{"gene":"RCAN3","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2006,"finding":"RCAN3 (DSCR1L2) protein interacts with human cardiac troponin I (TNNI3), the heart-specific inhibitory subunit of the troponin complex; the interaction was demonstrated by yeast two-hybrid analysis, yeast cotransformation, and GST fusion protein assay, with exon 2 of RCAN3 identified as sufficient for binding to TNNI3.","method":"Yeast two-hybrid screening of human heart cDNA library, yeast cotransformation, and GST fusion protein pull-down assay","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — three orthogonal in vitro/yeast methods in a single lab, domain mapping with exon-deletion isoforms","pmids":["16516408"],"is_preprint":false},{"year":2007,"finding":"Novel RCAN3 splice isoforms lacking exon 3 or exon 4 also interact with TNNI3, and the presence of exon 2 is sufficient for TNNI3 binding across all RCAN3 isoforms, as confirmed by yeast cotransformation and GST fusion protein assay.","method":"RT-PCR cloning of novel isoforms, yeast cotransformation, GST fusion protein pull-down assay","journal":"Gene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two orthogonal methods replicating and extending the TNNI3 interaction finding from the same lab","pmids":["18022329"],"is_preprint":false},{"year":2015,"finding":"RCAN3 inhibits tumor growth and tumor angiogenesis in an orthotopic breast cancer model in a calcineurin (CN)-dependent manner; mutation of the conserved CIC (calcipressin inhibitor of calcineurin) motif abolishes the tumor suppressor effect, and RCAN3 inhibits the CN-NFATc signaling pathway and NFATc-dependent COX-2 gene induction.","method":"Overexpression and CIC-motif mutagenesis in orthotopic xenograft mouse model, CN-NFATc pathway reporter assays, COX-2 expression analysis","journal":"Carcinogenesis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional mutagenesis (CIC motif) combined with in vivo orthotopic model and pathway reporter assays, single lab","pmids":["25916653"],"is_preprint":false},{"year":2022,"finding":"The PxIxIT motif-containing RCAN3-derived peptide (EGFP-R3(178-210)) binds calcineurin and inhibits NFAT-mediated cytokine gene expression without affecting calcineurin phosphatase activity, and suppresses tumor growth and angiogenesis in a syngeneic immunocompetent TNBC mouse model, confirming RCAN3's tumor suppressor activity is maintained in the presence of a functional immune system.","method":"Orthotopic syngeneic TNBC mouse model (immunocompetent), CN binding assay, NFAT-dependent gene expression assay, peptide with native PxIxIT sequence","journal":"Carcinogenesis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo syngeneic model replicating prior nude mouse results plus biochemical CN-binding/phosphatase assay, single lab","pmids":["35640493"],"is_preprint":false}],"current_model":"RCAN3 is an endogenous regulator of calcineurin (CN) that inhibits the CN-NFATc signaling pathway via its conserved CIC/PxIxIT motif (which competes with NFATc for CN binding without inhibiting CN phosphatase activity), suppresses tumor growth and angiogenesis in breast cancer models, and also interacts with cardiac troponin I (TNNI3) through its exon-2-encoded domain, suggesting an additional role in cardiac contractile regulation."},"narrative":{"mechanistic_narrative":"RCAN3 (DSCR1L2) is an endogenous regulator of the calcineurin (CN)–NFATc signaling pathway that functions as a tumor suppressor [PMID:25916653]. It binds calcineurin through a conserved CIC/PxIxIT motif and inhibits NFATc-dependent transcription—including NFATc-driven COX-2 induction and cytokine gene expression—without affecting calcineurin's intrinsic phosphatase activity, indicating that it acts by competitively occupying the CN substrate-docking site rather than by catalytic inhibition [PMID:25916653, PMID:35640493]. Through this CIC-motif-dependent mechanism, RCAN3 suppresses tumor growth and tumor angiogenesis in orthotopic breast cancer models, and a PxIxIT-containing RCAN3-derived peptide reproduces this anti-tumor and anti-angiogenic effect in an immunocompetent syngeneic triple-negative breast cancer model [PMID:25916653, PMID:35640493]. Independently, RCAN3 interacts with cardiac troponin I (TNNI3) via its exon-2-encoded domain, an interaction conserved across multiple splice isoforms, implicating it in cardiac contractile regulation [PMID:16516408, PMID:18022329]. Beyond these calcineurin-regulatory and TNNI3-binding activities, no further mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2006,"claim":"Established the first physical binding partner of RCAN3 by showing it directly interacts with cardiac troponin I, raising the possibility of a role in cardiac contractile regulation.","evidence":"Yeast two-hybrid screen of a human heart cDNA library with yeast cotransformation and GST pull-down, mapping the binding determinant to exon 2","pmids":["16516408"],"confidence":"Medium","gaps":["Interaction shown only in yeast/in vitro systems, not in cardiomyocytes","Functional consequence for troponin function or cardiac contraction not tested","No reciprocal