium","gaps":["Direct SNX10-OSTM1 interaction not shown","Mechanism coupling peripheral lysosome position to fusion control incomplete"]},{"year":2025,"claim":"Proposed surface La protein as a downstream effector of OSTM1 loss in osteoclast hyperfusion.","evidence":"Surface immunofluorescence and inhibitory antibody rescue of fusion/resorption in OSTM1-KO osteoclasts (preprint)","pmids":["bio_10.1101_2025.09.07.674639"],"confidence":"Low","gaps":["No biochemical OSTM1-La interaction data","Single lab preprint, not peer-reviewed","Mechanism of La surface elevation unknown"]},{"year":2026,"claim":"Identified a moonlighting E3 ubiquitin ligase activity for cytosolic non-glycosylated OSTM1 that degrades PDE3B to sustain cAMP/PKA/CREB tumor suppression in B cells.","evidence":"Whole-genome CRISPR screen, B-cell conditional knockout mice, E3 ligase and PDE3B ubiquitination/degradation assays (preprint)","pmids":["41659680"],"confidence":"Medium","gaps":["Preprint, not yet peer-reviewed","Structural basis of ligase activity unknown","Relationship between cytosolic ligase pool and membrane CLC-7 pool unresolved"]},{"year":null,"claim":"How OSTM1's distinct activities—CLC-7 β-subunit, KIF5B-linked trafficking adaptor, and cytosolic E3 ligase—are partitioned and coordinated within a single protein remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unifying model linking glycosylated membrane and non-glycosylated cytosolic pools","Substrate range of the E3 ligase activity beyond PDE3B unknown","Mechanistic basis for tissue-specific phenotypes incomplete"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,2,3]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[9,14]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[15]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[15]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[0,9,14]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,9]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[9]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[9]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[11,16]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[9,15]}],"pathway":[{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[0,3,4]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[8]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[9,14]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[10,13]}],"complexes":["CLC-7/OSTM1 chloride/proton exchanger"],"partners":["CLCN7","KIF5B","SNX10","PDE3B"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86WC4","full_name":"Osteopetrosis-associated transmembrane protein 1","aliases":["Chloride channel 7 beta subunit"],"length_aa":334,"mass_kda":37.3,"function":"Required for osteoclast and melanocyte maturation and function","subcellular_location":"Lysosome membrane","url":"https://www.uniprot.org/uniprotkb/Q86WC4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/OSTM1","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CLCN7","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/search/OSTM1","total_profiled":1310},"omim":[{"mim_id":"607649","title":"OSTEOPETROSIS-ASSOCIATED TRANSMEMBRANE PROTEIN 1; OSTM1","url":"https://www.omim.org/entry/607649"},{"mim_id":"602727","title":"CHLORIDE CHANNEL 7; CLCN7","url":"https://www.omim.org/entry/602727"},{"mim_id":"602726","title":"CHLORIDE CHANNEL 6; CLCN6","url":"https://www.omim.org/entry/602726"},{"mim_id":"259720","title":"OSTEOPETROSIS, AUTOSOMAL RECESSIVE 5; OPTB5","url":"https://www.omim.org/entry/259720"},{"mim_id":"259710","title":"OSTEOPETROSIS, AUTOSOMAL RECESSIVE 2; OPTB2","url":"https://www.omim.org/entry/259710"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Vesicles","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/OSTM1"},"hgnc":{"alias_symbol":["HSPC019","GL"],"prev_symbol":[]},"alphafold":{"accession":"Q86WC4","domains":[{"cath_id":"1.20.58","chopping":"81-170","consensus_level":"medium","plddt":89.7884,"start":81,"end":170},{"cath_id":"1.20.58","chopping":"181-305","consensus_level":"medium","plddt":85.1989,"start":181,"end":305}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86WC4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86WC4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86WC4-F1-predicted_aligned_error_v6.png","plddt_mean":73.