{"gene":"PPP1R35","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2018,"finding":"PPP1R35 is a resident centrosomal protein located in the proximal lumen above the cartwheel. Loss of PPP1R35 results in decreased centrosome number and shortened centrioles lacking distal and microtubule wall-associated proteins required for centriole elongation. PPP1R35 acts downstream of, and forms a complex with, the microcephaly protein RTTN in the centriole elongation pathway.","method":"Quantitative super-resolution microscopy mapping, live-cell imaging, BioID proximity proteomics, loss-of-function experiments","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (super-resolution microscopy, live-cell imaging, co-complex demonstration), clear epistasis with RTTN established","pmids":["30168418"],"is_preprint":false},{"year":2018,"finding":"PPP1R35 is enriched at newborn daughter centrioles in S/G2 phase and is required for centriole-to-centrosome conversion (CCC). In the absence of PPP1R35, nascent centrioles fail to recruit CEP295 (an essential CCC factor) and disintegrate after mitosis upon cartwheel removal, indicating PPP1R35 acts upstream of CEP295. Neither the centriolar localization nor the CCC function of PPP1R35 requires its putative PP1-interacting motif.","method":"Immunofluorescence, loss-of-function (PPP1R35-null cells), epistasis analysis with CEP295, domain mutant analysis","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal epistasis with CEP295 and domain-function dissection in null cells, single lab but multiple orthogonal approaches","pmids":["30230954"],"is_preprint":false},{"year":2020,"finding":"Loss of Ppp1r35 in mouse embryos results in absence of primary cilia, irregular and discontinuous notochord, failure to specify the floor plate of the neural tube, increased cell death (particularly in the neural tube), and cell-cycle stalling in prometaphase, demonstrating an essential in vivo role for PPP1R35 in ciliogenesis and centriole homeostasis during mammalian development.","method":"Mouse loss-of-function (homozygous knockout), histological analysis, molecular marker analysis, cell death and proliferation assays","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — in vivo KO with multiple defined cellular and developmental phenotypes (cilia, notochord, cell cycle), consistent with in vitro findings","pmids":["32628936"],"is_preprint":false},{"year":2024,"finding":"PPP1R35 is directly phosphorylated by the protein kinase CDKL5 on a serine residue within the CDKL5 consensus motif, as identified by unbiased phosphoproteomics in human iPSC-derived neurons and validated by complementary approaches. PPP1R35 also interacts with CEP131, a known CDKL5 phospho-target.","method":"Phosphoproteomics (iPSC-derived neurons), in vitro kinase assay validation, co-immunoprecipitation with CEP131","journal":"Cellular and molecular life sciences : CMLS","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — phosphoproteomics plus stated complementary validation, single lab, abstract does not detail all validation methods","pmids":["39136782"],"is_preprint":false}],"current_model":"PPP1R35 is a resident centrosomal protein in the proximal centriole lumen that promotes centriole elongation by acting downstream of RTTN and upstream of CEP295 to drive centriole-to-centrosome conversion; it is required in vivo for primary cilia formation, notochord integrity, and cell-cycle progression, and is itself directly phosphorylated by the kinase CDKL5."},"narrative":{"mechanistic_narrative":"PPP1R35 is a resident centriolar protein that drives centriole elongation and the conversion of nascent daughter centrioles into functional centrosomes during the cell cycle [PMID:30168418, PMID:30230954]. It occupies the proximal centriole lumen above the cartwheel, where it acts downstream of and in complex with the microcephaly protein RTTN; loss of PPP1R35 yields fewer centrioles, shortened structures lacking distal and microtubule-wall proteins, and failure of centriole elongation [PMID:30168418]. PPP1R35 is enriched at newborn daughter centrioles in S/G2 phase and is required for centriole-to-centrosome conversion, acting upstream of CEP295: without PPP1R35, nascent centrioles fail to recruit CEP295 and disintegrate after mitosis when the cartwheel is removed, and this function is independent of its putative PP1-interacting motif [PMID:30230954]. In vivo, Ppp1r35 is essential for primary cilia formation, notochord integrity, floor-plate specification, and cell-cycle progression, with its loss causing prometaphase stalling and increased cell death during mammalian development [PMID:32628936]. PPP1R35 is a direct phosphorylation substrate of the kinase CDKL5 and interacts with the CDKL5 phospho-target CEP131 [PMID:39136782].","teleology":[{"year":2018,"claim":"Established that PPP1R35 is a