endogenous co-IP in cardiac tissue"]},{"year":2007,"claim":"Defined the structural basis of TNNI3 binding by demonstrating exon 2 is necessary and sufficient across splice isoforms, distinguishing the troponin-binding domain from variable exons.","evidence":"RT-PCR cloning of exon-3- and exon-4-lacking isoforms with yeast cotransformation and GST pull-down","pmids":["18022329"],"confidence":"Medium","gaps":["Physiological role of distinct isoforms not established","No in vivo or cellular validation of the isoform interactions","Functional impact of TNNI3 binding still undetermined"]},{"year":2015,"claim":"Defined RCAN3 as a calcineurin-dependent tumor suppressor and identified the CIC motif as the critical functional element for inhibiting CN-NFATc signaling and downstream COX-2 induction.","evidence":"Overexpression and CIC-motif mutagenesis in an orthotopic breast cancer xenograft model with CN-NFATc reporter and COX-2 expression assays","pmids":["25916653"],"confidence":"Medium","gaps":["Performed in immunodeficient host, leaving immune contribution unaddressed","Endogenous (non-overexpression) role of RCAN3 not established","Direct CN binding biochemistry not yet resolved in this study"]},{"year":2022,"claim":"Resolved the mechanism of calcineurin inhibition—competitive PxIxIT docking that blocks NFAT signaling without inhibiting phosphatase activity—and confirmed tumor suppression in an immunocompetent setting.","evidence":"RCAN3-derived PxIxIT peptide (EGFP-R3(178-210)) tested in CN binding and phosphatase assays, NFAT-dependent gene expression assays, and a syngeneic immunocompetent TNBC mouse model","pmids":["35640493"],"confidence":"Medium","gaps":["Peptide surrogate rather than full-length protein in vivo","Structural model of the RCAN3–CN interface not determined","Specificity versus other PxIxIT-containing CN regulators not delineated"]},{"year":null,"claim":"Whether RCAN3's calcineurin-regulatory and TNNI3-binding activities are functionally integrated, and what RCAN3 does in cardiac physiology at endogenous levels, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No demonstrated cardiac phenotype or in vivo cardiac function for RCAN3","No link established between the exon-2 TNNI3 interaction and the CIC/PxIxIT CN-regulatory function","Endogenous loss-of-function studies and tissue-level localization absent from the corpus"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,3]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[2,3]}],"localization":[],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,3]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[2,3]}],"complexes":[],"partners":["PPP3CA","TNNI3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UKA8","full_name":"Calcipressin-3","aliases":["Down syndrome candidate region 1-like protein 2","Myocyte-enriched calcineurin-interacting protein 3","MCIP3","Regulator of calcineurin 3"],"length_aa":241,"mass_kda":27.5,"function":"Inhibits calcineurin-dependent transcriptional responses by binding to the catalytic domain of calcineurin A. Could play a role during central nervous system development (By similarity)","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q9UKA8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RCAN3","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RCAN3","total_profiled":1310},"omim":[{"mim_id":"605860","title":"RCAN FAMILY MEMBER 3; RCAN3","url":"https://www.omim.org/entry/605860"},{"mim_id":"602917","title":"REGULATOR OF CALCINEURIN 1; RCAN1","url":"https://www.omim.org/entry/602917"},{"mim_id":"191044","title":"TROPONIN I, CARDIAC; TNNI3","url":"https://www.omim.org/entry/191044"},{"mim_id":"114105","title":"PROTEIN PHOSPHATASE 3, CATALYTIC SUBUNIT, ALPHA ISOFORM; PPP3CA","url":"https://www.omim.org/entry/114105"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nuclear speckles","reliability":"Approved"},{"location":"Nucleoli fibrillar center","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"prostate","ntpm":31.7}],"url":"https://www.proteinatlas.org/search/RCAN3"},"hgnc":{"alias_symbol":[],"prev_symbol":["DSCR1L2"]},"alphafold":{"accession":"Q9UKA8","domains":[{"cath_id":"3.30.70.330","chopping":"47-120","consensus_level":"high","plddt":94.0378,"start":47,"end":120}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UKA8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UKA8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UKA8-F1-predicted_aligned_error_v6.png","plddt_mean":74.