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=OSTM1","jax_strain_url":"https://www.jax.org/strain/search?query=OSTM1"},"sequence":{"accession":"Q86WC4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86WC4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86WC4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86WC4"}},"corpus_meta":[{"pmid":"16525474","id":"PMC_16525474","title":"ClC-7 requires Ostm1 as a beta-subunit to support bone resorption and lysosomal function.","date":"2006","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/16525474","citation_count":271,"is_preprint":false},{"pmid":"16813530","id":"PMC_16813530","title":"Mutations in OSTM1 (grey lethal) define a particularly severe form of autosomal recessive osteopetrosis with neural involvement.","date":"2006","source":"Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research","url":"https://pubmed.ncbi.nlm.nih.gov/16813530","citation_count":81,"is_preprint":false},{"pmid":"17105730","id":"PMC_17105730","title":"The expression of Clcn7 and Ostm1 in osteoclasts is coregulated by microphthalmia transcription factor.","date":"2006","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/17105730","citation_count":64,"is_preprint":false},{"pmid":"32749217","id":"PMC_32749217","title":"Cryo-EM structure of the lysosomal chloride-proton exchanger CLC-7 in complex with OSTM1.","date":"2020","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/32749217","citation_count":59,"is_preprint":false},{"pmid":"21107136","id":"PMC_21107136","title":"Distinct neuropathologic phenotypes after disrupting the chloride transport proteins ClC-6 or ClC-7/Ostm1.","date":"2010","source":"Journal of neuropathology and experimental neurology","url":"https://pubmed.ncbi.nlm.nih.gov/21107136","citation_count":53,"is_preprint":false},{"pmid":"32851177","id":"PMC_32851177","title":"Molecular insights into the human CLC-7/Ostm1 transporter.","date":"2020","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/32851177","citation_count":50,"is_preprint":false},{"pmid":"24820037","id":"PMC_24820037","title":"Transport activity and presence of ClC-7/Ostm1 complex account for different cellular functions.","date":"2014","source":"EMBO 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Part A","url":"https://pubmed.ncbi.nlm.nih.gov/36369659","citation_count":1,"is_preprint":false},{"pmid":"41408708","id":"PMC_41408708","title":"The molecular and functional interplay between the osteopetrosis-associated proteins SNX10, OSTM1, and CLC-7 during mouse osteoclastogenesis.","date":"2025","source":"Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research","url":"https://pubmed.ncbi.nlm.nih.gov/41408708","citation_count":0,"is_preprint":false},{"pmid":"41659680","id":"PMC_41659680","title":"OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway.","date":"2026","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41659680","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.03.31.646258","title":"The molecular and cellular interplay between the osteopetrosis-associated proteins SNX10, OSTM1, and CLC-7 during osteoclastogenesis","date":"2025-03-31","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.31.646258","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.09.07.25335133","title":"GWAS for Periodontitis Phenotypes Using Multi-Ancestry All of Us Research Platform","date":"2025-09-08","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.07.25335133","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.09.07.674639","title":"Elevated surface La promotes hyperfusion and contributes to impaired resorption in osteopetrosis","date":"2025-09-08","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.07.674639","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.07.11.659973","title":"Context-dependent regulatory variants in Alzheimer’s disease","date":"2025-07-11","source":"bioRxiv","url":"https://doi.org/10.1101/2025.07.11.659973","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":20083,"output_tokens":4582,"usd":0.06449,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12695,"output_tokens":5084,"usd":0.095287,"stage2_stop_reason":"end_turn"},"total_usd":0.159777,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"OSTM1 (Ostm1) forms a molecular complex with ClC-7, co-localizing in late endosomes and lysosomes and in the ruffled border of bone-resorbing osteoclasts, functioning as a β-subunit of ClC-7. ClC-7 is required for Ostm1 to reach lysosomes, where the highly glycosylated Ostm1 luminal domain is cleaved. In Ostm1-deficient (grey-lethal) mice, ClC-7 protein levels fall below 10% of normal, indicating Ostm1 is required for ClC-7 protein stability.\",\n      \"method\": \"Co-immunoprecipitation, subcellular co-localization (immunofluorescence/fractionation), protein level analysis in grey-lethal mice\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, direct localization with functional consequence, protein stability data; replicated and foundational study\",\n      \"pmids\": [\"16525474\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Cryo-EM structures of CLC-7 alone and in complex with OSTM1 at up to 2.8 Å resolution show that the luminal surface of CLC-7 is entirely covered by a dimer of heavily glycosylated and disulfide-bonded OSTM1, which protects CLC-7 from the degradative lysosomal lumen. OSTM1 binding causes only minor conformational changes in the ion-conduction pathway of CLC-7, potentially contributing to its regulatory role.