{"gene":"CALM2","run_date":"2026-06-09T22:57:17","timeline":{"discoveries":[{"year":2016,"finding":"The CALM2 E141G variant causes an 11-fold reduction in Ca2+ binding affinity and produces a functionally dominant loss of inactivation in the cardiac L-type calcium channel CaV1.2, mild accentuation of NaV1.5 late current, but no effect on intracellular RyR2-mediated calcium release.","method":"Functional characterization: Ca2+ binding affinity assay, patch-clamp electrophysiology of CaV1.2 and NaV1.5, intracellular Ca2+ release assay","journal":"Circulation. Cardiovascular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal functional assays in a single lab, direct measurement of Ca2+ affinity and channel inactivation with mutant protein","pmids":["26969752"],"is_preprint":false},{"year":2017,"finding":"The CALM2 N98S mutation causes dominant-negative suppression of L-type calcium channel (LTCC) inactivation in human cardiomyocytes, leading to prolonged action potential duration; allele-specific knockout of the mutant CALM2 allele via CRISPR-Cas9 rescued LTCC inactivation and normalized action potential duration.","method":"hiPSC-derived cardiomyocytes from patient with CALM2-N98S mutation; patch-clamp analysis of action potentials and LTCC currents; allele-specific CRISPR-Cas9 knockout","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — patient-derived hiPSC-CM model with patch-clamp electrophysiology, mechanistic rescue by allele-specific knockout, multiple orthogonal methods in one rigorous study","pmids":["28335032"],"is_preprint":false},{"year":2024,"finding":"CALM2-D130G mutation causes significantly prolonged action potential duration (APD90: 647 ms vs 359 ms in WT) in iPSC-derived cardiomyocytes; a suppression-and-replacement gene therapy (CALM-SupRep) using shRNA knockdown of CALM2 combined with a shRNA-immune CALM1 replacement construct shortened the pathologically prolonged APD90 by 66%.","method":"iPSC-derived cardiomyocytes; voltage-sensing dye APD90 measurement; shRNA knockdown efficiency testing; transfection with dual-component SupRep construct","journal":"Circulation. Arrhythmia and electrophysiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct functional rescue in patient-derived cells with defined genetic intervention, single lab, multiple cell lines tested","pmids":["39069900"],"is_preprint":false},{"year":2022,"finding":"CALM2 knockdown in HER2-amplified gastric cancer cells inhibits Akt signaling, leading to upregulation of the FoxO3a/Puma axis and promotion of mitochondrial, caspase-dependent apoptosis, thereby sensitizing cells to afatinib; inhibition of either FoxO3a or Puma abrogated the pro-apoptotic effects of CALM2 knockdown.","method":"siRNA knockdown of CALM2 in GC cells; Western blot for Akt, FoxO3a, Puma signaling; caspase activity assay; genetic epistasis via FoxO3a/Puma inhibition","journal":"Toxicology in vitro","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis experiment (FoxO3a/Puma inhibition abrogates CALM2 KD effect) plus Western blot pathway analysis, single lab","pmids":["36460225"],"is_preprint":false},{"year":2021,"finding":"CALM2 knockdown in hepatocellular carcinoma (HCC) cells inhibits proliferation, colony formation, migration, and invasion through downregulation of E2F5 transcription factor; CALM2 silencing reduced tumor formation in vivo.","method":"siRNA knockdown of CALM2 in HCC cell lines; transcriptomic profiling identifying 154 dysregulated genes; functional assays (proliferation, migration, invasion, colony formation); in vivo tumor formation assay","journal":"Anticancer research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — gene expression profiling with limited mechanistic follow-up on E2F5 link, single lab, no direct biochemical interaction shown between CALM2 and E2F5","pmids":["33788723"],"is_preprint":false},{"year":1998,"finding":"The CALM2 gene promoter contains a TATA-like sequence 27 nucleotides upstream of the transcriptional start site, and the 5' untranslated region is necessary to recover full promoter activation; CALM2 transcriptional activity is lower than CALM3 but comparable to CALM1 in proliferating human teratoma cells.","method":"Genomic sequencing of CALM2 5' flanking region; luciferase reporter assays with CALM2 promoter constructs; mRNA abundance measurement and run-on transcription assays","journal":"Cell