{"gene":"ANKRD13A","run_date":"2026-06-09T22:02:43","timeline":{"discoveries":[{"year":2016,"finding":"ANKRD13A (Ankrd13 family) contains ubiquitin-interacting motifs (UIMs) that bind preferentially to Lys-63-linked polyubiquitin chains on Caveolin-1 (Cav-1), forming a ternary complex with VCP/p97 on endosomal membranes to facilitate lysosomal trafficking of ubiquitinated Cav-1 oligomers.","method":"Co-immunoprecipitation, mass spectrometry (ubiquitin chain-type analysis), UIM-deletion mutagenesis, overexpression phenotypic assay (enlarged hollow late endosomes), interaction studies with IBMPFD-associated VCP mutants","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (Co-IP, MS ubiquitin linkage analysis, domain mutagenesis, phenotypic rescue) in a single rigorous study","pmids":["26797118"],"is_preprint":false},{"year":2020,"finding":"ANKRD13A forms a complex with RNF11 (RING finger protein 11) in vivo via its UIMs, and this interaction is modulated by EGF stimulation. A ternary complex of ANKRD13A, RNF11, and activated EGFR is transiently assembled during early receptor endocytosis. Loss of ITCH E3 ligase abrogates ANKRD13A ubiquitination while loss of RNF11 increases it; the ubiquitination status of ANKRD13A controls its ability to bind activated EGFR, thereby regulating EGFR sorting for lysosomal degradation.","method":"SILAC-based co-immunoprecipitation proteomics, in vivo Co-IP with UIM-deletion mutants, EGF stimulation time-course assays, loss-of-function (RNAi) of ITCH and RNF11 with ubiquitination readout","journal":"The FEBS journal","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, SILAC proteomics, domain mutagenesis, and functional loss-of-function in a single study with multiple orthogonal methods","pmids":["31985874"],"is_preprint":false},{"year":2021,"finding":"ANKRD13A acts as a novel component of TNF signaling complex-II (death-inducing complex). It binds to ubiquitinated RIP1 via its UIM domain and limits the association of FADD and caspase-8 with RIP1, thereby setting a higher threshold for TNF-induced cell death without affecting NF-κB activation. ANKRD13A deficiency shifts the cellular response to TNF from survival to apoptosis.","method":"Co-immunoprecipitation of ANKRD13A with ubiquitinated RIP1, complex-II assembly assays, ANKRD13A knockout/knockdown with TNF-induced cell death and NF-κB reporter readouts, UIM-dependent interaction studies","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, genetic knockout with defined phenotype, pathway epistasis (NF-κB vs. complex-II), multiple orthogonal methods in one study","pmids":["34839354"],"is_preprint":false},{"year":2025,"finding":"ANKRD13A relocates to depolarized mitochondria upon PINK1/Parkin activation and promotes mitophagy by recruiting VCP/p97 to the mitochondrial outer membrane (OMM). VCP and its recruitment factors including ANKRD13A are required for OMM rupture, which exposes inner mitochondrial membrane mitophagy receptors for autophagic recognition.","method":"Live-cell fluorescence imaging (novel OMM-rupture biosensor), ANKRD13A localization assay (fractionation/imaging of depolarized mitochondria), Co-IP with mitochondrial proteins, loss-of-function (knockdown/knockout) with mitophagy and OMM-rupture readouts","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Moderate — novel biosensor for direct visualization, Co-IP, loss-of-function with specific phenotypic readout (OMM rupture, mitophagy flux), multiple orthogonal methods","pmids":["40975168"],"is_preprint":false},{"year":2023,"finding":"ANKRD13A is recruited to ubiquitinated Toxoplasma gondii parasitophorous vacuoles (PVs) in IFNγ-stimulated endothelial cells together with p97/VCP and UBXD1. PV ubiquitination is a prerequisite for ANKRD13A recruitment, and its deposition directs Tg PVs to acidification, restricting parasite survival.","method":"Genetic knockdown/knockout with parasite restriction assay, immunofluorescence localization of ANKRD13A to ubiquitinated PVs, IFNγ stimulation experiments, co-depletion