\",\n      \"method\": \"Cryo-electron microscopy (cryo-EM) structural determination\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution cryo-EM structure with functional interpretation, independent of prior co-IP data\",\n      \"pmids\": [\"32749217\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Cryo-EM structure of human CLC-7/Ostm1 complex reveals that Ostm1 functions as a lid positioned above CLC-7, interacting extensively with CLC-7 within the membrane. Structural analyses and electrophysiology studies indicate that the domain interaction interfaces between the amino terminus, TMD, and CBS domains of CLC-7 affect the slow gating kinetics of CLC-7/Ostm1.\",\n      \"method\": \"Cryo-EM structural determination combined with electrophysiology\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure plus electrophysiology in a single study, orthogonal methods\",\n      \"pmids\": [\"32851177\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Slow voltage-dependent activation of ClC-7/Ostm1 operates via common gating (acting on both subunits of the dimer simultaneously, not protopore gates). The CBS domain-containing C-terminus is required for currents and slow gating; when ClC-7 was truncated after the last intramembrane helix, currents were abolished but restored by co-expression of the C-terminus alone or fused to the Ostm1 C-terminus.\",\n      \"method\": \"Electrophysiology with ClC-7 mutants and trans-complementation of truncated constructs in heterologous expression\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of gating using mutagenesis and electrophysiology, multiple mutant combinations tested\",\n      \"pmids\": [\"23983121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Using ion transport-deficient ClC-7 knock-in mice (Clcn7td/td), it was established that both protein-protein interactions (presence of ClC-7/Ostm1 complex) and ion transport activity are mechanistically separable contributors to different ClC-7-related disease phenotypes: osteopetrosis requires both, whereas hair pigmentation requires only protein presence (not transport activity), and neurodegeneration is exacerbated by Cl− conductance.\",\n      \"method\": \"In vivo knock-in mouse models with defined transport-deficient mutations, phenotypic analysis\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with defined knock-in alleles, multiple phenotypes dissected in vivo\",\n      \"pmids\": [\"24820037\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"MITF transcription factor directly binds a single M-box in the Ostm1 promoter, as shown by EMSA with anti-MITF supershift and abolition of binding by M-box mutation, and by chromatin immunoprecipitation. MITF co-regulates Ostm1 expression during osteoclastogenesis in concert with Clcn7.\",\n      \"method\": \"EMSA, ChIP, reporter gene assay, microarray\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — EMSA with supershift and mutagenesis plus ChIP, single lab\",\n      \"pmids\": [\"17105730\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"OSTM1 is required for Wnt/β-catenin canonical signaling: overexpression of OSTM1 in F9 cells increased Wnt3a-responsive β-catenin accumulation and Lef/Tcf-sensitive transcription, while knockdown attenuated Wnt3a signaling. Wild-type OSTM1 stimulated the Wnt-dependent association of β-catenin with Lef1, whereas an osteopetrosis-associated C-terminal deletion mutant inhibited this interaction and Lef/Tcf transcription even with constitutively active β-catenin, but not with a β-catenin/Lef chimera.\",\n      \"method\": \"Overexpression and knockdown in F9 cells, reporter gene assays, co-immunoprecipitation of β-catenin/Lef1\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — co-IP and reporter assays, single lab, two orthogonal functional readouts\",\n      \"pmids\": [\"18296023\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The gl (Ostm1-null) osteopetrotic defect is non-cell autonomous: conditional Ostm1 transgene targeted only to committed osteoclasts did not rescue the bone phenotype, but expression driven by PU.1 (broader hematopoietic cells) rescued osteoclast function as well as B- and T-lymphoid lineage phenotypes, establishing an essential role for Ostm1 in multiple hematopoietic cell types beyond osteoclasts.\",\n      \"method\": \"Conditional transgenic mouse rescue experiments, flow cytometric analysis of hematopoietic lineages\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis via cell-type-specific transgenic rescue, single lab\",\n      \"pmids\": [\"18790735\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In Ostm1-null mice, severe neurodegeneration is accompanied by accumulation of autophagosomes causing axonal swelling, downregulation of mTOR signaling, and storage of carbohydrates, lipids, and ubiquitinated proteins in neurons. Cell-type-specific transgenic rescue showed that Ostm1 has a primary and autonomous role in neuronal homeostasis independent of the hematopoietic lineage.