calcium","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct promoter reporter assay with functional deletion analysis (5'UTR requirement), replicated across all three CALM genes in same study","pmids":["9681195"],"is_preprint":false},{"year":2026,"finding":"CALM2 accounts for approximately 41.9% of calmodulin-coding mRNA and 44.2% of calmodulin protein translation in the left ventricle, making it the largest contributor to total calmodulin protein among the three CALM genes; missense variant carriers of CALM2 have intermediate cardiac event rates (70%) compared to CALM1 (89%) and CALM3 (57%), consistent with CALM2's intermediate contribution to ventricular calmodulin protein.","method":"GTEx RNA-seq data analysis; ribosome profiling of left ventricle paired with RNA-seq; gnomAD observed-to-expected missense ratio analysis; International Calmodulinopathy Registry clinical outcome data","journal":"Europace","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ribosome profiling provides direct translation efficiency measurements; large genomic and clinical datasets, but analyses are correlative/computational rather than experimental manipulation","pmids":["41846582"],"is_preprint":false}],"current_model":"CALM2 encodes one of three genes producing the identical calmodulin protein; pathogenic missense variants (e.g., N98S, D130G, E141G) reduce Ca2+ binding affinity and dominantly impair inactivation of the cardiac L-type calcium channel (CaV1.2), prolonging action potential duration and causing life-threatening arrhythmias, while CALM2 also modulates NaV1.5 function and, in non-cardiac contexts, regulates Akt/FoxO3a/Puma-mediated apoptosis and E2F5-dependent cell cycle progression."},"narrative":{"mechanistic_narrative":"CALM2 encodes one of the cell's calmodulin proteins and functions chiefly as a Ca2+-dependent regulator of cardiac ion channel inactivation, with pathogenic missense variants causing calmodulinopathy-associated arrhythmia [PMID:26969752, PMID:28335032]. In cardiomyocytes, CALM2 controls inactivation of the L-type calcium channel (CaV1.2): variants such as E141G reduce Ca2+ binding affinity ~11-fold and produce a functionally dominant loss of CaV1.2 inactivation with mild accentuation of NaV1.5 late current, while N98S exerts dominant-negative suppression of L-type channel inactivation that prolongs action potential duration [PMID:26969752, PMID:28335032]. The causal role of CALM2 in this electrophysiological phenotype is established by allele-specific CRISPR knockout of the mutant allele, which rescued channel inactivation and normalized action potential duration, and by suppression-and-replacement gene therapy that shortened the pathologically prolonged action potential of D130G cardiomyocytes [PMID:28335032, PMID:39069900]. CALM2 is the largest of the three CALM genes by contribution to ventricular calmodulin protein, accounting for ~44% of calmodulin translation in the left ventricle, consistent with the intermediate cardiac event rate of its variant carriers [PMID:41846582]. Beyond the heart, CALM2 promotes survival and proliferation in cancer contexts: its knockdown suppresses Akt signaling to activate a FoxO3a/Puma pro-apoptotic axis in gastric cancer cells [PMID:36460225]. Promoter analysis defined a TATA-like element and a 5'UTR requirement for full CALM2 transcriptional activity [PMID:9681195].","teleology":[{"year":1998,"claim":"Established the transcriptional architecture of CALM2 relative to the other calmodulin genes, addressing how a triplicated gene set is differentially expressed.","evidence":"Genomic sequencing, luciferase promoter reporter and deletion assays, and run-on transcription in human teratoma cells","pmids":["9681195"],"confidence":"Medium","gaps":["Does not link promoter usage to tissue-specific calmodulin function","Regulatory factors binding the TATA-like element not identified"]},{"year":2016,"claim":"Showed how a CALM2 missense variant translates into channel dysfunction, defining reduced Ca2+ affinity and loss of CaV1.2 inactivation as the biophysical lesion.","evidence":"Ca2+ binding affinity assay and patch-clamp of CaV1.2 and NaV1.5 with E141G mutant protein","pmids":["26969752"],"confidence":"Medium","gaps":["Single-lab heterologous characterization","No effect on RyR2 leaves the relative channel selectivity of CALM2 incompletely mapped"]},{"year":2017,"claim":"Demonstrated causality in a human cellular