{"gene":"ANKRD35","run_date":"2026-06-09T22:02:43","timeline":{"discoveries":[{"year":2023,"finding":"RBCK1 (an E3 ubiquitin ligase) promotes ubiquitin-dependent proteasomal degradation of ANKRD35 in ccRCC cells, reducing ANKRD35 protein levels.","method":"In vitro and in vivo studies in ccRCC cell lines and patient specimens; ubiquitin-proteasome pathway assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro and in vivo functional studies in a single lab, mechanistic follow-up with pathway analysis but abstract-level detail only","pmids":["36732658"],"is_preprint":false},{"year":2023,"finding":"ANKRD35 destabilizes MITD1 by binding with SUMO2 in ccRCC cells, placing ANKRD35 as a regulator of MITD1 stability downstream of RBCK1.","method":"Binding/interaction studies (ANKRD35-SUMO2 interaction) and functional destabilization assays in ccRCC cells","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single lab, interaction and functional data from in vitro/in vivo studies, but abstract lacks detail on method rigor (e.g., no mention of mutagenesis or reciprocal Co-IP)","pmids":["36732658"],"is_preprint":false},{"year":2023,"finding":"The RBCK1-ANKRD35-MITD1-ANXA1 axis regulates phosphorylation of AKT and ERK signaling in ccRCC, thereby contributing to sunitinib sensitivity.","method":"In vitro and in vivo epistasis/pathway studies with inhibition of RBCK1 and downstream readouts of AKT/MAPK pathway activity and sunitinib response","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis via ordered axis established in single lab with in vitro and in vivo experiments, but abstract-level detail limits full tier assessment","pmids":["36732658"],"is_preprint":false}],"current_model":"ANKRD35 is a substrate of the E3 ubiquitin ligase RBCK1, which targets it for proteasomal degradation; when present, ANKRD35 binds SUMO2 and destabilizes MITD1, thereby suppressing ANXA1 expression and dampening AKT/ERK phosphorylation to maintain sunitinib sensitivity in clear cell renal cell carcinoma."},"narrative":{"mechanistic_narrative":"ANKRD35 functions as a signaling intermediate in clear cell renal cell carcinoma (ccRCC) whose abundance is controlled by the E3 ubiquitin ligase RBCK1, which drives its ubiquitin-dependent proteasomal degradation [PMID:36732658]. When stabilized, ANKRD35 binds SUMO2 and destabilizes MITD1 [PMID:36732658], operating within an RBCK1-ANKRD35-MITD1-ANXA1 axis that modulates AKT and ERK phosphorylation and thereby tunes sunitinib sensitivity in ccRCC [PMID:36732658]. Beyond this axis defined in ccRCC, no further biochemical or structural characterization of ANKRD35 has been established in the available corpus.","teleology":[{"year":2023,"claim":"Establishing how ANKRD35 protein levels are controlled identified it as a degradation substrate of the E3 ligase RBCK1, linking it to the ubiquitin-proteasome system in ccRCC.","evidence":"Ubiquitin-proteasome pathway assays in ccRCC cell lines and patient specimens, in vitro and in vivo","pmids":["36732658"],"confidence":"Medium","gaps":["Direct ubiquitination sites on ANKRD35 not mapped","Whether RBCK1 ubiquitinates ANKRD35 directly versus via an adaptor not resolved","Single-lab abstract-level detail without reciprocal validation"]},{"year":2023,"claim":"Defining ANKRD35's downstream action showed it binds SUMO2 and destabilizes MITD1, placing it as an effector immediately downstream of RBCK1.","evidence":"Interaction and functional destabilization assays in ccRCC cells","pmids":["36732658"],"confidence":"Medium","gaps":["No mutagenesis or reciprocal Co-IP reported to confirm the ANKRD35-SUMO2 interaction","Mechanism by which ANKRD35 destabilizes MITD1 unresolved","Whether SUMO2 binding is required for MITD1 destabilization untested"]},{"year":2023,"claim":"Ordering the full RBCK1-ANKRD35-MITD1-ANXA1 axis connected ANKRD35 to AKT/ERK signaling and drug response, framing its role in sunitinib sensitivity.","evidence":"In vitro and in vivo epistasis studies with RBCK1 inhibition and AKT/MAPK and sunitinib-response readouts","pmids":["36732658"],"confidence":"Medium","gaps":["Causal contribution of ANKRD35 versus other axis members to AKT/ERK changes not isolated","Generalizability beyond ccRCC unknown","How ANXA1 expression is mechanistically coupled to MITD1 not detailed"]},{"year":null,"claim":"The intrinsic molecular activity, domain function, and physiological role of ANKRD35 outside the ccRCC sunitinib-sensitivity context remain uncharacterized.