\",\n      \"method\": \"Conditional transgenic mouse rescue, immunohistochemistry, autophagosome and mTOR pathway markers, cell-type specific targeting\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-autonomous rescue in defined CNS subpopulations, multiple cellular markers, single lab\",\n      \"pmids\": [\"24719316\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Ostm1 is a type I transmembrane protein (immature 34 kDa) that undergoes post-translational N-glycosylation to ~60 kDa mature form. It localizes to the endoplasmic reticulum, trans-Golgi network, and endosomes/lysosomes. A direct interaction between Ostm1 and kinesin 5B (KIF5B) heavy chains was demonstrated, placing Ostm1 in a cytosolic scaffolding multiprotein complex that acts as a trafficking adaptor for cargo movement from the ER to late endosomal/lysosomal compartments.\",\n      \"method\": \"Protein screen, co-immunoprecipitation, subcellular fractionation and localization, biochemical analysis of glycosylation\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct co-IP interaction with KIF5B validated, localization and trafficking demonstrated, single lab\",\n      \"pmids\": [\"26598607\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Conditional deletion of the Ostm1 transmembrane domain in osteoclasts alone reproduced the full osteopetrotic phenotype, demonstrating osteoclast-intrinsic deficiency is sufficient. Ostm1 loss of transmembrane domain causes oversized osteoclasts with enhanced multinucleation, elevated intracellular calcium, NFATc1 nuclear re-localization, and upregulation of NFATc1 target genes, establishing Ostm1 as a negative regulator of preosteoclast fusion. Mature osteoclasts show appropriate acidification levels but mislocalized endolysosomes, and TRAP/cathepsin K are sequestered intracellularly rather than secreted.\",\n      \"method\": \"Conditional mouse knock-in (transmembrane domain deletion), osteoclast culture, calcium imaging, NFATc1 nuclear localization assay, lysosomal trafficking analysis\",\n      \"journal\": \"Journal of bone and mineral research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional genetic model with multiple orthogonal cellular phenotype readouts, single lab\",\n      \"pmids\": [\"29297601\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"A secreted truncated form of OSTM1 (lacking the transmembrane domain) binds to the cell surface of osteoclast precursors and inhibits multinucleated osteoclast formation by reducing cell fusion and survival, acting through downregulation of the BLIMP1-NFATc1 transcriptional axis. In vivo, truncated OSTM1 reduced LPS-induced bone destruction.\",\n      \"method\": \"Cell surface binding assay, osteoclast differentiation assay, gene expression analysis, in vivo bone destruction model\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — cell binding and functional osteoclast assays with pathway marker analysis, single lab\",\n      \"pmids\": [\"25359771\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"A missense mutation (Y750Q) in the CBS2 domain of ClC-7 largely preserves lysosomal localization and assembly of the ClC-7/Ostm1 complex but drastically accelerates voltage-dependent gating of ClC-7/Ostm1, causing osteopetrosis in cattle. This provides direct evidence that accelerated ClC-7/Ostm1 gating per se is pathogenic, demonstrating a physiological requirement for slow voltage activation.\",\n      \"method\": \"Autozygosity mapping, genome sequencing, electrophysiology, lysosomal localization assay in cell models\",\n      \"journal\": \"Disease models & mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — natural mutation characterized by electrophysiology and localization with disease phenotype, single study\",\n      \"pmids\": [\"24159188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Ostm1 is an essential regulator of T cell ontogeny: Ostm1 ablation caused a cell-autonomous defect in early T cell precursors (ETP, DN subpopulations) in the thymus. Transcriptome analysis identified an Ostm1 crosstalk with a Foxo1-Klf2-S1pr1-Gnai1-Rac1 signaling axis in DN1 T cells. Transgenic rescue of Ostm1 in DN1 cells partially rescued T cell subpopulations from ETP onwards.\",\n      \"method\": \"Conditional transgenic rescue, flow cytometry of T cell subpopulations, transcriptome analysis\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-autonomous rescue with transcriptomic pathway identification, single lab\",\n      \"pmids\": [\"35434560\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SNX10 physically interacts with CLC-7 (co-immunoprecipitation), and loss of SNX10 reduces peripheral LAMP1-positive lysosomes containing CLC-7 and OSTM1. Loss of CLC-7 also depletes peripheral OSTM1-containing lysosomes. All three proteins (SNX10, CLC-7, OSTM1) co-localize in LAMP1-positive lysosomes and regulate lysosome trafficking to the cell periphery, which controls both fusion arrest and functionality of mature osteoclasts.