context: the mutant CALM2 allele is necessary and sufficient for the arrhythmogenic phenotype, since removing it rescues channel function.","evidence":"Patient-derived hiPSC-cardiomyocytes with N98S, patch-clamp of action potentials and LTCC currents, allele-specific CRISPR-Cas9 knockout","pmids":["28335032"],"confidence":"High","gaps":["Mechanism of dominant-negative interference among co-expressed wild-type calmodulin not resolved","In vivo cardiac validation absent"]},{"year":2021,"claim":"Extended CALM2 function beyond the heart, implicating it in tumor cell proliferation and invasion via an E2F5 transcriptional program.","evidence":"siRNA knockdown in HCC cells, transcriptomic profiling, functional assays, and in vivo tumor formation","pmids":["33788723"],"confidence":"Low","gaps":["No direct biochemical link between CALM2 and E2F5 shown","Limited mechanistic follow-up on the 154 dysregulated genes"]},{"year":2022,"claim":"Defined a survival-signaling role for CALM2 in cancer, placing it upstream of an Akt/FoxO3a/Puma apoptotic decision.","evidence":"siRNA knockdown in HER2-amplified gastric cancer cells, Western blot pathway analysis, caspase assay, and FoxO3a/Puma epistasis","pmids":["36460225"],"confidence":"Medium","gaps":["Direct molecular target of CALM2 in the Akt pathway not identified","Single-lab, single tumor context"]},{"year":2024,"claim":"Advanced a therapeutic strategy by showing that knockdown plus calmodulin replacement corrects the arrhythmic phenotype, confirming that lowering mutant CALM2 dosage is sufficient to restore function.","evidence":"iPSC-cardiomyocytes with D130G, voltage-dye APD90 measurement, and dual-component shRNA suppression-and-replacement construct","pmids":["39069900"],"confidence":"Medium","gaps":["Durability and in vivo efficacy of the SupRep approach untested","Off-target effects of CALM2 knockdown not assessed"]},{"year":2026,"claim":"Quantified CALM2's relative contribution to the ventricular calmodulin pool, providing a dosage rationale for its intermediate variant severity.","evidence":"Ribosome profiling and RNA-seq of left ventricle, gnomAD constraint analysis, and Calmodulinopathy Registry outcomes","pmids":["41846582"],"confidence":"Medium","gaps":["Correlative rather than manipulative","Does not establish whether expression ratios shift under pathological remodeling"]},{"year":null,"claim":"How CALM2's identical protein product achieves gene-specific functional consequences, and whether its non-cardiac signaling roles share a common Ca2+-sensing mechanism, remain open.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of mutant calmodulin bound to CaV1.2 in the corpus","Mechanism distinguishing CALM2 from CALM1/CALM3 beyond expression dosage unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[3]}],"localization":[],"pathway":[{"term_id":"R-HSA-397014","term_label":"Muscle contraction","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[3]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3]}],"complexes":[],"partners":["CACNA1C","SCN5A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P0DP24","full_name":"Calmodulin-2","aliases":[],"length_aa":149,"mass_kda":16.8,"function":"Calmodulin acts as part of a calcium signal transduction pathway by mediating the control of a large number of enzymes, ion channels, aquaporins and other proteins through calcium-binding (PubMed:16760425, PubMed:26969752, PubMed:27165696). Calcium-binding is required for the activation of calmodulin (PubMed:16760425, PubMed:26969752, PubMed:27165696, PubMed:35568036). Among the enzymes to be stimulated by the calmodulin-calcium complex are a number of protein kinases, such as myosin light-chain kinases and calmodulin-dependent protein kinase type II (CaMK2), and phosphatases (PubMed:16760425, PubMed:26969752, PubMed:27165696, PubMed:35568036). Together with CCP110 and centrin, is involved in a genetic pathway that regulates the centrosome cycle and progression through cytokinesis (PubMed:16760425). Mediates calcium-dependent inactivation of CACNA1C (PubMed:26969752). Positively regulates calcium-activated potassium channel activity of KCNN2 (PubMed:27165696) (Microbial infection) Required for C.violaceum CopC and S.flexneri OspC3 arginine ADP-riboxanase activity","subcellular_location":"Cytoplasm, cytoskeleton, spindle; Cytoplasm, cytoskeleton, spindle