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No subcellular localization established","No structural model of ANKRD35 or its interaction interfaces","No evidence in non-renal tissues or normal physiology"]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["RBCK1","SUMO2","MITD1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8N283","full_name":"Ankyrin repeat domain-containing protein 35","aliases":[],"length_aa":1001,"mass_kda":109.9,"function":"","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q8N283/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ANKRD35","classification":"Not Classified","n_dependent_lines":30,"n_total_lines":1208,"dependency_fraction":0.024834437086092714},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ANKRD35","total_profiled":1310},"omim":[{"mim_id":"621505","title":"ANKYRIN REPEAT DOMAIN-CONTAINING PROTEIN 35; ANKRD35","url":"https://www.omim.org/entry/621505"},{"mim_id":"621486","title":"MICROTUBULE-INTERACTING AND TRAFFICKING DOMAIN-CONTAINING PROTEIN 1; MITD1","url":"https://www.omim.org/entry/621486"},{"mim_id":"610924","title":"RANBP-TYPE AND C3HC4-TYPE ZINC FINGER-CONTAINING 1; RBCK1","url":"https://www.omim.org/entry/610924"},{"mim_id":"151690","title":"ANNEXIN A1; ANXA1","url":"https://www.omim.org/entry/151690"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Plasma membrane","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Vesicles","reliability":"Additional"},{"location":"Primary cilium","reliability":"Additional"},{"location":"Primary cilium transition zone","reliability":"Additional"},{"location":"Basal body","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"skin 1","ntpm":58.1}],"url":"https://www.proteinatlas.org/search/ANKRD35"},"hgnc":{"alias_symbol":["FLJ25124"],"prev_symbol":[]},"alphafold":{"accession":"Q8N283","domains":[{"cath_id":"1.25.40.20","chopping":"20-248","consensus_level":"medium","plddt":89.7372,"start":20,"end":248},{"cath_id":"-","chopping":"973-1001","consensus_level":"medium","plddt":68.2217,"start":973,"end":1001}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N283","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N283-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N283-F1-predicted_aligned_error_v6.png","plddt_mean":65.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ANKRD35","jax_strain_url":"https://www.jax.org/strain/search?query=ANKRD35"},"sequence":{"accession":"Q8N283","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N283.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N283/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N283"}},"corpus_meta":[{"pmid":"36732658","id":"PMC_36732658","title":"The E3 ligase RBCK1 reduces the sensitivity of ccRCC to sunitinib through the ANKRD35-MITD1-ANXA1 axis.","date":"2023","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/36732658","citation_count":11,"is_preprint":false},{"pmid":"33203765","id":"PMC_33203765","title":"Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits.","date":"2020","source":"Genome research","url":"https://pubmed.ncbi.nlm.nih.gov/33203765","citation_count":4,"is_preprint":false},{"pmid":"39306676","id":"PMC_39306676","title":"Functional landscape of genome-wide postzygotic somatic mutations between monozygotic twins.","date":"2024","source":"DNA research : an international journal for rapid publication of reports on genes and genomes","url":"https://pubmed.ncbi.nlm.nih.gov/39306676","citation_count":2,"is_preprint":false},{"pmid":"38938903","id":"PMC_38938903","title":"Dynein axonemal heavy chain 9 M4374I variation may have an effect on imatinib mesylate resistance in CML.","date":"2022","source":"Medicine international","url":"https://pubmed.ncbi.nlm.nih.gov/38938903","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4162,"output_tokens":738,"usd":0.011778,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":14282,"output_tokens":2737,"usd":0.104753,"resynth_parse_fail":true,"stage2_stop_reason":"end_turn"},"total_usd":0.116531,"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\": 2023,\n      \"finding\": \"RBCK1 (an E3 ubiquitin ligase) promotes ubiquitin-dependent proteasomal degradation of ANKRD35 in ccRCC cells, reducing ANKRD35 protein levels.\",\n      \"method\": \"In vitro and in vivo studies in ccRCC cell lines and patient specimens; ubiquitin-proteasome pathway assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro and in vivo functional studies in a single lab, mechanistic follow-up with pathway analysis but abstract-level detail only\",\n      \"pmids\": [\"36732658\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ANKRD35 destabilizes MITD1 by binding with SUMO2 in ccRCC cells, placing ANKRD35 as a regulator of MITD1 stability downstream of RBCK1.