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence co-localization, knockout cell culture, lysosome distribution analysis\",\n      \"journal\": \"Journal of bone and mineral research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus localization in KO cells with functional phenotype, single lab\",\n      \"pmids\": [\"41408708\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"A cytosolic, non-glycosylated fraction of OSTM1 functions as an E3 ubiquitin ligase that targets phosphodiesterase 3B (PDE3B) for proteasomal degradation. Loss of OSTM1 stabilizes PDE3B, which increases conversion of cAMP to AMP and suppresses the cAMP/PKA/CREB tumor suppressive pathway, thereby promoting B-cell lymphomagenesis.\",\n      \"method\": \"Whole-genome CRISPR screen, B-cell-specific Ostm1 conditional knockout mouse, E3 ligase activity assay, PDE3B ubiquitination and degradation assays, cAMP/PKA/CREB pathway analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR screen plus mechanistic follow-up with substrate degradation assay and pathway analysis; preprint, not yet peer-reviewed\",\n      \"pmids\": [\"41659680\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"La protein is greatly elevated at the surface of osteoclasts upon loss of OSTM1 (or SNX10). Inhibitory antibodies against La suppressed excessive osteoclast fusion and restored resorptive function in OSTM1-deficient osteoclasts, establishing a functional link between OSTM1 loss and dysregulated surface La in osteoclast hyperfusion.\",\n      \"method\": \"Immunofluorescence surface labeling, inhibitory antibody treatment, osteoclast fusion and resorption assays in OSTM1-KO cells\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab preprint, surface labeling and antibody inhibition, no biochemical interaction data for OSTM1-La\",\n      \"pmids\": [\"bio_10.1101_2025.09.07.674639\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"OSTM1 is a type I transmembrane glycoprotein that functions as the obligate β-subunit of the lysosomal CLC-7 Cl⁻/H⁺ exchanger—covering and protecting CLC-7's luminal face, stabilizing CLC-7 protein, and modulating its slow voltage-dependent gating—while also acting as a cytosolic scaffolding adaptor (via KIF5B) for endolysosomal trafficking, a negative regulator of preosteoclast fusion through the NFATc1 axis, an essential factor in neuronal autophagy homeostasis, a regulator of T cell ontogeny through the Foxo1-Klf2-S1pr1-Gnai1-Rac1 axis, and, in its non-glycosylated cytosolic fraction, an E3 ubiquitin ligase that degrades PDE3B to sustain the cAMP/PKA/CREB tumor-suppressive pathway in B cells.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"OSTM1 is a type I transmembrane glycoprotein that functions as the obligate β-subunit of the lysosomal CLC-7 Cl⁻/H⁺ exchanger, governing endolysosomal ion homeostasis in osteoclasts and neurons [#0, #1]. It forms a molecular complex with CLC-7 in late endosomes, lysosomes, and the osteoclast ruffled border, where a glycosylated dimer of OSTM1 covers the entire luminal surface of CLC-7 to shield it from lysosomal degradation and stabilize CLC-7 protein levels [#0, #1]. Beyond stabilization, OSTM1 contributes to the slow common gating of the CLC-7 complex through interactions involving the CLC-7 N-terminus, transmembrane domain, and CBS domains, and physiologically slow voltage activation is itself required—accelerated gating alone is pathogenic [#2, #3, #12]. Protein-protein interaction and ion transport are separable functions: osteopetrosis requires both, hair pigmentation requires only complex presence, and neurodegeneration is exacerbated by Cl⁻ conductance [#4]. OSTM1 also acts as a cytosolic scaffolding adaptor that binds KIF5B heavy chains to direct trafficking of cargo toward late endosomal/lysosomal compartments [#9], and it positions lysosomes at the cell periphery together with SNX10 and CLC-7 to control osteoclast fusion arrest and resorptive function [#14]. Loss of OSTM1 in osteoclasts causes oversized, hyperfused cells with elevated intracellular calcium and NFATc1 nuclear relocalization, establishing OSTM1 as a negative regulator of preosteoclast fusion [#10, #11]. OSTM1 is independently essential for neuronal autophagy homeostasis, with its loss causing autophagosome accumulation, mTOR downregulation, and storage of undegraded macromolecules [#8], and for cell-autonomous T cell ontogeny via a Foxo1-Klf2-S1pr1-Gnai1-Rac1 axis [#13]. Mutations disrupting OSTM1 or the CLC-7/OSTM1 complex cause osteopetrosis [#4, #12].