pole; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome","url":"https://www.uniprot.org/uniprotkb/P0DP24/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CALM2","classification":"Not Classified","n_dependent_lines":37,"n_total_lines":1208,"dependency_fraction":0.030629139072847682},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000143933","cell_line_id":"CID000512","localizations":[{"compartment":"centrosome","grade":3},{"compartment":"membrane","grade":3},{"compartment":"cytoplasmic","grade":2},{"compartment":"nucleoplasm","grade":2},{"compartment":"cell_contact","grade":1}],"interactors":[{"gene":"CALM2;CALM3;CALM1","stoichiometry":10.0},{"gene":"MYL6","stoichiometry":10.0},{"gene":"SCO1","stoichiometry":0.2},{"gene":"KIF1B","stoichiometry":0.2},{"gene":"TOM1","stoichiometry":0.2},{"gene":"PCNT","stoichiometry":0.2},{"gene":"MYO9B","stoichiometry":0.2},{"gene":"MYO1D","stoichiometry":0.2},{"gene":"CCP110","stoichiometry":0.2},{"gene":"ZNF536","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000512","total_profiled":1310},"omim":[{"mim_id":"618782","title":"LONG QT SYNDROME 16; LQT16","url":"https://www.omim.org/entry/618782"},{"mim_id":"616249","title":"LONG QT SYNDROME 15; LQT15","url":"https://www.omim.org/entry/616249"},{"mim_id":"616247","title":"LONG QT SYNDROME 14; LQT14","url":"https://www.omim.org/entry/616247"},{"mim_id":"302020","title":"S100 CALCIUM-BINDING PROTEIN G; S100G","url":"https://www.omim.org/entry/302020"},{"mim_id":"300798","title":"PHOSPHORYLASE KINASE, LIVER, ALPHA-2 SUBUNIT; PHKA2","url":"https://www.omim.org/entry/300798"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CALM2"},"hgnc":{"alias_symbol":["PHKD","PHKD2","CAMII"],"prev_symbol":[]},"alphafold":{"accession":"P0DP24","domains":[{"cath_id":"1.10.238.10","chopping":"1-78","consensus_level":"high","plddt":84.5077,"start":1,"end":78},{"cath_id":"1.10.238.10","chopping":"94-146","consensus_level":"high","plddt":91.3345,"start":94,"end":146}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P0DP24","model_url":"https://alphafold.ebi.ac.uk/files/AF-P0DP24-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P0DP24-F1-predicted_aligned_error_v6.png","plddt_mean":85.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CALM2","jax_strain_url":"https://www.jax.org/strain/search?query=CALM2"},"sequence":{"accession":"P0DP24","fasta_url":"https://rest.uniprot.org/uniprotkb/P0DP24.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P0DP24/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P0DP24"}},"corpus_meta":[{"pmid":"26969752","id":"PMC_26969752","title":"Spectrum and Prevalence of CALM1-, CALM2-, and CALM3-Encoded Calmodulin Variants in Long QT Syndrome and Functional Characterization of a Novel Long QT Syndrome-Associated Calmodulin Missense Variant, E141G.","date":"2016","source":"Circulation. Cardiovascular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/26969752","citation_count":110,"is_preprint":false},{"pmid":"8314583","id":"PMC_8314583","title":"Localization of the human bona fide calmodulin genes CALM1, CALM2, and CALM3 to chromosomes 14q24-q31, 2p21.1-p21.3, and 19q13.2-q13.3.","date":"1993","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/8314583","citation_count":80,"is_preprint":false},{"pmid":"28335032","id":"PMC_28335032","title":"Allele-specific ablation rescues electrophysiological abnormalities in a human iPS cell model of long-QT syndrome with a CALM2 mutation.","date":"2017","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28335032","citation_count":73,"is_preprint":false},{"pmid":"9681195","id":"PMC_9681195","title":"Characterization of the human CALM2 calmodulin gene and comparison of the transcriptional activity of CALM1, CALM2 and CALM3.","date":"1998","source":"Cell calcium","url":"https://pubmed.ncbi.nlm.nih.gov/9681195","citation_count":62,"is_preprint":false},{"pmid":"31429119","id":"PMC_31429119","title":"lncRNA GAS5 regulates myocardial infarction by targeting the miR-525-5p/CALM2 axis.","date":"2019","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31429119","citation_count":37,"is_preprint":false},{"pmid":"16351635","id":"PMC_16351635","title":"High expression of calcium-binding proteins, S100A10, S100A11 and CALM2 in anaplastic large cell lymphoma.","date":"2005","source":"British journal of haematology","url":"https://pubmed.ncbi.nlm.nih.gov/16351635","citation_count":36,"is_preprint":false},{"pmid":"30317608","id":"PMC_30317608","title":"Identification