epistasis with p97/VCP","journal":"mSphere","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — loss-of-function with defined phenotype (parasite restriction, PV acidification) and direct localization, but single study","pmids":["37975677"],"is_preprint":false},{"year":2013,"finding":"Ankrd13A controls focal adhesion formation and distribution in lens and neural crest cells. miR-204 directly targets Ankrd13A; elevated Ankrd13A (from miR-204 inactivation) causes abnormal focal adhesion dynamics, reduced cell motility, and aberrant lens morphogenesis. In vivo restoration of Ankrd13A levels rescued the lens phenotype.","method":"Morpholino-mediated miR-204 knockdown and Ankrd13A overexpression in medaka (live imaging), in vitro focal adhesion assays, miR-204 target validation (3'UTR reporter), in vivo rescue experiment","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — live imaging epistasis (miR-204/Ankrd13A/focal adhesions), in vivo rescue, but mechanistic detail on ANKRD13A's direct biochemical role in focal adhesion regulation not fully resolved","pmids":["23620728"],"is_preprint":false},{"year":2021,"finding":"ANKRD13A recognizes Lys-63-linked polyubiquitin chains on HLA class I (HLA-I), and elevated ANKRD13A expression (induced by lncRNA USP30-AS1 via H3K4me3/H3K27Ac chromatin changes) promotes HLA-I internalization from the cell membrane, contributing to immune evasion in AML cells.","method":"USP30-AS1 knockdown/overexpression, ANKRD13A knockdown, cell surface HLA-I assay (flow cytometry/imaging), ChIP analysis for histone marks","journal":"Human cell","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, limited direct biochemical validation of ANKRD13A–Lys63-Ub–HLA-I interaction; primarily functional readout with indirect mechanistic inference","pmids":["34694569"],"is_preprint":false}],"current_model":"ANKRD13A is a UIM-containing scaffold protein that selectively recognizes Lys-63-linked polyubiquitin chains on diverse substrates (Caveolin-1, EGFR, RIP1, HLA-I, mitochondrial outer membrane proteins) to coordinate VCP/p97-dependent membrane remodeling (lysosomal trafficking of Cav-1, EGFR endosomal sorting, mitochondrial outer membrane rupture during mitophagy) and modulates cell-death signaling by binding ubiquitinated RIP1 at TNF complex-II to limit FADD/caspase-8 recruitment, thereby acting as a gatekeeper against TNF-induced apoptosis."},"narrative":{"mechanistic_narrative":"ANKRD13A is a ubiquitin-interacting-motif (UIM) scaffold protein that selectively recognizes Lys-63-linked polyubiquitin chains on diverse membrane and signaling substrates to direct VCP/p97-dependent membrane remodeling and trafficking [PMID:26797118, PMID:40975168]. Through its UIMs it binds ubiquitinated Caveolin-1 and assembles a ternary complex with VCP/p97 on endosomal membranes to route Cav-1 oligomers for lysosomal trafficking [PMID:26797118], and it cooperates with the E3 ligase RNF11 and the ITCH-dependent ubiquitination of ANKRD13A itself to gate binding to activated EGFR and its sorting toward lysosomal degradation [PMID:31985874]. Upon PINK1/Parkin-driven mitochondrial depolarization, ANKRD13A relocates to depolarized mitochondria and recruits VCP/p97 to the outer membrane to promote membrane rupture required for mitophagy [PMID:40975168], and it is similarly recruited to ubiquitinated Toxoplasma parasitophorous vacuoles with VCP/p97 and UBXD1 to drive their acidification and restrict the parasite [PMID:37975677]. Beyond trafficking, ANKRD13A binds ubiquitinated RIP1 within TNF complex-II via its UIM and limits FADD/caspase-8 recruitment, raising the threshold for TNF-induced apoptosis without affecting NF-κB activation [PMID:34839354].","teleology":[{"year":2016,"claim":"Established ANKRD13A's core biochemical activity: that its UIMs read Lys-63-linked polyubiquitin and couple a ubiquitinated cargo (Cav-1) to VCP/p97 for lysosomal delivery, defining it as a ubiquitin-selective trafficking adaptor.","evidence":"Co-IP, MS ubiquitin-linkage analysis, UIM-deletion