structural centriole-lumen protein required for centriole elongation, placing it in a defined pathway downstream of RTTN.","evidence":"Super-resolution mapping, live-cell imaging, BioID proximity proteomics, and loss-of-function in human cells","pmids":["30168418"],"confidence":"High","gaps":["The molecular activity by which PPP1R35 promotes elongation is undefined","Whether the RTTN complex is direct or bridged by other factors is not resolved","No structural model of PPP1R35 in the centriole lumen"]},{"year":2018,"claim":"Defined PPP1R35's cell-cycle-staged role in centriole-to-centrosome conversion, ordering it upstream of CEP295 and showing its function is independent of the predicted PP1-interacting motif.","evidence":"Immunofluorescence, PPP1R35-null cells, epistasis with CEP295, and domain-mutant analysis","pmids":["30230954"],"confidence":"High","gaps":["How PPP1R35 enables CEP295 recruitment mechanistically is unknown","The function of the conserved PP1-interacting motif, if any, is unexplained","Whether PPP1R35 binds a phosphatase at all remains untested"]},{"year":2020,"claim":"Demonstrated that PPP1R35 is essential in vivo, linking its centriole/cilia function to embryonic patterning and cell-cycle homeostasis.","evidence":"Mouse homozygous knockout with histological, molecular-marker, cell-death, and proliferation analyses","pmids":["32628936"],"confidence":"High","gaps":["Tissue-specific requirements versus a general centriole defect are not separated","Whether ciliary and notochord phenotypes are direct or secondary to cell-cycle stalling is unresolved"]},{"year":2024,"claim":"Identified PPP1R35 as a direct CDKL5 phosphorylation substrate, introducing regulatory control over the protein and a link to centriolar satellite biology via CEP131.","evidence":"Phosphoproteomics in iPSC-derived neurons, in vitro kinase assay, and co-IP with CEP131","pmids":["39136782"],"confidence":"Medium","gaps":["Functional consequence of the CDKL5 phosphosite on centriole elongation or CCC is untested","Whether the CEP131 interaction is direct or part of a larger complex is unclear","Single lab; full validation methods not detailed"]},{"year":null,"claim":"The biochemical activity of PPP1R35 and how its phosphorylation by CDKL5 modulates centriole elongation and conversion remain unknown.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No defined enzymatic or scaffolding activity assigned","No structural basis for RTTN or CEP295 functional dependence","No mechanistic link between CDKL5 phosphorylation and centriole function"]}],"mechanism_profile":{"molecular_activity":[],"localization":[{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[0,1]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,1]}],"complexes":[],"partners":["RTTN","CEP295","CDKL5","CEP131"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8TAP8","full_name":"Protein phosphatase 1 regulatory subunit 35","aliases":[],"length_aa":253,"mass_kda":28.0,"function":"During centriole duplication, plays a role in the centriole elongation by promoting the recruitment of the microtubule-binding elongation machinery through its interaction with RTTN, leading to the centriole to centrosome conversion (PubMed:30168418, PubMed:30230954). In addition, may play a role in the primary cilia assembly (By similarity)","subcellular_location":"Cytoplasm, cytoskeleton, microtubule organizing center, centrosome; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriole","url":"https://www.uniprot.org/uniprotkb/Q8TAP8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PPP1R35","classification":"Not Classified","n_dependent_lines":50,"n_total_lines":1208,"dependency_fraction":0.041390728476821195},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PPP1R35","total_profiled":1310},"omim":[{"mim_id":"618937","title":"PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 35; PPP1R35","url":"https://www.omim.org/entry/618937"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"testis","ntpm":50.6}],"url":"https://www.proteinatlas.org/search/PPP1R35"},"hgnc":{"alias_symbol":["MGC22793"],"prev_symbol":["C7orf47"]},"alphafold":{"accession":"Q8TAP8","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TAP8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TAP8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TAP8-F1-predicted_aligned_error_v6.png","plddt_mean":68.