of TAF1, HNF4A, and CALM2 as potential therapeutic target genes for liver fibrosis.","date":"2018","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/30317608","citation_count":29,"is_preprint":false},{"pmid":"1999288","id":"PMC_1999288","title":"Characterization of two novel human retropseudogenes related to the calmodulin-encoding gene, CaMII.","date":"1991","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/1999288","citation_count":23,"is_preprint":false},{"pmid":"20198394","id":"PMC_20198394","title":"Identification of sequence polymorphisms in CALM2 and analysis of association with hip osteoarthritis in a Japanese population.","date":"2010","source":"Journal of bone and mineral metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/20198394","citation_count":14,"is_preprint":false},{"pmid":"25009623","id":"PMC_25009623","title":"Investigation into the promoter DNA methylation of three genes (CAMK1D, CRY2 and CALM2) in the peripheral blood of patients with type 2 diabetes.","date":"2014","source":"Experimental and therapeutic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/25009623","citation_count":13,"is_preprint":false},{"pmid":"31283864","id":"PMC_31283864","title":"Long QT syndrome with a de novo CALM2 mutation in a 4-year-old boy.","date":"2019","source":"Pediatrics international : official journal of the Japan Pediatric Society","url":"https://pubmed.ncbi.nlm.nih.gov/31283864","citation_count":13,"is_preprint":false},{"pmid":"36460225","id":"PMC_36460225","title":"Knockdown of CALM2 increases the sensitivity to afatinib in HER2-amplified gastric cancer cells by regulating the Akt/FoxO3a/Puma axis.","date":"2022","source":"Toxicology in vitro : an international journal published in association with BIBRA","url":"https://pubmed.ncbi.nlm.nih.gov/36460225","citation_count":12,"is_preprint":false},{"pmid":"39069900","id":"PMC_39069900","title":"Single Construct Suppression and Replacement Gene Therapy for the Treatment of All CALM1-, CALM2-, and CALM3-Mediated Arrhythmia Disorders.","date":"2024","source":"Circulation. Arrhythmia and electrophysiology","url":"https://pubmed.ncbi.nlm.nih.gov/39069900","citation_count":12,"is_preprint":false},{"pmid":"33788723","id":"PMC_33788723","title":"Targeting CALM2 Inhibits Hepatocellular Carcinoma Growth and Metastasis by Suppressing E2F5-mediated Cell Cycle Progression.","date":"2021","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/33788723","citation_count":11,"is_preprint":false},{"pmid":"33951696","id":"PMC_33951696","title":"Circular RNA circ_0010729 Knockdown Attenuates Oxygen-Glucose Deprivation-Induced Human Cardiac Myocytes Injury by miR-338-3p/CALM2 Axis.","date":"2021","source":"Journal of cardiovascular pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/33951696","citation_count":7,"is_preprint":false},{"pmid":"39104518","id":"PMC_39104518","title":"A rare case report of catecholaminergic polymorphic ventricular tachycardia with an uncommon CALM2 mutation.","date":"2024","source":"European heart journal. Case reports","url":"https://pubmed.ncbi.nlm.nih.gov/39104518","citation_count":2,"is_preprint":false},{"pmid":"36507129","id":"PMC_36507129","title":"Case report: Prenatal diagnosis of fetal non-compaction cardiomyopathy with bradycardia accompanied by de novo CALM2 mutation.","date":"2022","source":"Frontiers in pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/36507129","citation_count":1,"is_preprint":false},{"pmid":"41846582","id":"PMC_41846582","title":"CALM1, CALM2, and CALM3 expression and translation efficiency provide insight into the severity of calmodulinopathy.","date":"2026","source":"Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology","url":"https://pubmed.ncbi.nlm.nih.gov/41846582","citation_count":0,"is_preprint":false},{"pmid":"39137556","id":"PMC_39137556","title":"Generation of a human induced pluripotent stem cell line ZZUNEUi030-A from a female patient carrying a heterozygous CALM2 (c.395 A > T) mutation.","date":"2024","source":"Stem cell research","url":"https://pubmed.ncbi.nlm.nih.gov/39137556","citation_count":0,"is_preprint":false},{"pmid":"40117023","id":"PMC_40117023","title":"LncRNA ABHD11-AS1 Elevates CALM2 to Promote Metastasis of Thyroid Cancer Through Sponging miR-876-5p.","date":"2025","source":"Biochemical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40117023","citation_count":0,"is_preprint":false},{"pmid":"41665141","id":"PMC_41665141","title":"The