{"gene":"PPP1R35","run_date":"2026-04-28T19:45:44","timeline":{"discoveries":[{"year":2018,"finding":"PPP1R35 is a resident centrosomal protein located in the proximal lumen above the cartwheel, required for centriole elongation. Loss of PPP1R35 results in shortened centrioles lacking distal and microtubule wall-associated proteins required for elongation. PPP1R35 acts downstream of and forms a complex with RTTN (a microcephaly protein required for distal centriole elongation).","method":"Quantitative super-resolution microscopy mapping, live-cell imaging, siRNA knockdown, BioID proximity proteomics, Co-IP/complex formation assay","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods including super-resolution localization, live imaging, functional knockdown with defined phenotype, and complex formation validated in single study","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 PPP1R35-null cells, nascent centrioles assemble normally but fail to form active centrosomes or recruit CEP295 (an essential CCC factor); centrioles disintegrate after mitosis upon cartwheel removal. The putative PP1-interacting motif is dispensable for PPP1R35 centriolar localization and CCC function, placing PPP1R35 upstream of CEP295 in the CCC pathway.","method":"CRISPR/Cas9 knockout, immunofluorescence, epistasis (CEP295 recruitment assay), domain mutagenesis","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined cellular phenotype, epistasis placing PPP1R35 upstream of CEP295, and domain mutagenesis ruling out PP1 motif requirement","pmids":["30230954"],"is_preprint":false},{"year":2020,"finding":"Loss of Ppp1r35 in mouse embryos abolishes primary cilia formation, disrupts notochord development, impairs floor plate specification, increases cell death in the neural tube, and causes cell-cycle delay/stalling (increased prometaphase cells), confirming an essential in vivo role for PPP1R35 in centriole homeostasis and ciliogenesis.","method":"Homozygous loss-of-function mouse model, histology, immunofluorescence, molecular marker analysis","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 — in vivo knockout with multiple orthogonal phenotypic readouts consistent with in vitro findings","pmids":["32628936"],"is_preprint":false},{"year":2024,"finding":"PPP1R35 is a direct phosphorylation substrate of the kinase CDKL5; the phosphoserine residue lies within the CDKL5 consensus motif. PPP1R35 also interacts with CEP131, a known CDKL5 phospho-target, linking CDKL5 signaling to the centriole elongation/cilia pathway.","method":"Phosphoproteomic screen (unbiased), in vitro kinase validation of direct phosphorylation, Co-IP (PPP1R35–CEP131 interaction), iPSC-derived neurons","journal":"Cellular and molecular life sciences : CMLS","confidence":"Medium","confidence_rationale":"Tier 2 — direct phosphorylation validated by complementary approaches in single study; interaction with CEP131 by single Co-IP","pmids":["39136782"],"is_preprint":false}],"current_model":"PPP1R35 is a resident centrosomal protein in the proximal centriole lumen that acts downstream of RTTN to promote centriole elongation and upstream of CEP295 to drive centriole-to-centrosome conversion, thereby maintaining centriole homeostasis and enabling ciliogenesis; it is also a direct substrate of the kinase CDKL5 and interacts with CEP131, connecting it to a broader centrosome/cilia signaling network."},"narrative":{"teleology":[{"year":2018,"claim":"Defining where PPP1R35 resides within the centriole and what happens when it is lost established it as a core structural regulator of centriole elongation acting in complex with the microcephaly protein RTTN.","evidence":"Quantitative super-resolution microscopy, siRNA knockdown, BioID proximity proteomics, and Co-IP in human cells","pmids":["30168418"],"confidence":"High","gaps":["Whether PPP1R35 has catalytic activity or acts solely as a scaffold remains unknown","Structural basis of the PPP1R35–RTTN interaction is unresolved","How PPP1R35 recruits or stabilizes distal centriole components is not mechanistically defined"]},{"year":2018,"claim":"Demonstrating that PPP1R35-null cells form nascent centrioles that fail to recruit CEP295 and disintegrate after mitosis placed PPP1R35 as the earliest known factor required for centriole-to-centrosome conversion, independent of its putative PP1-binding motif.","evidence":"CRISPR/Cas9 knockout, epistasis analysis of CEP295 recruitment, and domain mutagenesis in human cells","pmids":["30230954"],"confidence":"High","gaps":["The molecular mechanism by which PPP1R35 promotes CEP295 recruitment is unknown","Whether PPP1R35 engages PP1 phosphatase in any other context remains untested","The relationship between centriole elongation and CCC functions of PPP1R35 is not disentangled"]},{"year":2020,"claim":"In vivo validation in a mouse knockout model confirmed that PPP1R35 is essential for primary cilia formation, neural tube patterning, and cell-cycle progression, extending the cell-culture findings to organismal physiology.","evidence":"Homozygous loss-of-function mouse model with histology, immunofluorescence, and molecular marker analysis","pmids":["32628936"],"confidence":"High","gaps":["Tissue-specific and conditional requirements for PPP1R35 have not been examined","Whether the cell-cycle delay is a direct consequence of centriole loss or a checkpoint response is unresolved","No human Mendelian disease link has been