mutagenesis and overexpression phenotypes (enlarged late endosomes) in cells, including IBMPFD VCP mutants","pmids":["26797118"],"confidence":"High","gaps":["No structural model of UIM–Lys63-Ub recognition","Whether VCP recruitment is direct or bridged by additional cofactors not resolved"]},{"year":2020,"claim":"Extended the adaptor role to receptor tyrosine kinase sorting and showed ANKRD13A's own ubiquitination state is a regulatory switch, governed by ITCH and RNF11, for binding activated EGFR.","evidence":"SILAC Co-IP proteomics, UIM-deletion mutants, EGF time-course, and RNAi of ITCH and RNF11 with ubiquitination readouts","pmids":["31985874"],"confidence":"High","gaps":["Site(s) of ANKRD13A ubiquitination not mapped","Functional consequence for EGFR degradation kinetics in vivo not quantified"]},{"year":2021,"claim":"Identified a death-signaling function distinct from trafficking: ANKRD13A binds ubiquitinated RIP1 in TNF complex-II to limit FADD/caspase-8 assembly, positioning it as a checkpoint balancing survival versus apoptosis.","evidence":"Co-IP with ubiquitinated RIP1, complex-II assembly assays, knockout/knockdown with TNF death and NF-κB reporter readouts, UIM-dependent interaction studies","pmids":["34839354"],"confidence":"High","gaps":["Whether VCP/p97 participates in the complex-II function not addressed","Linkage type of RIP1 ubiquitin recognized not directly defined here"]},{"year":2023,"claim":"Showed the ANKRD13A–VCP module is deployed in cell-autonomous immunity, recruited to ubiquitinated pathogen vacuoles to drive their acidification.","evidence":"Knockdown/knockout parasite restriction assay, immunofluorescence localization to ubiquitinated PVs, IFNγ stimulation, co-depletion epistasis with p97/VCP and UBXD1","pmids":["37975677"],"confidence":"Medium","gaps":["Single study","Direct biochemical demonstration of ANKRD13A binding PV ubiquitin not shown"]},{"year":2025,"claim":"Demonstrated ANKRD13A drives mitochondrial outer-membrane rupture during mitophagy by recruiting VCP/p97 to depolarized mitochondria, generalizing its VCP-recruiting trafficking role to organelle quality control.","evidence":"Live-cell OMM-rupture biosensor imaging, localization on depolarized mitochondria, Co-IP with mitochondrial proteins, loss-of-function with mitophagy/OMM-rupture readouts","pmids":["40975168"],"confidence":"High","gaps":["Identity of the ubiquitinated OMM substrate(s) read by ANKRD13A not defined","Relationship to other VCP mitophagy cofactors not delineated"]},{"year":2021,"claim":"Implicated ANKRD13A in tumor immune evasion by promoting Lys-63-Ub-dependent internalization of HLA class I, downstream of lncRNA-driven chromatin activation.","evidence":"USP30-AS1 perturbation, ANKRD13A knockdown, cell-surface HLA-I flow/imaging, ChIP for histone marks in AML cells","pmids":["34694569"],"confidence":"Low","gaps":["Direct ANKRD13A–Lys63-Ub–HLA-I interaction not biochemically validated","Mechanism inferred largely from functional readouts","Single lab"]},{"year":2013,"claim":"Earliest functional link, placing Ankrd13A downstream of miR-204 in regulating focal adhesion dynamics and lens/neural crest morphogenesis.","evidence":"Morpholino miR-204 knockdown and Ankrd13A overexpression with live imaging in medaka, focal adhesion assays, 3'UTR reporter, in vivo rescue","pmids":["23620728"],"confidence":"Medium","gaps":["Direct biochemical role of ANKRD13A in focal adhesion regulation unresolved","Connection to its ubiquitin-trafficking activity not established"]},{"year":null,"claim":"How ANKRD13A discriminates among its many ubiquitinated substrates and is targeted to specific membranes/complexes in a context-dependent manner remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural basis for substrate/linkage selectivity","Determinants of subcellular targeting across endosomes, mitochondria, vacuoles, and complex-II not defined","Whether a unifying VCP-handoff mechanism operates across all contexts unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0031386","term_label":"protein