Alternative titles; symbols
HGNC Approved Gene Symbol: CALM3
Cytogenetic location: 19q13.32 Genomic coordinates (GRCh38) : 19:46,601,074-46,610,782 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 19q13.32 | ?Ventricular tachycardia, catecholaminergic polymorphic 6 | 618782 | Autosomal dominant | 3 |
| Long QT syndrome 16 | 618782 | Autosomal dominant | 3 |
Calmodulin (CaM) is an essential calcium-binding protein with multiple cellular targets. Humans have 3 CaM genes, CALM1 (114180), CALM2 (114182), and CALM3, all encoding an identical protein with 4 EF-hand calcium-binding motifs (summary by Gomez-Hurtado et al., 2016).
Fischer et al. (1988) cloned CALM3 from human brain and teratoma cDNA libraries. CALM3 is identical in amino acid sequence to CALM1 (114180) and CALM2 (114182), but within the coding regions, CALM3 shares only 82% and 81% nucleotide identity with CALM1 and CALM2, respectively. The untranslated regions contain no significant homologies. Using an N-terminal sequence to probe a Northern blot, Fischer et al. (1988) detected 0.8- and 2.3-kb transcripts in fibroblast, erythroleukemia, and teratoma cell lines. Only the 2.3-kb transcript was revealed with a C-terminal probe, suggesting use of an alternate polyadenylation signal.
Toutenhoofd et al. (1998) measured the mRNA abundance and transcriptional activity of the 3 CALM genes in proliferating human teratoma cells. All 5 possible mRNA transcripts were detected in these cells, with highest abundance of CALM3. CALM3 was 5-fold more actively transcribed than CALM1 and CALM2.
Fischer et al. (1988) determined that the CALM3 gene contains 6 exons.
Koller and Strehler (1993) determined that the 5-prime flanking region of CALM3 is GC rich and contains a canonical CAAT box but no TATA box. There are several clustered SP1 (189906)-binding sites and 7 AGGA elements, which are found in genes encoding Ca(2+)-binding proteins. Using a promoter-reporter construct transfected into several cell lines, Koller and Strehler (1993) found that CALM3 promoter activity was neither cell type nor species specific.
McPherson et al. (1991) assigned the CALM3 gene to chromosome 19 by study of somatic cell hybrids. By PCR-based amplification of CALM3-specific sequences using DNA from human/hamster cell hybrids as template, Berchtold et al. (1993) confirmed the assignment to chromosome 19 and regionalized the gene to chromosome 19q13.2-q13.3 by in situ hybridization.
Long QT Syndrome 16
In a 6-month-old boy with severe long QT syndrome (LQT16; 618782), Reed et al. (2015) identified heterozygosity for a de novo missense mutation in the CALM3 gene (D130G; 114183.0001).
In a Spanish girl who died at age 5 years with LQTS, negative for mutation in 8 LQTS-associated genes, Wren et al. (2019) analyzed the 3 calmodulin genes and identified a heterozygous missense mutation in the CALM3 gene (E141K; 114183.0003). The mutation was not found in her asymptomatic father or in the gnomAD database; however, the asymptomatic mother carried the mutation in approximately 25% of sequencing reads, consistent with somatic mosaicism and presumed germline mosaicism, due to transmission of the variant. The same E141K variant was identified in heterozygosity in a Saudi Arabian boy with LQTS, who was alive at 21 months of age. In another family with LQTS in which 5 of 6 sibs died suddenly in early childhood, exon sequencing revealed heterozygosity for the D130G mutation in CALM3 in the 2 affected sibs for whom DNA was available. Exome sequencing did not detect the mutation in either unaffected parent or an unaffected sister; however, single-molecule molecular inversion probes revealed the c.389A-G variant (D130G) in 6% of captured molecules in the father's DNA, consistent with somatic mosaicism.
Catecholaminergic Polymorphic Ventricular Tachycardia-6
In a cohort of 12 patients with clinically diagnosed CPVT who were negative for mutation in known CPVT-associated genes, Gomez-Hurtado et al. (2016) identified a 31-year-old woman (CPVT6; see 618782) who was heterozygous for a missense mutation in the CALM3 gene (A103V; 114183.0002).