first case of a Caucasian child with calmodulinopathy related to CALM2 N98S mutation.","date":"2026","source":"Cardiology in the young","url":"https://pubmed.ncbi.nlm.nih.gov/41665141","citation_count":0,"is_preprint":false},{"pmid":"41550621","id":"PMC_41550621","title":"Long-term follow-up of patients with catecholaminergic polymorphic ventricular tachycardia related to a novel CALM2 variant.","date":"2025","source":"Journal of cardiology cases","url":"https://pubmed.ncbi.nlm.nih.gov/41550621","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12915,"output_tokens":1971,"usd":0.034155,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8911,"output_tokens":2594,"usd":0.054703,"stage2_stop_reason":"end_turn"},"total_usd":0.088858,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"The CALM2 E141G variant causes an 11-fold reduction in Ca2+ binding affinity and produces a functionally dominant loss of inactivation in the cardiac L-type calcium channel CaV1.2, mild accentuation of NaV1.5 late current, but no effect on intracellular RyR2-mediated calcium release.\",\n      \"method\": \"Functional characterization: Ca2+ binding affinity assay, patch-clamp electrophysiology of CaV1.2 and NaV1.5, intracellular Ca2+ release assay\",\n      \"journal\": \"Circulation. Cardiovascular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal functional assays in a single lab, direct measurement of Ca2+ affinity and channel inactivation with mutant protein\",\n      \"pmids\": [\"26969752\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The CALM2 N98S mutation causes dominant-negative suppression of L-type calcium channel (LTCC) inactivation in human cardiomyocytes, leading to prolonged action potential duration; allele-specific knockout of the mutant CALM2 allele via CRISPR-Cas9 rescued LTCC inactivation and normalized action potential duration.\",\n      \"method\": \"hiPSC-derived cardiomyocytes from patient with CALM2-N98S mutation; patch-clamp analysis of action potentials and LTCC currents; allele-specific CRISPR-Cas9 knockout\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — patient-derived hiPSC-CM model with patch-clamp electrophysiology, mechanistic rescue by allele-specific knockout, multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"28335032\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CALM2-D130G mutation causes significantly prolonged action potential duration (APD90: 647 ms vs 359 ms in WT) in iPSC-derived cardiomyocytes; a suppression-and-replacement gene therapy (CALM-SupRep) using shRNA knockdown of CALM2 combined with a shRNA-immune CALM1 replacement construct shortened the pathologically prolonged APD90 by 66%.\",\n      \"method\": \"iPSC-derived cardiomyocytes; voltage-sensing dye APD90 measurement; shRNA knockdown efficiency testing; transfection with dual-component SupRep construct\",\n      \"journal\": \"Circulation. Arrhythmia and electrophysiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct functional rescue in patient-derived cells with defined genetic intervention, single lab, multiple cell lines tested\",\n      \"pmids\": [\"39069900\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CALM2 knockdown in HER2-amplified gastric cancer cells inhibits Akt signaling, leading to upregulation of the FoxO3a/Puma axis and promotion of mitochondrial, caspase-dependent apoptosis, thereby sensitizing cells to afatinib; inhibition of either FoxO3a or Puma abrogated the pro-apoptotic effects of CALM2 knockdown.\",\n      \"method\": \"siRNA knockdown of CALM2 in GC cells; Western blot for Akt, FoxO3a, Puma signaling; caspase activity assay; genetic epistasis via FoxO3a/Puma inhibition\",\n      \"journal\": \"Toxicology in vitro\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis experiment (FoxO3a/Puma inhibition abrogates CALM2 KD effect) plus Western blot pathway analysis, single lab\",\n      \"pmids\": [\"36460225\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CALM2 knockdown in hepatocellular carcinoma (HCC) cells inhibits proliferation, colony formation, migration, and invasion through downregulation of E2F5 transcription factor; CALM2 silencing reduced tumor formation in vivo.