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Established the foundational identity of OSTM1 as the β-subunit of CLC-7, answering what molecular partner explains the shared osteopetrotic phenotype of Ostm1 and Clcn7 loss.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation, subcellular co-localization, and CLC-7 protein-level analysis in grey-lethal mice\",\n      \"pmids\": [\"16525474\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the structural basis of the interaction\", \"Did not separate the stabilization role from a gating/regulatory role\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Identified how OSTM1 expression is transcriptionally coupled to osteoclastogenesis, showing MITF directly drives Ostm1 in concert with Clcn7.\",\n      \"evidence\": \"EMSA with anti-MITF supershift and M-box mutation, ChIP, and reporter assays during osteoclast differentiation\",\n      \"pmids\": [\"17105730\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Does not address post-transcriptional or trafficking regulation of OSTM1\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Demonstrated that OSTM1 function extends beyond osteoclasts into multiple hematopoietic lineages, reframing the osteopetrotic defect as non-cell-autonomous at the committed-osteoclast stage.\",\n      \"evidence\": \"Cell-type-specific conditional transgenic rescue (osteoclast-restricted vs PU.1-driven) and flow cytometry of hematopoietic lineages\",\n      \"pmids\": [\"18790735\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular function in lymphoid lineages not defined\", \"Apparent tension with later osteoclast-intrinsic rescue data\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Linked OSTM1 to Wnt/β-catenin signaling, proposing a function distinct from its lysosomal CLC-7 role.\",\n      \"evidence\": \"Overexpression/knockdown in F9 cells, Lef/Tcf reporter assays, and β-catenin/Lef1 co-IP\",\n      \"pmids\": [\"18296023\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab and cell line\", \"Mechanistic connection to the lysosomal/CLC-7 function unresolved\", \"No in vivo confirmation\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Defined the biophysical mechanism of CLC-7/OSTM1 gating, showing slow activation is common gating dependent on the CBS-containing C-terminus.\",\n      \"evidence\": \"Electrophysiology with CLC-7 mutants and trans-complementation of truncated constructs in heterologous cells\",\n      \"pmids\": [\"23983121\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish OSTM1's direct contribution to gating\", \"Physiological role of slow gating not yet demonstrated\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Provided causal evidence that slow gating is physiologically required, identifying a CBS2 mutation that accelerates gating and causes osteopetrosis despite intact complex assembly.\",\n      \"evidence\": \"Autozygosity mapping, genome sequencing, electrophysiology, and lysosomal localization in bovine osteopetrosis\",\n      \"pmids\": [\"24159188\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single natural mutation\", \"Mechanism linking gating speed to bone resorption not detailed\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Dissected protein-presence versus ion-transport contributions, establishing that distinct CLC-7/OSTM1-related phenotypes have separable molecular requirements.\",\n      \"evidence\": \"Transport-deficient CLC-7 knock-in mice with multi-phenotype analysis\",\n      \"pmids\": [\"24820037\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not explain why pigmentation tolerates transport loss\", \"Downstream effectors of Cl⁻ conductance in neurodegeneration unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Revealed a cell-autonomous neuronal role for OSTM1 in autophagy homeostasis independent of the hematopoietic compartment.\",\n      \"evidence\": \"Cell-type-specific transgenic rescue, autophagosome/mTOR markers, and storage-material histology in Ostm1-null mice\",\n      \"pmids\": [\"24719316\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether autophagy defect is downstream of CLC-7 dysfunction unresolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showed a secreted truncated OSTM1 can act extracellularly to inhibit osteoclast fusion, introducing a ligand-like activity for the protein.\",\n      \"evidence\": \"Cell-surface binding, osteoclast differentiation assays, BLIMP1-NFATc1 expression analysis, and in vivo bone destruction model\",\n      \"pmids\": [\"25359771\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Surface receptor for truncated OSTM1 not identified\", \"Relationship to full-length membrane function unclear\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identified a cytosolic scaffolding/trafficking function for OSTM1, showing direct binding to KIF5B that links it to motor-driven cargo transport.