established"]},{"year":2024,"claim":"Identification of PPP1R35 as a direct CDKL5 kinase substrate and CEP131 interaction partner connected the centriole elongation/cilia pathway to CDKL5 signaling, suggesting a regulatory input controlling PPP1R35 function.","evidence":"Unbiased phosphoproteomics, in vitro kinase assay, and Co-IP in iPSC-derived neurons","pmids":["39136782"],"confidence":"Medium","gaps":["CEP131 interaction relies on a single Co-IP without reciprocal validation","Functional consequence of CDKL5-mediated phosphorylation on PPP1R35 activity or localization is unknown","Whether CDKL5 phosphorylation regulates centriole elongation or CCC has not been tested"]},{"year":null,"claim":"The molecular mechanism by which PPP1R35 coordinates centriole elongation and centriole-to-centrosome conversion — including its direct binding partners on the centriole wall and how CDKL5 phosphorylation modulates its function — remains to be defined.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of PPP1R35 or its complexes exists","Whether PPP1R35 dysfunction underlies a human ciliopathy or microcephaly syndrome is untested","The relationship between CDKL5-dependent phosphorylation and the PPP1R35–RTTN or PPP1R35–CEP295 pathways has not been examined"]}],"mechanism_profile":{"molecular_activity":[],"localization":[{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[0,1,2]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,1,2]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[1,2]}],"complexes":[],"partners":["RTTN","CEP295","CEP131","CDKL5"],"other_free_text":[]},"mechanistic_narrative":"PPP1R35 is a resident centrosomal protein localized to the proximal centriole lumen, where it serves dual roles in centriole elongation and centriole-to-centrosome conversion (CCC). It acts downstream of the microcephaly protein RTTN to promote distal centriole elongation and upstream of CEP295 to drive CCC, with its putative PP1-interacting motif being dispensable for both localization and CCC function [PMID:30168418, PMID:30230954]. Loss of PPP1R35 in mouse embryos abolishes primary cilia formation, disrupts notochord development, and causes cell-cycle stalling, confirming an essential in vivo role in centriole homeostasis and ciliogenesis [PMID:32628936]. PPP1R35 is a direct phosphorylation substrate of CDKL5 and interacts with the centrosomal protein CEP131, connecting centriole biogenesis to CDKL5 kinase signaling [PMID:39136782]."},"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":2,"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":4346,"output_tokens":1151,"usd":0.015152},"stage2":{"model":"claude-opus-4-6","input_tokens":4354,"output_tokens":1528,"usd":0.089955},"total_usd":0.105107,"stage1_batch_id":"msgbatch_01SUR8NDzVrNmyszWyJeCct7","stage2_batch_id":"msgbatch_01G7Yfutko3cDWzejrwH5AMx","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, required for centriole elongation. Loss of PPP1R35 results in shortened centrioles lacking distal and microtubule wall-associated proteins required for elongation. PPP1R35 acts downstream of and forms a complex with RTTN (a microcephaly protein required for distal centriole elongation).\",\n      \"method\": \"Quantitative super-resolution microscopy mapping, live-cell imaging, siRNA knockdown, BioID proximity proteomics, Co-IP/complex formation assay\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including super-resolution localization, live imaging, functional knockdown with defined phenotype, and complex formation validated in single study\",\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 PPP1R35-null cells, nascent centrioles assemble normally but fail to form active centrosomes or recruit CEP295 (an essential CCC factor); centrioles disintegrate after mitosis upon cartwheel removal. The putative PP1-interacting motif is dispensable for PPP1R35 centriolar localization and CCC function, placing PPP1R35 upstream of CEP295 in the CCC pathway.\",\n      \"method\": \"CRISPR/Cas9 knockout, immunofluorescence, epistasis (CEP295 recruitment assay), domain mutagenesis\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined cellular phenotype, epistasis placing PPP1R35 upstream of CEP295, and domain mutagenesis ruling out PP1 motif requirement\",\n      \"pmids\": [\"30230954\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Loss of Ppp1r35 in mouse embryos abolishes primary cilia formation, disrupts notochord development, impairs floor plate specification, increases cell death in the neural tube, and causes cell-cycle delay/stalling (increased prometaphase cells), confirming an essential in vivo role for PPP1R35 in centriole homeostasis and ciliogenesis.\",\n      \"method\": \"Homozygous loss-of-function mouse model, histology, immunofluorescence, molecular marker analysis\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo knockout with multiple orthogonal phenotypic readouts consistent with in vitro findings\",\n      \"pmids\": [\"32628936\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PPP1R35 is a direct phosphorylation substrate of the kinase CDKL5; the phosphoserine residue lies within the CDKL5 consensus motif. PPP1R35 also interacts with CEP131, a known CDKL5 phospho-target, linking CDKL5 signaling to the centriole elongation/cilia pathway.