tag activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[3,4]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[2]}],"complexes":["TNF complex-II"],"partners":["VCP","RNF11","ITCH","EGFR","RIPK1","CAVEOLIN-1","UBXD1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8IZ07","full_name":"Ankyrin repeat domain-containing protein 13A","aliases":["Protein KE03"],"length_aa":590,"mass_kda":67.6,"function":"Ubiquitin-binding protein that specifically recognizes and binds 'Lys-63'-linked ubiquitin. Does not bind 'Lys-48'-linked ubiquitin. Positively regulates the internalization of ligand-activated EGFR by binding to the Ub moiety of ubiquitinated EGFR at the cell membrane","subcellular_location":"Cell membrane; Late endosome","url":"https://www.uniprot.org/uniprotkb/Q8IZ07/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ANKRD13A","classification":"Not Classified","n_dependent_lines":5,"n_total_lines":1208,"dependency_fraction":0.0041390728476821195},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000076513","cell_line_id":"CID001396","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"vesicles","grade":2}],"interactors":[{"gene":"RPS27A;UBC;UBB;UBA52","stoichiometry":0.2},{"gene":"RHOB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001396","total_profiled":1310},"omim":[{"mim_id":"615126","title":"ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 13D; ANKRD13D","url":"https://www.omim.org/entry/615126"},{"mim_id":"615124","title":"ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 13B; ANKRD13B","url":"https://www.omim.org/entry/615124"},{"mim_id":"615123","title":"ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 13A; ANKRD13A","url":"https://www.omim.org/entry/615123"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Plasma membrane","reliability":"Supported"},{"location":"Vesicles","reliability":"Additional"},{"location":"Primary cilium","reliability":"Additional"},{"location":"Primary cilium tip","reliability":"Additional"},{"location":"Primary cilium transition zone","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ANKRD13A"},"hgnc":{"alias_symbol":["NY-REN-25"],"prev_symbol":["ANKRD13"]},"alphafold":{"accession":"Q8IZ07","domains":[{"cath_id":"1.25.40.20","chopping":"11-106","consensus_level":"medium","plddt":92.0119,"start":11,"end":106},{"cath_id":"-","chopping":"227-425","consensus_level":"medium","plddt":78.4132,"start":227,"end":425}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IZ07","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IZ07-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IZ07-F1-predicted_aligned_error_v6.png","plddt_mean":73.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ANKRD13A","jax_strain_url":"https://www.jax.org/strain/search?query=ANKRD13A"},"sequence":{"accession":"Q8IZ07","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8IZ07.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8IZ07/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IZ07"}},"corpus_meta":[{"pmid":"23620728","id":"PMC_23620728","title":"miR-204 targeting of Ankrd13A controls both mesenchymal neural crest and lens cell migration.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23620728","citation_count":29,"is_preprint":false},{"pmid":"34694569","id":"PMC_34694569","title":"LncRNA USP30-AS1 promotes the survival of acute myeloid leukemia cells by cis-regulating USP30 and ANKRD13A.","date":"2021","source":"Human cell","url":"https://pubmed.ncbi.nlm.nih.gov/34694569","citation_count":26,"is_preprint":false},{"pmid":"26797118","id":"PMC_26797118","title":"The Ankrd13 Family of Ubiquitin-interacting Motif-bearing Proteins Regulates Valosin-containing Protein/p97 Protein-mediated Lysosomal Trafficking of Caveolin 1.","date":"2016","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26797118","citation_count":25,"is_preprint":false},{"pmid":"33396258","id":"PMC_33396258","title":"Blood-Based Detection of Colorectal Cancer Using Cancer-Specific DNA Methylation Markers.","date":"2020","source":"Diagnostics (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/33396258","citation_count":22,"is_preprint":false},{"pmid":"31985874","id":"PMC_31985874","title":"Ring Finger Protein 11 acts on ligand-activated EGFR via the direct interaction with the UIM region of ANKRD13 protein family.","date":"2020","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/31985874","citation_count":17,"is_preprint":false},{"pmid":"35401688","id":"PMC_35401688","title":"Population Genetic Structure and Selection Signature Analysis of Beijing Black Pig.