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PPP1R35","jax_strain_url":"https://www.jax.org/strain/search?query=PPP1R35"},"sequence":{"accession":"Q8TAP8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8TAP8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8TAP8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TAP8"}},"corpus_meta":[{"pmid":"30168418","id":"PMC_30168418","title":"PPP1R35 is a novel centrosomal protein that regulates centriole length in concert with the microcephaly protein RTTN.","date":"2018","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/30168418","citation_count":29,"is_preprint":false},{"pmid":"30230954","id":"PMC_30230954","title":"PPP1R35 ensures centriole homeostasis by promoting centriole-to-centrosome conversion.","date":"2018","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/30230954","citation_count":13,"is_preprint":false},{"pmid":"32628936","id":"PMC_32628936","title":"Protein phosphatase 1 regulatory subunit 35 is required for ciliogenesis, notochord morphogenesis, and cell-cycle progression during murine development.","date":"2020","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/32628936","citation_count":6,"is_preprint":false},{"pmid":"36598158","id":"PMC_36598158","title":"A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly.","date":"2023","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/36598158","citation_count":3,"is_preprint":false},{"pmid":"39136782","id":"PMC_39136782","title":"Novel CDKL5 targets identified in human iPSC-derived neurons.","date":"2024","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/39136782","citation_count":3,"is_preprint":false},{"pmid":"40650042","id":"PMC_40650042","title":"Identifying Molecular Modulators of the Vascular Invasion in Rectal Carcinoma: Role of ADAMTS8 and Its Co-Dependent Genes.","date":"2025","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/40650042","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5112,"output_tokens":1125,"usd":0.016105,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7680,"output_tokens":1903,"usd":0.042987,"stage2_stop_reason":"end_turn"},"total_usd":0.059092,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2018,\n      \"finding\": \"PPP1R35 is a resident centrosomal protein located in the proximal lumen above the cartwheel. Loss of PPP1R35 results in decreased centrosome number and shortened centrioles lacking distal and microtubule wall-associated proteins required for centriole elongation. PPP1R35 acts downstream of, and forms a complex with, the microcephaly protein RTTN in the centriole elongation pathway.\",\n      \"method\": \"Quantitative super-resolution microscopy mapping, live-cell imaging, BioID proximity proteomics, loss-of-function experiments\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (super-resolution microscopy, live-cell imaging, co-complex demonstration), clear epistasis with RTTN established\",\n      \"pmids\": [\"30168418\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PPP1R35 is enriched at newborn daughter centrioles in S/G2 phase and is required for centriole-to-centrosome conversion (CCC). In the absence of PPP1R35, nascent centrioles fail to recruit CEP295 (an essential CCC factor) and disintegrate after mitosis upon cartwheel removal, indicating PPP1R35 acts upstream of CEP295. Neither the centriolar localization nor the CCC function of PPP1R35 requires its putative PP1-interacting motif.\",\n      \"method\": \"Immunofluorescence, loss-of-function (PPP1R35-null cells), epistasis analysis with CEP295, domain mutant analysis\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal epistasis with CEP295 and domain-function dissection in null cells, single lab but multiple orthogonal approaches\",\n      \"pmids\": [\"30230954\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Loss of Ppp1r35 in mouse embryos results in absence of primary cilia, irregular and discontinuous notochord, failure to specify the floor plate of the neural tube, increased cell death (particularly in the neural tube), and cell-cycle stalling in prometaphase, demonstrating an essential in vivo role for PPP1R35 in ciliogenesis and centriole homeostasis during mammalian development.\",\n      \"method\": \"Mouse loss-of-function (homozygous knockout), histological analysis, molecular marker analysis, cell death and proliferation assays\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo KO with multiple defined cellular and developmental phenotypes (cilia, notochord, cell cycle), consistent with in vitro findings\",\n      \"pmids\": [\"32628936\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PPP1R35 is directly phosphorylated by the protein kinase CDKL5 on a serine residue within the CDKL5 consensus motif, as identified by unbiased phosphoproteomics in human iPSC-derived neurons and validated by complementary approaches. PPP1R35 also interacts with CEP131, a known CDKL5 phospho-target.