Reviews
Crotti et al. (2019) reviewed 74 patients, from both the International Calmodulinopathy Registry and the published literature, who had mutations in the CALM1, CALM2, or CALM3 genes (36, 23, and 15 patients, respectively). The 2 prevalent phenotypes were LQTS (49%) and CPVT (28%). The majority of variants (80%) affected amino acid residues on the EF-hand Ca(2+)-binding loops III and IV, and almost 90% of them affected 1 of the 4 residues principally involved in Ca(2+) binding (Asp, Asp, Asp/Asn, and Glu, at positions 1, 3, 5, and 12, respectively, from the beginning of each 12-residue loop). Three residues appeared to be relative hotspots, with N98S, D130G, and F142L identified in 10, 5, and 4 families, respectively. The authors noted that LQTS-associated calmodulin variants, located primarily in EF hands III and IV, show a strong dominant-negative reduction in Ca(2+)-dependent inactivation of the L-type Ca(2+) channel Ca(v)1.2 (CACNA1C; 114205), which results in repolarization delay However, the major effect of CPVT-associated variants, mostly located in either EF hand III or in the inter-EF hand I-II linker, appears to be a higher binding affinity for RyR2 (180902), promoting its open conformation and increasing the frequency of Ca(2+) waves. The authors added that no gene-specific phenotypic correlations could be made since mutations in all 3 calmodulin genes may give rise to different phenotypes.
In a 6-month-old boy with severe long QT syndrome (LQT16; 618782), Reed et al. (2015) identified heterozygosity for a de novo c.389A-G transition in the CALM3 gene, resulting in an asp130-to-gly (D130G) substitution. The mutation was not found in his unaffected parents.
In a deceased sister and brother (family D) with LQT syndrome, Wren et al. (2019) identified heterozygosity for the D130G mutation in CALM3. In the family, 3 additional sibs had died suddenly in childhood, but their DNA was unavailable for study. Exome sequencing did not detect the mutation in either unaffected parent or an unaffected sister; however, single-molecule molecular inversion probes revealed the c.389A-G variant in 6% of captured molecules in the father's DNA, consistent with somatic mosaicism.
In a 31-year-old woman diagnosed with catecholaminergic polymorphic ventricular tachycardia (CPVT6; see 618782), Gomez-Hurtado et al. (2016) identified heterozygosity for an ala103-to-val (A103V) substitution in CALM3. Her mother, who had a history of fainting episodes in her youth and showed exercise-induced PVCs on stress testing, was also heterozygous for the A103V mutation, which was not found in her unaffected father. Ca(2+) titration curves showed a 3-fold reduction in Ca(2+)-binding affinity in the C domain with the A103V mutant compared to wildtype calmodulin. Permeabilized mouse ventricular myocytes showed significantly increased spark frequency and reduced sarcoplasmic reticulum Ca(2+) content with the mutant compared to wildtype calmodulin. The cardiomyocytes also showed increased spontaneous Ca(2+) release in the form of regular propagated Ca(2+) waves, and with increased amplitude of the Ca(2+) waves, with the mutant compared to wildtype calmodulin. The mutant demonstrated a dominant effect, with significantly higher Ca(2+) wave frequencies even in the presence of 3-fold excess of wildtype calmodulin. The spontaneous Ca(2+) releases induced by the A103V mutation generated delayed afterdepolarizations that triggered spontaneous action potentials, which the authors noted was consistent with the clinical phenotype of CPVT.
In a Spanish girl (family A) who died at age 5 years with LQTS (LQTS16; 618782), Wren et al. (2019) identified heterozygosity for a c.421G-A transition in the CALM3 gene, resulting in a glu141-to-lys (E141K) substitution at a strictly conserved residue within the fourth Ca(2+)-binding EF-hand motif of the calmodulin C domain. The mutation was not found in her asymptomatic father or in the gnomAD database; however, the asymptomatic mother, who had normal basal and exercise electrocardiograms, carried the mutation in approximately 25% of sequencing reads, consistent with somatic mosaicism and presumed germline mosaicism. The same E141K variant was identified in a Saudi Arabian boy with LQTS (family B), who was alive at 21 months of age. The variant was not found in either parent, consistent with a de novo mutation; his unaffected twin sister also did not carry the mutation. Fluorescence assay revealed diminished amplitude of fluorescence change with the E141K mutant compared to wildtype calmodulin, suggesting that the mutated C domain binds Ca(2+) ions weakly; this was confirmed by 2-dimensional 15N-1H NMR spectra. Studies in transfected human induced pluripotent stem cell-derived cardiomyocytes demonstrated that channel inactivation was slower and less complete for E141K-expressing cells, with significant differences in peak and late Ca(2+) currents compared to control cells. Ca(2+)-dependent inactivation was blunted substantially in cells transfected with the E141K mutant, with significantly larger inactivation time constants and longer action potential duration than cells expressing wildtype calmodulin, consistent with a cellular arrhythmogenic substrate underlying clinical LQTS.