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35401688","citation_count":17,"is_preprint":false},{"pmid":"34839354","id":"PMC_34839354","title":"ANKRD13a controls early cell-death checkpoint by interacting with RIP1 independent of NF-κB.","date":"2021","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/34839354","citation_count":13,"is_preprint":false},{"pmid":"37975677","id":"PMC_37975677","title":"p97/VCP targets Toxoplasma gondii vacuoles for parasite restriction in interferon-stimulated human cells.","date":"2023","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/37975677","citation_count":6,"is_preprint":false},{"pmid":"34320404","id":"PMC_34320404","title":"Dose-dependent transcriptional effects of lithium and adverse effect burden in a psychiatric cohort.","date":"2021","source":"Progress in neuro-psychopharmacology & biological psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/34320404","citation_count":6,"is_preprint":false},{"pmid":"40975168","id":"PMC_40975168","title":"The ubiquitin-binding protein ANKRD13A mediates VCP-dependent mitochondrial outer membrane rupture during PINK1/Parkin-mediated mitophagy.","date":"2025","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40975168","citation_count":1,"is_preprint":false},{"pmid":"40465099","id":"PMC_40465099","title":"Identification and validation of a thirteen-gene signature based on ubiquitin related genes in cervical cancer.","date":"2025","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/40465099","citation_count":0,"is_preprint":false},{"pmid":"39406802","id":"PMC_39406802","title":"Mitophagy related diagnostic biomarkers for coronary in-stent restenosis identified using machine learning and bioinformatics.","date":"2024","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/39406802","citation_count":0,"is_preprint":false},{"pmid":"41717448","id":"PMC_41717448","title":"A New biosensor illuminates the driving force behind mitochondrial outer membrane rupture.","date":"2026","source":"Autophagy reports","url":"https://pubmed.ncbi.nlm.nih.gov/41717448","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.04.07.25325355","title":"Hierarchical representation learning of preeclampsia interactome connecting endometrial maturation, placentation, chorioamnionitis, and HELLP syndrome","date":"2025-04-07","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.07.25325355","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9390,"output_tokens":2218,"usd":0.03072,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9269,"output_tokens":2970,"usd":0.060297,"stage2_stop_reason":"end_turn"},"total_usd":0.091017,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"ANKRD13A (Ankrd13 family) contains ubiquitin-interacting motifs (UIMs) that bind preferentially to Lys-63-linked polyubiquitin chains on Caveolin-1 (Cav-1), forming a ternary complex with VCP/p97 on endosomal membranes to facilitate lysosomal trafficking of ubiquitinated Cav-1 oligomers.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry (ubiquitin chain-type analysis), UIM-deletion mutagenesis, overexpression phenotypic assay (enlarged hollow late endosomes), interaction studies with IBMPFD-associated VCP mutants\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (Co-IP, MS ubiquitin linkage analysis, domain mutagenesis, phenotypic rescue) in a single rigorous study\",\n      \"pmids\": [\"26797118\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ANKRD13A forms a complex with RNF11 (RING finger protein 11) in vivo via its UIMs, and this interaction is modulated by EGF stimulation. A ternary complex of ANKRD13A, RNF11, and activated EGFR is transiently assembled during early receptor endocytosis. Loss of ITCH E3 ligase abrogates ANKRD13A ubiquitination while loss of RNF11 increases it; the ubiquitination status of ANKRD13A controls its ability to bind activated EGFR, thereby regulating EGFR sorting for lysosomal degradation.