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RCAN3","jax_strain_url":"https://www.jax.org/strain/search?query=RCAN3"},"sequence":{"accession":"Q9UKA8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UKA8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UKA8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UKA8"}},"corpus_meta":[{"pmid":"10756093","id":"PMC_10756093","title":"A new gene family including DSCR1 (Down Syndrome Candidate Region 1) and ZAKI-4: characterization from yeast to human and identification of DSCR1-like 2, a novel human member (DSCR1L2).","date":"2000","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/10756093","citation_count":67,"is_preprint":false},{"pmid":"25916653","id":"PMC_25916653","title":"A novel role for an RCAN3-derived peptide as a tumor suppressor in breast cancer.","date":"2015","source":"Carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/25916653","citation_count":18,"is_preprint":false},{"pmid":"16516408","id":"PMC_16516408","title":"Proteins encoded by human Down syndrome critical region gene 1-like 2 (DSCR1L2) mRNA and by a novel DSCR1L2 mRNA isoform interact with cardiac troponin I (TNNI3).","date":"2006","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/16516408","citation_count":15,"is_preprint":false},{"pmid":"18022329","id":"PMC_18022329","title":"Identification and analysis of human RCAN3 (DSCR1L2) mRNA and protein isoforms.","date":"2007","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/18022329","citation_count":12,"is_preprint":false},{"pmid":"21961037","id":"PMC_21961037","title":"Complexity of bidirectional transcription and alternative splicing at human RCAN3 locus.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21961037","citation_count":12,"is_preprint":false},{"pmid":"32345470","id":"PMC_32345470","title":"Functional implications of miR-145/RCAN3 axis in the progression of cervical cancer.","date":"2020","source":"Reproductive biology","url":"https://pubmed.ncbi.nlm.nih.gov/32345470","citation_count":4,"is_preprint":false},{"pmid":"35640493","id":"PMC_35640493","title":"The PxIxIT motif of the RCAN3 inhibits angiogenesis and tumor progression in Triple Negative breast cancer in immunocompetent mice.","date":"2022","source":"Carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/35640493","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.03.15.643421","title":"Spatial single-cell interactome and niche-specific molecular signatures in alcohol-related liver disease","date":"2025-03-17","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.15.643421","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6972,"output_tokens":1121,"usd":0.018866,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7674,"output_tokens":2065,"usd":0.044998,"stage2_stop_reason":"end_turn"},"total_usd":0.063864,"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\": 2006,\n      \"finding\": \"RCAN3 (DSCR1L2) protein interacts with human cardiac troponin I (TNNI3), the heart-specific inhibitory subunit of the troponin complex; the interaction was demonstrated by yeast two-hybrid analysis, yeast cotransformation, and GST fusion protein assay, with exon 2 of RCAN3 identified as sufficient for binding to TNNI3.\",\n      \"method\": \"Yeast two-hybrid screening of human heart cDNA library, yeast cotransformation, and GST fusion protein pull-down assay\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — three orthogonal in vitro/yeast methods in a single lab, domain mapping with exon-deletion isoforms\",\n      \"pmids\": [\"16516408\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Novel RCAN3 splice isoforms lacking exon 3 or exon 4 also interact with TNNI3, and the presence of exon 2 is sufficient for TNNI3 binding across all RCAN3 isoforms, as confirmed by yeast cotransformation and GST fusion protein assay.\",\n      \"method\": \"RT-PCR cloning of novel isoforms, yeast cotransformation, GST fusion protein pull-down assay\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two orthogonal methods replicating and extending the TNNI3 interaction finding from the same lab\",\n      \"pmids\": [\"18022329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"RCAN3 inhibits tumor growth and tumor angiogenesis in an orthotopic breast cancer model in a calcineurin (CN)-dependent manner; mutation of the conserved CIC (calcipressin inhibitor of calcineurin) motif abolishes the tumor suppressor effect, and RCAN3 inhibits the CN-NFATc signaling pathway and NFATc-dependent COX-2 gene induction.\",\n      \"method\": \"Overexpression and CIC-motif mutagenesis in orthotopic xenograft mouse model, CN-NFATc pathway reporter assays, COX-2 expression analysis\",\n      \"journal\": \"Carcinogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional mutagenesis (CIC motif) combined with in vivo orthotopic model and pathway reporter assays, single lab\",\n      \"pmids\": [\"25916653\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The PxIxIT motif-containing RCAN3-derived peptide (EGFP-R3(178-210)) binds calcineurin and inhibits NFAT-mediated cytokine gene expression without affecting calcineurin phosphatase activity, and suppresses tumor growth and angiogenesis in a syngeneic immunocompetent TNBC mouse model, confirming RCAN3's tumor suppressor activity is maintained in the presence of a functional immune system.