\",\n      \"method\": \"Phosphoproteomics (iPSC-derived neurons), in vitro kinase assay validation, co-immunoprecipitation with CEP131\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — phosphoproteomics plus stated complementary validation, single lab, abstract does not detail all validation methods\",\n      \"pmids\": [\"39136782\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPP1R35 is a resident centrosomal protein in the proximal centriole lumen that promotes centriole elongation by acting downstream of RTTN and upstream of CEP295 to drive centriole-to-centrosome conversion; it is required in vivo for primary cilia formation, notochord integrity, and cell-cycle progression, and is itself directly phosphorylated by the kinase CDKL5.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PPP1R35 is a resident centriolar protein that drives centriole elongation and the conversion of nascent daughter centrioles into functional centrosomes during the cell cycle [#0, #1]. It occupies the proximal centriole lumen above the cartwheel, where it acts downstream of and in complex with the microcephaly protein RTTN; loss of PPP1R35 yields fewer centrioles, shortened structures lacking distal and microtubule-wall proteins, and failure of centriole elongation [#0]. PPP1R35 is enriched at newborn daughter centrioles in S/G2 phase and is required for centriole-to-centrosome conversion, acting upstream of CEP295: without PPP1R35, nascent centrioles fail to recruit CEP295 and disintegrate after mitosis when the cartwheel is removed, and this function is independent of its putative PP1-interacting motif [#1]. In vivo, Ppp1r35 is essential for primary cilia formation, notochord integrity, floor-plate specification, and cell-cycle progression, with its loss causing prometaphase stalling and increased cell death during mammalian development [#2]. PPP1R35 is a direct phosphorylation substrate of the kinase CDKL5 and interacts with the CDKL5 phospho-target CEP131 [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Established that PPP1R35 is a structural centriole-lumen protein required for centriole elongation, placing it in a defined pathway downstream of RTTN.\",\n      \"evidence\": \"Super-resolution mapping, live-cell imaging, BioID proximity proteomics, and loss-of-function in human cells\",\n      \"pmids\": [\"30168418\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The molecular activity by which PPP1R35 promotes elongation is undefined\",\n        \"Whether the RTTN complex is direct or bridged by other factors is not resolved\",\n        \"No structural model of PPP1R35 in the centriole lumen\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined PPP1R35's cell-cycle-staged role in centriole-to-centrosome conversion, ordering it upstream of CEP295 and showing its function is independent of the predicted PP1-interacting motif.\",\n      \"evidence\": \"Immunofluorescence, PPP1R35-null cells, epistasis with CEP295, and domain-mutant analysis\",\n      \"pmids\": [\"30230954\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How PPP1R35 enables CEP295 recruitment mechanistically is unknown\",\n        \"The function of the conserved PP1-interacting motif, if any, is unexplained\",\n        \"Whether PPP1R35 binds a phosphatase at all remains untested\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Demonstrated that PPP1R35 is essential in vivo, linking its centriole/cilia function to embryonic patterning and cell-cycle homeostasis.\",\n      \"evidence\": \"Mouse homozygous knockout with histological, molecular-marker, cell-death, and proliferation analyses\",\n      \"pmids\": [\"32628936\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Tissue-specific requirements versus a general centriole defect are not separated\",\n        \"Whether ciliary and notochord phenotypes are direct or secondary to cell-cycle stalling is unresolved\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified PPP1R35 as a direct CDKL5 phosphorylation substrate, introducing regulatory control over the protein and a link to centriolar satellite biology via CEP131.\",\n      \"evidence\": \"Phosphoproteomics in iPSC-derived neurons, in vitro kinase assay, and co-IP with CEP131\",\n      \"pmids\": [\"39136782\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequence of the CDKL5 phosphosite on centriole elongation or CCC is untested\",\n        \"Whether the CEP131 interaction is direct or part of a larger complex is unclear\",\n        \"Single lab; full validation methods not detailed\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The biochemical activity of PPP1R35 and how its phosphorylation by CDKL5 modulates centriole elongation and conversion remain unknown.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No defined enzymatic or scaffolding activity assigned\",\n        \"No structural basis for RTTN or CEP295 functional dependence\",\n        \"No mechanistic link between CDKL5 phosphorylation and centriole function\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005814\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RTTN\", \"CEP295\", \"CDKL5\", \"CEP131\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}