\",\n      \"method\": \"SILAC-based co-immunoprecipitation proteomics, in vivo Co-IP with UIM-deletion mutants, EGF stimulation time-course assays, loss-of-function (RNAi) of ITCH and RNF11 with ubiquitination readout\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, SILAC proteomics, domain mutagenesis, and functional loss-of-function in a single study with multiple orthogonal methods\",\n      \"pmids\": [\"31985874\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ANKRD13A acts as a novel component of TNF signaling complex-II (death-inducing complex). It binds to ubiquitinated RIP1 via its UIM domain and limits the association of FADD and caspase-8 with RIP1, thereby setting a higher threshold for TNF-induced cell death without affecting NF-κB activation. ANKRD13A deficiency shifts the cellular response to TNF from survival to apoptosis.\",\n      \"method\": \"Co-immunoprecipitation of ANKRD13A with ubiquitinated RIP1, complex-II assembly assays, ANKRD13A knockout/knockdown with TNF-induced cell death and NF-κB reporter readouts, UIM-dependent interaction studies\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, genetic knockout with defined phenotype, pathway epistasis (NF-κB vs. complex-II), multiple orthogonal methods in one study\",\n      \"pmids\": [\"34839354\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ANKRD13A relocates to depolarized mitochondria upon PINK1/Parkin activation and promotes mitophagy by recruiting VCP/p97 to the mitochondrial outer membrane (OMM). VCP and its recruitment factors including ANKRD13A are required for OMM rupture, which exposes inner mitochondrial membrane mitophagy receptors for autophagic recognition.\",\n      \"method\": \"Live-cell fluorescence imaging (novel OMM-rupture biosensor), ANKRD13A localization assay (fractionation/imaging of depolarized mitochondria), Co-IP with mitochondrial proteins, loss-of-function (knockdown/knockout) with mitophagy and OMM-rupture readouts\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — novel biosensor for direct visualization, Co-IP, loss-of-function with specific phenotypic readout (OMM rupture, mitophagy flux), multiple orthogonal methods\",\n      \"pmids\": [\"40975168\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ANKRD13A is recruited to ubiquitinated Toxoplasma gondii parasitophorous vacuoles (PVs) in IFNγ-stimulated endothelial cells together with p97/VCP and UBXD1. PV ubiquitination is a prerequisite for ANKRD13A recruitment, and its deposition directs Tg PVs to acidification, restricting parasite survival.\",\n      \"method\": \"Genetic knockdown/knockout with parasite restriction assay, immunofluorescence localization of ANKRD13A to ubiquitinated PVs, IFNγ stimulation experiments, co-depletion epistasis with p97/VCP\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — loss-of-function with defined phenotype (parasite restriction, PV acidification) and direct localization, but single study\",\n      \"pmids\": [\"37975677\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Ankrd13A controls focal adhesion formation and distribution in lens and neural crest cells. miR-204 directly targets Ankrd13A; elevated Ankrd13A (from miR-204 inactivation) causes abnormal focal adhesion dynamics, reduced cell motility, and aberrant lens morphogenesis. In vivo restoration of Ankrd13A levels rescued the lens phenotype.