\",\n      \"method\": \"Orthotopic syngeneic TNBC mouse model (immunocompetent), CN binding assay, NFAT-dependent gene expression assay, peptide with native PxIxIT sequence\",\n      \"journal\": \"Carcinogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo syngeneic model replicating prior nude mouse results plus biochemical CN-binding/phosphatase assay, single lab\",\n      \"pmids\": [\"35640493\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RCAN3 is an endogenous regulator of calcineurin (CN) that inhibits the CN-NFATc signaling pathway via its conserved CIC/PxIxIT motif (which competes with NFATc for CN binding without inhibiting CN phosphatase activity), suppresses tumor growth and angiogenesis in breast cancer models, and also interacts with cardiac troponin I (TNNI3) through its exon-2-encoded domain, suggesting an additional role in cardiac contractile regulation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RCAN3 (DSCR1L2) is an endogenous regulator of the calcineurin (CN)–NFATc signaling pathway that functions as a tumor suppressor [#2]. It binds calcineurin through a conserved CIC/PxIxIT motif and inhibits NFATc-dependent transcription—including NFATc-driven COX-2 induction and cytokine gene expression—without affecting calcineurin's intrinsic phosphatase activity, indicating that it acts by competitively occupying the CN substrate-docking site rather than by catalytic inhibition [#2, #3]. Through this CIC-motif-dependent mechanism, RCAN3 suppresses tumor growth and tumor angiogenesis in orthotopic breast cancer models, and a PxIxIT-containing RCAN3-derived peptide reproduces this anti-tumor and anti-angiogenic effect in an immunocompetent syngeneic triple-negative breast cancer model [#2, #3]. Independently, RCAN3 interacts with cardiac troponin I (TNNI3) via its exon-2-encoded domain, an interaction conserved across multiple splice isoforms, implicating it in cardiac contractile regulation [#0, #1]. Beyond these calcineurin-regulatory and TNNI3-binding activities, no further mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Established the first physical binding partner of RCAN3 by showing it directly interacts with cardiac troponin I, raising the possibility of a role in cardiac contractile regulation.\",\n      \"evidence\": \"Yeast two-hybrid screen of a human heart cDNA library with yeast cotransformation and GST pull-down, mapping the binding determinant to exon 2\",\n      \"pmids\": [\"16516408\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Interaction shown only in yeast/in vitro systems, not in cardiomyocytes\",\n        \"Functional consequence for troponin function or cardiac contraction not tested\",\n        \"No reciprocal endogenous co-IP in cardiac tissue\"\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Defined the structural basis of TNNI3 binding by demonstrating exon 2 is necessary and sufficient across splice isoforms, distinguishing the troponin-binding domain from variable exons.\",\n      \"evidence\": \"RT-PCR cloning of exon-3- and exon-4-lacking isoforms with yeast cotransformation and GST pull-down\",\n      \"pmids\": [\"18022329\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Physiological role of distinct isoforms not established\",\n        \"No in vivo or cellular validation of the isoform interactions\",\n        \"Functional impact of TNNI3 binding still undetermined\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined RCAN3 as a calcineurin-dependent tumor suppressor and identified the CIC motif as the critical functional element for inhibiting CN-NFATc signaling and downstream COX-2 induction.\",\n      \"evidence\": \"Overexpression and CIC-motif mutagenesis in an orthotopic breast cancer xenograft model with CN-NFATc reporter and COX-2 expression assays\",\n      \"pmids\": [\"25916653\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Performed in immunodeficient host, leaving immune contribution unaddressed\",\n        \"Endogenous (non-overexpression) role of RCAN3 not established\",\n        \"Direct CN binding biochemistry not yet resolved in this study\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Resolved the mechanism of calcineurin inhibition—competitive PxIxIT docking that blocks NFAT signaling without inhibiting phosphatase activity—and confirmed tumor suppression in an immunocompetent setting.\",\n      \"evidence\": \"RCAN3-derived PxIxIT peptide (EGFP-R3(178-210)) tested in CN binding and phosphatase assays, NFAT-dependent gene expression assays, and a syngeneic immunocompetent TNBC mouse model\",\n      \"pmids\": [\"35640493\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Peptide surrogate rather than full-length protein in vivo\",\n        \"Structural model of the RCAN3–CN interface not determined\",\n        \"Specificity versus other PxIxIT-containing CN regulators not delineated\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether RCAN3's calcineurin-regulatory and TNNI3-binding activities are functionally integrated, and what RCAN3 does in cardiac physiology at endogenous levels, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No demonstrated cardiac phenotype or in vivo cardiac function for RCAN3\",\n        \"No link established between the exon-2 TNNI3 interaction and the CIC/PxIxIT CN-regulatory function\",\n        \"Endogenous loss-of-function studies and tissue-level localization absent from the corpus\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PPP3CA\", \"TNNI3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}