\",\n      \"method\": \"Binding/interaction studies (ANKRD35-SUMO2 interaction) and functional destabilization assays in ccRCC cells\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single lab, interaction and functional data from in vitro/in vivo studies, but abstract lacks detail on method rigor (e.g., no mention of mutagenesis or reciprocal Co-IP)\",\n      \"pmids\": [\"36732658\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The RBCK1-ANKRD35-MITD1-ANXA1 axis regulates phosphorylation of AKT and ERK signaling in ccRCC, thereby contributing to sunitinib sensitivity.\",\n      \"method\": \"In vitro and in vivo epistasis/pathway studies with inhibition of RBCK1 and downstream readouts of AKT/MAPK pathway activity and sunitinib response\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis via ordered axis established in single lab with in vitro and in vivo experiments, but abstract-level detail limits full tier assessment\",\n      \"pmids\": [\"36732658\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ANKRD35 is a substrate of the E3 ubiquitin ligase RBCK1, which targets it for proteasomal degradation; when present, ANKRD35 binds SUMO2 and destabilizes MITD1, thereby suppressing ANXA1 expression and dampening AKT/ERK phosphorylation to maintain sunitinib sensitivity in clear cell renal cell carcinoma.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ANKRD35 functions as a signaling intermediate in clear cell renal cell carcinoma (ccRCC) whose abundance is controlled by the E3 ubiquitin ligase RBCK1, which drives its ubiquitin-dependent proteasomal degradation [#0]. When stabilized, ANKRD35 binds SUMO2 and destabilizes MITD1 [#1], operating within an RBCK1-ANKRD35-MITD1-ANXA1 axis that modulates AKT and ERK phosphorylation and thereby tunes sunitinib sensitivity in ccRCC [#2]. Beyond this axis defined in ccRCC, no further biochemical or structural characterization of ANKRD35 has been established in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Establishing how ANKRD35 protein levels are controlled identified it as a degradation substrate of the E3 ligase RBCK1, linking it to the ubiquitin-proteasome system in ccRCC.\",\n      \"evidence\": \"Ubiquitin-proteasome pathway assays in ccRCC cell lines and patient specimens, in vitro and in vivo\",\n      \"pmids\": [\"36732658\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct ubiquitination sites on ANKRD35 not mapped\",\n        \"Whether RBCK1 ubiquitinates ANKRD35 directly versus via an adaptor not resolved\",\n        \"Single-lab abstract-level detail without reciprocal validation\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defining ANKRD35's downstream action showed it binds SUMO2 and destabilizes MITD1, placing it as an effector immediately downstream of RBCK1.\",\n      \"evidence\": \"Interaction and functional destabilization assays in ccRCC cells\",\n      \"pmids\": [\"36732658\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No mutagenesis or reciprocal Co-IP reported to confirm the ANKRD35-SUMO2 interaction\",\n        \"Mechanism by which ANKRD35 destabilizes MITD1 unresolved\",\n        \"Whether SUMO2 binding is required for MITD1 destabilization untested\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Ordering the full RBCK1-ANKRD35-MITD1-ANXA1 axis connected ANKRD35 to AKT/ERK signaling and drug response, framing its role in sunitinib sensitivity.\",\n      \"evidence\": \"In vitro and in vivo epistasis studies with RBCK1 inhibition and AKT/MAPK and sunitinib-response readouts\",\n      \"pmids\": [\"36732658\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Causal contribution of ANKRD35 versus other axis members to AKT/ERK changes not isolated\",\n        \"Generalizability beyond ccRCC unknown\",\n        \"How ANXA1 expression is mechanistically coupled to MITD1 not detailed\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The intrinsic molecular activity, domain function, and physiological role of ANKRD35 outside the ccRCC sunitinib-sensitivity context remain uncharacterized.\",\n      \"evidence\": null,\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No subcellular localization established\",\n        \"No structural model of ANKRD35 or its interaction interfaces\",\n        \"No evidence in non-renal tissues or normal physiology\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [\"RBCK1\", \"SUMO2\", \"MITD1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":2,"faith_total":2,"faith_pct":100.0}}