Berchtold, M. W., Egli, R., Rhyner, J. A., Hameister, H., Strehler, E. E. 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. Genomics 16: 461-465, 1993. [PubMed: 8314583] [Full Text: https://doi.org/10.1006/geno.1993.1211]
Crotti, L., Spazzolini, C., Tester, D. J., Ghidoni, A., Baruteau, A.-E., Beckmann, B.-M., Behr, E. R., Bennet, J. S., Bezzina, C. R., Bhuiyan, Z. A., Celiker, A., Cerrone, M., and 29 others. Calmodulin mutations and life-threatening cardiac arrhythmias: insights from the International Calmodulinopathy Registry. Europ. Heart J. 40: 2964-2975, 2019. [PubMed: 31170290] [Full Text: https://doi.org/10.1093/eurheartj/ehz311]
Fischer, R., Koller, M., Flura, M., Mathews, S., Strehler-Page, M.-A., Krebs, J., Penniston, J. T., Carafoli, E., Strehler, E. E. Multiple divergent mRNAs code for a single human calmodulin. J. Biol. Chem. 263: 17055-17062, 1988. [PubMed: 3182832]
Gomez-Hurtado, N., Boczek, N. J., Kryshtal, D. O., Johnson, C. N., Sun, J., Nitu, F. R., Cornea, R. L., Chazin, W. J., Calvert, M. L., Tester, D. J., Ackerman, M. J., Knollmann, B. C. Novel CPVT-associated calmodulin mutation in CALM3 (CALM3-A103V) activates arrhythmogenic Ca waves and sparks. Circ. Arrhythm. Electrophysiol. 9: e004161, 2016. Note: Electronic Article. [PubMed: 27516456] [Full Text: https://doi.org/10.1161/CIRCEP.116.004161]
Koller, M., Strehler, E. E. Functional analysis of the promoters of the human CaMIII calmodulin gene and of the intronless gene coding for a calmodulin-like protein. Biochim. Biophys. Acta 1163: 1-9, 1993. [PubMed: 8476923] [Full Text: https://doi.org/10.1016/0167-4838(93)90271-r]
McPherson, J. D., Hickie, R. A., Wasmuth, J. J., Meyskens, F. L., Perham, R. N., Strehler, E. E., Graham, M. T. Chromosomal localization of multiple genes encoding calmodulin. (Abstract) Cytogenet. Cell Genet. 58: 1951 only, 1991.
Reed, G. J., Boczek, N. J., Etheridge, S. P., Ackerman, M. J. CALM3 mutation associated with long QT syndrome. Heart Rhythm 12: 419-422, 2015. [PubMed: 25460178] [Full Text: https://doi.org/10.1016/j.hrthm.2014.10.035]
Toutenhoofd, S. L., Foletti, D., Wicki, R., Rhyner, J. A., Garcia, F., Tolon, R., Strehler, E. E. Characterization of the human CALM2 calmodulin gene and comparison of the transcriptional activity of CALM1, CALM2, and CALM3. Cell Calcium 23: 323-338, 1998. [PubMed: 9681195] [Full Text: https://doi.org/10.1016/s0143-4160(98)90028-8]
Wren, L. M., Jimenez-Jaimez, J., Al-Ghamdi, S., Al-Aama, J. Y., Bdeir, pectra., Al-Hassnan, Z. N., Kuan, J. L., Foo, R. Y., Potet, F., Johnson, C. N., Aziz, M. C., Carvill, G. L., and 9 others. Genetic mosaicism in calmodulinopathy. Circ. Genom. Precis. Med. 12: e002581, 2019. Note: Electronic Article.