\",\n      \"evidence\": \"Protein screen, co-IP with KIF5B, subcellular fractionation, and glycosylation analysis\",\n      \"pmids\": [\"26598607\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cargo identity incompletely defined\", \"How trafficking role coordinates with CLC-7 β-subunit role unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Established osteoclast-intrinsic sufficiency and defined OSTM1 as a negative regulator of preosteoclast fusion acting through calcium and NFATc1.\",\n      \"evidence\": \"Conditional transmembrane-domain deletion in osteoclasts, calcium imaging, NFATc1 nuclear localization, and endolysosomal trafficking analysis\",\n      \"pmids\": [\"29297601\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking OSTM1 loss to calcium elevation unresolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Resolved the structural architecture of the complex, showing an OSTM1 dimer caps and shields the CLC-7 luminal face while the membrane-embedded interface tunes slow gating.\",\n      \"evidence\": \"Cryo-EM structures of CLC-7 alone and CLC-7/OSTM1 with accompanying electrophysiology\",\n      \"pmids\": [\"32749217\", \"32851177\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Conformational states underlying gating transitions not fully captured\", \"Structural basis of disease mutations not all mapped\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extended OSTM1's essential role to T cell development, identifying a Foxo1-Klf2-S1pr1-Gnai1-Rac1 axis disrupted by its loss.\",\n      \"evidence\": \"Conditional transgenic rescue, flow cytometry of thymic T cell subsets, and transcriptome analysis\",\n      \"pmids\": [\"35434560\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular link between OSTM1 and the signaling axis not defined\", \"Whether lysosomal or scaffolding activity drives the phenotype unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placed OSTM1 in a SNX10/CLC-7 lysosome-positioning module controlling osteoclast fusion arrest and resorption.\",\n      \"evidence\": \"Co-IP, immunofluorescence co-localization, and lysosome distribution analysis in knockout cells\",\n      \"pmids\": [\"41408708\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct SNX10-OSTM1 interaction not shown\", \"Mechanism coupling peripheral lysosome position to fusion control incomplete\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Proposed surface La protein as a downstream effector of OSTM1 loss in osteoclast hyperfusion.\",\n      \"evidence\": \"Surface immunofluorescence and inhibitory antibody rescue of fusion/resorption in OSTM1-KO osteoclasts (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.09.07.674639\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No biochemical OSTM1-La interaction data\", \"Single lab preprint, not peer-reviewed\", \"Mechanism of La surface elevation unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified a moonlighting E3 ubiquitin ligase activity for cytosolic non-glycosylated OSTM1 that degrades PDE3B to sustain cAMP/PKA/CREB tumor suppression in B cells.\",\n      \"evidence\": \"Whole-genome CRISPR screen, B-cell conditional knockout mice, E3 ligase and PDE3B ubiquitination/degradation assays (preprint)\",\n      \"pmids\": [\"41659680\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not yet peer-reviewed\", \"Structural basis of ligase activity unknown\", \"Relationship between cytosolic ligase pool and membrane CLC-7 pool unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How OSTM1's distinct activities—CLC-7 β-subunit, KIF5B-linked trafficking adaptor, and cytosolic E3 ligase—are partitioned and coordinated within a single protein remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unifying model linking glycosylated membrane and non-glycosylated cytosolic pools\", \"Substrate range of the E3 ligase activity beyond PDE3B unknown\", \"Mechanistic basis for tissue-specific phenotypes incomplete\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 2, 3]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [9, 14]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [15]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [0, 9, 14]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 9]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [11, 16]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [9, 15]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [0, 3, 4]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [9, 14]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [10, 13]}\n    ],\n    \"complexes\": [\"CLC-7/OSTM1 chloride/proton exchanger\"],\n    \"partners\": [\"CLCN7\", \"KIF5B\", \"SNX10\", \"PDE3B\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}