\",\n      \"method\": \"Phosphoproteomic screen (unbiased), in vitro kinase validation of direct phosphorylation, Co-IP (PPP1R35–CEP131 interaction), iPSC-derived neurons\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct phosphorylation validated by complementary approaches in single study; interaction with CEP131 by single Co-IP\",\n      \"pmids\": [\"39136782\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPP1R35 is a resident centrosomal protein in the proximal centriole lumen that acts downstream of RTTN to promote centriole elongation and upstream of CEP295 to drive centriole-to-centrosome conversion, thereby maintaining centriole homeostasis and enabling ciliogenesis; it is also a direct substrate of the kinase CDKL5 and interacts with CEP131, connecting it to a broader centrosome/cilia signaling network.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"PPP1R35 is a resident centrosomal protein localized to the proximal centriole lumen, where it serves dual roles in centriole elongation and centriole-to-centrosome conversion (CCC). It acts downstream of the microcephaly protein RTTN to promote distal centriole elongation and upstream of CEP295 to drive CCC, with its putative PP1-interacting motif being dispensable for both localization and CCC function [PMID:30168418, PMID:30230954]. Loss of PPP1R35 in mouse embryos abolishes primary cilia formation, disrupts notochord development, and causes cell-cycle stalling, confirming an essential in vivo role in centriole homeostasis and ciliogenesis [PMID:32628936]. PPP1R35 is a direct phosphorylation substrate of CDKL5 and interacts with the centrosomal protein CEP131, connecting centriole biogenesis to CDKL5 kinase signaling [PMID:39136782].\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Defining where PPP1R35 resides within the centriole and what happens when it is lost established it as a core structural regulator of centriole elongation acting in complex with the microcephaly protein RTTN.\",\n      \"evidence\": \"Quantitative super-resolution microscopy, siRNA knockdown, BioID proximity proteomics, and Co-IP in human cells\",\n      \"pmids\": [\"30168418\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether PPP1R35 has catalytic activity or acts solely as a scaffold remains unknown\",\n        \"Structural basis of the PPP1R35–RTTN interaction is unresolved\",\n        \"How PPP1R35 recruits or stabilizes distal centriole components is not mechanistically defined\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Demonstrating that PPP1R35-null cells form nascent centrioles that fail to recruit CEP295 and disintegrate after mitosis placed PPP1R35 as the earliest known factor required for centriole-to-centrosome conversion, independent of its putative PP1-binding motif.\",\n      \"evidence\": \"CRISPR/Cas9 knockout, epistasis analysis of CEP295 recruitment, and domain mutagenesis in human cells\",\n      \"pmids\": [\"30230954\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The molecular mechanism by which PPP1R35 promotes CEP295 recruitment is unknown\",\n        \"Whether PPP1R35 engages PP1 phosphatase in any other context remains untested\",\n        \"The relationship between centriole elongation and CCC functions of PPP1R35 is not disentangled\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"In vivo validation in a mouse knockout model confirmed that PPP1R35 is essential for primary cilia formation, neural tube patterning, and cell-cycle progression, extending the cell-culture findings to organismal physiology.\",\n      \"evidence\": \"Homozygous loss-of-function mouse model with histology, immunofluorescence, and molecular marker analysis\",\n      \"pmids\": [\"32628936\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Tissue-specific and conditional requirements for PPP1R35 have not been examined\",\n        \"Whether the cell-cycle delay is a direct consequence of centriole loss or a checkpoint response is unresolved\",\n        \"No human Mendelian disease link has been established\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identification of PPP1R35 as a direct CDKL5 kinase substrate and CEP131 interaction partner connected the centriole elongation/cilia pathway to CDKL5 signaling, suggesting a regulatory input controlling PPP1R35 function.\",\n      \"evidence\": \"Unbiased phosphoproteomics, in vitro kinase assay, and Co-IP in iPSC-derived neurons\",\n      \"pmids\": [\"39136782\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"CEP131 interaction relies on a single Co-IP without reciprocal validation\",\n        \"Functional consequence of CDKL5-mediated phosphorylation on PPP1R35 activity or localization is unknown\",\n        \"Whether CDKL5 phosphorylation regulates centriole elongation or CCC has not been tested\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular mechanism by which PPP1R35 coordinates centriole elongation and centriole-to-centrosome conversion — including its direct binding partners on the centriole wall and how CDKL5 phosphorylation modulates its function — remains to be defined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No structural model of PPP1R35 or its complexes exists\",\n        \"Whether PPP1R35 dysfunction underlies a human ciliopathy or microcephaly syndrome is untested\",\n        \"The relationship between CDKL5-dependent phosphorylation and the PPP1R35–RTTN or PPP1R35–CEP295 pathways has not been examined\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"RTTN\", \"CEP295\", \"CEP131\", \"CDKL5\"],\n    \"other_free_text\": []\n  }\n}\n```"}