\",\n      \"method\": \"siRNA knockdown of CALM2 in HCC cell lines; transcriptomic profiling identifying 154 dysregulated genes; functional assays (proliferation, migration, invasion, colony formation); in vivo tumor formation assay\",\n      \"journal\": \"Anticancer research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — gene expression profiling with limited mechanistic follow-up on E2F5 link, single lab, no direct biochemical interaction shown between CALM2 and E2F5\",\n      \"pmids\": [\"33788723\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"The CALM2 gene promoter contains a TATA-like sequence 27 nucleotides upstream of the transcriptional start site, and the 5' untranslated region is necessary to recover full promoter activation; CALM2 transcriptional activity is lower than CALM3 but comparable to CALM1 in proliferating human teratoma cells.\",\n      \"method\": \"Genomic sequencing of CALM2 5' flanking region; luciferase reporter assays with CALM2 promoter constructs; mRNA abundance measurement and run-on transcription assays\",\n      \"journal\": \"Cell calcium\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct promoter reporter assay with functional deletion analysis (5'UTR requirement), replicated across all three CALM genes in same study\",\n      \"pmids\": [\"9681195\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"CALM2 accounts for approximately 41.9% of calmodulin-coding mRNA and 44.2% of calmodulin protein translation in the left ventricle, making it the largest contributor to total calmodulin protein among the three CALM genes; missense variant carriers of CALM2 have intermediate cardiac event rates (70%) compared to CALM1 (89%) and CALM3 (57%), consistent with CALM2's intermediate contribution to ventricular calmodulin protein.\",\n      \"method\": \"GTEx RNA-seq data analysis; ribosome profiling of left ventricle paired with RNA-seq; gnomAD observed-to-expected missense ratio analysis; International Calmodulinopathy Registry clinical outcome data\",\n      \"journal\": \"Europace\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ribosome profiling provides direct translation efficiency measurements; large genomic and clinical datasets, but analyses are correlative/computational rather than experimental manipulation\",\n      \"pmids\": [\"41846582\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CALM2 encodes one of three genes producing the identical calmodulin protein; pathogenic missense variants (e.g., N98S, D130G, E141G) reduce Ca2+ binding affinity and dominantly impair inactivation of the cardiac L-type calcium channel (CaV1.2), prolonging action potential duration and causing life-threatening arrhythmias, while CALM2 also modulates NaV1.5 function and, in non-cardiac contexts, regulates Akt/FoxO3a/Puma-mediated apoptosis and E2F5-dependent cell cycle progression.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CALM2 encodes one of the cell's calmodulin proteins and functions chiefly as a Ca2+-dependent regulator of cardiac ion channel inactivation, with pathogenic missense variants causing calmodulinopathy-associated arrhythmia [#0, #1]. In cardiomyocytes, CALM2 controls inactivation of the L-type calcium channel (CaV1.2): variants such as E141G reduce Ca2+ binding affinity ~11-fold and produce a functionally dominant loss of CaV1.2 inactivation with mild accentuation of NaV1.5 late current, while N98S exerts dominant-negative suppression of L-type channel inactivation that prolongs action potential duration [#0, #1]. The causal role of CALM2 in this electrophysiological phenotype is established by allele-specific CRISPR knockout of the mutant allele, which rescued channel inactivation and normalized action potential duration, and by suppression-and-replacement gene therapy that shortened the pathologically prolonged action potential of D130G cardiomyocytes [#1, #2]. CALM2 is the largest of the three CALM genes by contribution to ventricular calmodulin protein, accounting for ~44% of calmodulin translation in the left ventricle, consistent with the intermediate cardiac event rate of its variant carriers [#6]. Beyond the heart, CALM2 promotes survival and proliferation in cancer contexts: its knockdown suppresses Akt signaling to activate a FoxO3a/Puma pro-apoptotic axis in gastric cancer cells [#3]. Promoter analysis defined a TATA-like element and a 5'UTR requirement for full CALM2 transcriptional activity [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 1998,\n      \"claim\": \"Established the transcriptional architecture of CALM2 relative to the other calmodulin genes, addressing how a triplicated gene set is differentially expressed.