\",\n      \"method\": \"Morpholino-mediated miR-204 knockdown and Ankrd13A overexpression in medaka (live imaging), in vitro focal adhesion assays, miR-204 target validation (3'UTR reporter), in vivo rescue experiment\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — live imaging epistasis (miR-204/Ankrd13A/focal adhesions), in vivo rescue, but mechanistic detail on ANKRD13A's direct biochemical role in focal adhesion regulation not fully resolved\",\n      \"pmids\": [\"23620728\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ANKRD13A recognizes Lys-63-linked polyubiquitin chains on HLA class I (HLA-I), and elevated ANKRD13A expression (induced by lncRNA USP30-AS1 via H3K4me3/H3K27Ac chromatin changes) promotes HLA-I internalization from the cell membrane, contributing to immune evasion in AML cells.\",\n      \"method\": \"USP30-AS1 knockdown/overexpression, ANKRD13A knockdown, cell surface HLA-I assay (flow cytometry/imaging), ChIP analysis for histone marks\",\n      \"journal\": \"Human cell\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, limited direct biochemical validation of ANKRD13A–Lys63-Ub–HLA-I interaction; primarily functional readout with indirect mechanistic inference\",\n      \"pmids\": [\"34694569\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ANKRD13A is a UIM-containing scaffold protein that selectively recognizes Lys-63-linked polyubiquitin chains on diverse substrates (Caveolin-1, EGFR, RIP1, HLA-I, mitochondrial outer membrane proteins) to coordinate VCP/p97-dependent membrane remodeling (lysosomal trafficking of Cav-1, EGFR endosomal sorting, mitochondrial outer membrane rupture during mitophagy) and modulates cell-death signaling by binding ubiquitinated RIP1 at TNF complex-II to limit FADD/caspase-8 recruitment, thereby acting as a gatekeeper against TNF-induced apoptosis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ANKRD13A is a ubiquitin-interacting-motif (UIM) scaffold protein that selectively recognizes Lys-63-linked polyubiquitin chains on diverse membrane and signaling substrates to direct VCP/p97-dependent membrane remodeling and trafficking [#0, #3]. Through its UIMs it binds ubiquitinated Caveolin-1 and assembles a ternary complex with VCP/p97 on endosomal membranes to route Cav-1 oligomers for lysosomal trafficking [#0], and it cooperates with the E3 ligase RNF11 and the ITCH-dependent ubiquitination of ANKRD13A itself to gate binding to activated EGFR and its sorting toward lysosomal degradation [#1]. Upon PINK1/Parkin-driven mitochondrial depolarization, ANKRD13A relocates to depolarized mitochondria and recruits VCP/p97 to the outer membrane to promote membrane rupture required for mitophagy [#3], and it is similarly recruited to ubiquitinated Toxoplasma parasitophorous vacuoles with VCP/p97 and UBXD1 to drive their acidification and restrict the parasite [#4]. Beyond trafficking, ANKRD13A binds ubiquitinated RIP1 within TNF complex-II via its UIM and limits FADD/caspase-8 recruitment, raising the threshold for TNF-induced apoptosis without affecting NF-\\u03baB activation [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Established ANKRD13A's core biochemical activity: that its UIMs read Lys-63-linked polyubiquitin and couple a ubiquitinated cargo (Cav-1) to VCP/p97 for lysosomal delivery, defining it as a ubiquitin-selective trafficking adaptor.\",\n      \"evidence\": \"Co-IP, MS ubiquitin-linkage analysis, UIM-deletion mutagenesis and overexpression phenotypes (enlarged late endosomes) in cells, including IBMPFD VCP mutants\",\n      \"pmids\": [\"26797118\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural model of UIM\\u2013Lys63-Ub recognition\", \"Whether VCP recruitment is direct or bridged by additional cofactors not resolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Extended the adaptor role to receptor tyrosine kinase sorting and showed ANKRD13A's own ubiquitination state is a regulatory switch, governed by ITCH and RNF11, for binding activated EGFR.