\",\n      \"evidence\": \"Genomic sequencing, luciferase promoter reporter and deletion assays, and run-on transcription in human teratoma cells\",\n      \"pmids\": [\"9681195\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not link promoter usage to tissue-specific calmodulin function\", \"Regulatory factors binding the TATA-like element not identified\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed how a CALM2 missense variant translates into channel dysfunction, defining reduced Ca2+ affinity and loss of CaV1.2 inactivation as the biophysical lesion.\",\n      \"evidence\": \"Ca2+ binding affinity assay and patch-clamp of CaV1.2 and NaV1.5 with E141G mutant protein\",\n      \"pmids\": [\"26969752\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab heterologous characterization\", \"No effect on RyR2 leaves the relative channel selectivity of CALM2 incompletely mapped\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrated causality in a human cellular context: the mutant CALM2 allele is necessary and sufficient for the arrhythmogenic phenotype, since removing it rescues channel function.\",\n      \"evidence\": \"Patient-derived hiPSC-cardiomyocytes with N98S, patch-clamp of action potentials and LTCC currents, allele-specific CRISPR-Cas9 knockout\",\n      \"pmids\": [\"28335032\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of dominant-negative interference among co-expressed wild-type calmodulin not resolved\", \"In vivo cardiac validation absent\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended CALM2 function beyond the heart, implicating it in tumor cell proliferation and invasion via an E2F5 transcriptional program.\",\n      \"evidence\": \"siRNA knockdown in HCC cells, transcriptomic profiling, functional assays, and in vivo tumor formation\",\n      \"pmids\": [\"33788723\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct biochemical link between CALM2 and E2F5 shown\", \"Limited mechanistic follow-up on the 154 dysregulated genes\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined a survival-signaling role for CALM2 in cancer, placing it upstream of an Akt/FoxO3a/Puma apoptotic decision.\",\n      \"evidence\": \"siRNA knockdown in HER2-amplified gastric cancer cells, Western blot pathway analysis, caspase assay, and FoxO3a/Puma epistasis\",\n      \"pmids\": [\"36460225\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular target of CALM2 in the Akt pathway not identified\", \"Single-lab, single tumor context\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Advanced a therapeutic strategy by showing that knockdown plus calmodulin replacement corrects the arrhythmic phenotype, confirming that lowering mutant CALM2 dosage is sufficient to restore function.\",\n      \"evidence\": \"iPSC-cardiomyocytes with D130G, voltage-dye APD90 measurement, and dual-component shRNA suppression-and-replacement construct\",\n      \"pmids\": [\"39069900\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Durability and in vivo efficacy of the SupRep approach untested\", \"Off-target effects of CALM2 knockdown not assessed\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Quantified CALM2's relative contribution to the ventricular calmodulin pool, providing a dosage rationale for its intermediate variant severity.\",\n      \"evidence\": \"Ribosome profiling and RNA-seq of left ventricle, gnomAD constraint analysis, and Calmodulinopathy Registry outcomes\",\n      \"pmids\": [\"41846582\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Correlative rather than manipulative\", \"Does not establish whether expression ratios shift under pathological remodeling\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CALM2's identical protein product achieves gene-specific functional consequences, and whether its non-cardiac signaling roles share a common Ca2+-sensing mechanism, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of mutant calmodulin bound to CaV1.2 in the corpus\", \"Mechanism distinguishing CALM2 from CALM1/CALM3 beyond expression dosage unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-397014\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"CACNA1C\", \"SCN5A\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}