\",\n      \"evidence\": \"SILAC Co-IP proteomics, UIM-deletion mutants, EGF time-course, and RNAi of ITCH and RNF11 with ubiquitination readouts\",\n      \"pmids\": [\"31985874\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Site(s) of ANKRD13A ubiquitination not mapped\", \"Functional consequence for EGFR degradation kinetics in vivo not quantified\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified a death-signaling function distinct from trafficking: ANKRD13A binds ubiquitinated RIP1 in TNF complex-II to limit FADD/caspase-8 assembly, positioning it as a checkpoint balancing survival versus apoptosis.\",\n      \"evidence\": \"Co-IP with ubiquitinated RIP1, complex-II assembly assays, knockout/knockdown with TNF death and NF-\\u03baB reporter readouts, UIM-dependent interaction studies\",\n      \"pmids\": [\"34839354\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether VCP/p97 participates in the complex-II function not addressed\", \"Linkage type of RIP1 ubiquitin recognized not directly defined here\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed the ANKRD13A\\u2013VCP module is deployed in cell-autonomous immunity, recruited to ubiquitinated pathogen vacuoles to drive their acidification.\",\n      \"evidence\": \"Knockdown/knockout parasite restriction assay, immunofluorescence localization to ubiquitinated PVs, IFN\\u03b3 stimulation, co-depletion epistasis with p97/VCP and UBXD1\",\n      \"pmids\": [\"37975677\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single study\", \"Direct biochemical demonstration of ANKRD13A binding PV ubiquitin not shown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated ANKRD13A drives mitochondrial outer-membrane rupture during mitophagy by recruiting VCP/p97 to depolarized mitochondria, generalizing its VCP-recruiting trafficking role to organelle quality control.\",\n      \"evidence\": \"Live-cell OMM-rupture biosensor imaging, localization on depolarized mitochondria, Co-IP with mitochondrial proteins, loss-of-function with mitophagy/OMM-rupture readouts\",\n      \"pmids\": [\"40975168\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the ubiquitinated OMM substrate(s) read by ANKRD13A not defined\", \"Relationship to other VCP mitophagy cofactors not delineated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Implicated ANKRD13A in tumor immune evasion by promoting Lys-63-Ub-dependent internalization of HLA class I, downstream of lncRNA-driven chromatin activation.\",\n      \"evidence\": \"USP30-AS1 perturbation, ANKRD13A knockdown, cell-surface HLA-I flow/imaging, ChIP for histone marks in AML cells\",\n      \"pmids\": [\"34694569\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Direct ANKRD13A\\u2013Lys63-Ub\\u2013HLA-I interaction not biochemically validated\", \"Mechanism inferred largely from functional readouts\", \"Single lab\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Earliest functional link, placing Ankrd13A downstream of miR-204 in regulating focal adhesion dynamics and lens/neural crest morphogenesis.\",\n      \"evidence\": \"Morpholino miR-204 knockdown and Ankrd13A overexpression with live imaging in medaka, focal adhesion assays, 3'UTR reporter, in vivo rescue\",\n      \"pmids\": [\"23620728\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical role of ANKRD13A in focal adhesion regulation unresolved\", \"Connection to its ubiquitin-trafficking activity not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ANKRD13A discriminates among its many ubiquitinated substrates and is targeted to specific membranes/complexes in a context-dependent manner remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural basis for substrate/linkage selectivity\", \"Determinants of subcellular targeting across endosomes, mitochondria, vacuoles, and complex-II not defined\", \"Whether a unifying VCP-handoff mechanism operates across all contexts unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0031386\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\"TNF complex-II\"],\n    \"partners\": [\"VCP\", \"RNF11\", \"ITCH\", \"EGFR\", \"RIPK1\", \"Caveolin-1\", \"UBXD1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":4,"faith_total":4,"faith_pct":100.0}}