Alternative titles; symbols
HGNC Approved Gene Symbol: CACNA2D1
Cytogenetic location: 7q21.11 Genomic coordinates (GRCh38): 7:81,946,444-82,443,956 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 7q21.11 | Developmental and epileptic encephalopathy 110 | 620149 | Autosomal recessive | 3 |
The CACNA2D1 gene encodes the alpha-2/delta subunit of skeletal muscle and brain voltage-dependent calcium channels, which are heteromultimer complexes comprising 4 subunits: alpha-1 (see, e.g., CACNA1A; 601011), alpha-2/delta, beta-1 (CACNB1; 114207), and gamma (CACNG1; 114209) (Powers et al., 1994). CACNA2D1 alters the properties of pore-forming alpha-1 subunits of voltage-gated calcium channels, and it is posttranslationally processed into 2 peptides, an alpha-2 subunit and a delta subunit, that are held together by a disulfide bond. The alpha-2/delta protein is encoded by at least 4 different genes: CACNA2D1, CACNA2D2 (607082), CACNA2D3 (606399), and CACNA2D4 (608171) (Schleithoff et al., 1999; Field et al., 2006).
Williams et al. (1992) isolated a clone corresponding to a human voltage-dependent calcium channel alpha-2 subunit from human basal ganglia and human brainstem cDNA libraries. The deduced 1,091-amino acid protein has a calculated molecular mass of 123 kD. Various transcripts were identified in the brain, skeletal muscle, and aortic tissue.
Iles et al. (1994) cloned and partially sequenced the CACNL2A gene. The CACNL2A is expressed in many tissues, including skeletal muscle, brain, heart, and lung. A comparison of sequences of cDNAs representing the skeletal muscle and brain isoforms showed that they are encoded by a single gene.
Schleithoff et al. (1999) isolated overlapping cDNAs corresponding to the CACNA2D1 gene from a human phage library. The 'delta' portion, encoded by exons 37 to 40, is posttranscriptionally cleaved from the C-terminal 'alpha' portion of the protein. The membrane-spanning region of the delta portion is encoded by exon 40. Cotransfection of the full cDNA clone with alpha-1a and beta-4 (601949) subunits enhanced Q-type calcium currents 18-fold. The CACNA2D1 gene undergoes alternative splicing at exons 19 and 24, corresponding to muscle and brain isoforms, respectively.
Schleithoff et al. (1999) determined that the CACNA2D1 gene spans over 150 kb and contains 40 exons.
By PCR assay of Chinese hamster/human somatic cell hybrid DNAs, Powers et al. (1994) assigned the CACNL2A gene to chromosome 7. They refined the localization to 7q21-q22 by analysis of a panel of human/rodent somatic cell hybrids containing defined regions of human chromosome 7.
Iles et al. (1994) found that the CACNL2A gene and a neighboring polymorphic dinucleotide repeat marker, D7S849, were linked to the hepatocyte growth factor gene (HGF; 142409). Using a human chromosome 7-specific YAC library, they found that HGF was within approximately 110 to 380 kb of CACNL2A. They also mapped CACNL2A to 7q11.23-q21.1 by fluorescence in situ hybridization, the same location where D7S849 had been placed by analysis of human/hamster somatic cell hybrids.
By studies in Xenopus oocytes, Williams et al. (1992) found that the alpha-2 subunit enhanced activity of a dihydropyrimidine (DHP)-sensitive, high voltage-activated, long-lasting calcium channel when coexpressed with an alpha-1D (CACNA1D; 114206) and beta-2 (CACNB2; 600003) subunits. The results suggested that the alpha-2 subunit plays an accessory role.
Self-biting and other self-injurious behaviors occur in a number of By expression studies in Xenopus oocytes, Yamaguchi et al. (2000) showed that the beta-2a (CACNB2) and alpha-2/delta subunits cooperatively increased membrane expression of the alpha-1c subunit, whereas their effects on voltage-dependence of the channel complex were additive. Furthermore, the beta-2a subunit, but not the alpha-2/delta subunit, enhanced channel opening.
Marais et al. (2001) found that the alpha-2/delta subunit binds the antiepileptic drug gabapentin.
Hoppa et al. (2012) showed that a trafficking step probably sets synaptic voltage-gated calcium channel (VGCC) levels in rats, because overexpression of the pore-forming alpha-1A VGCC subunit (CACNA1A; 601011) fails to change synaptic VGCC abundance or function. Alpha-2-deltas are a family of glycosylphosphatidylinositol (GPI)-anchored VGCC-associated subunits that, in addition to being the target of the potent neuropathic analgesics gabapentin and pregabalin (alpha-2-delta-1 (CACNA2D1) and alpha-2-delta-2 (CACNA2D2)), were also identified in a forward genetic screen for pain genes (alpha-2-delta-3 (CACNA2D3)). Hoppa et al. (2012) showed that these proteins confer powerful modulation of presynaptic function through 2 distinct molecular mechanisms. First, alpha-2-delta subunits set synaptic VGCC abundance, as predicted from their chaperone-like function when expressed in nonneuronal cells. Second, alpha-2-deltas configure synaptic VGCCs to drive exocytosis through an extracellular metal ion-dependent adhesion site (MIDAS), a conserved set of amino acids within the predicted von Willebrand A domain of alpha-2-delta. Expression of alpha-2-delta with an intact MIDAS motif leads to an 80% increase in release probability, while simultaneously protecting exocytosis from blockade by an intracellular calcium chelator. Alpha-2-deltas harboring MIDAS site mutations still drive synaptic accumulation of VGCCs; however, they no longer change release probability or sensitivity to intracellular calcium chelators. Hoppa et al. (2012) concluded that their data revealed dual functionality of these clinically important VGCC subunits, allowing synapses to make more efficient use of calcium entry to drive neurotransmitter release.
Vergult et al. (2015) reported 3 unrelated girls with intellectual disability and epilepsy associated with a heterozygous genomic alteration that disrupted the CACNA2D1 gene. One female patient had a de novo apparently balanced reciprocal translocation 46,X,t(X;7)(p10;q21.2). There was 100% skewing of X-chromosome inactivation in favor of the abnormal chromosome. The second patient had a de novo 7.5-Mb deletion on 7q21.11-q21.12 including 14 genes, as well as a maternally inherited 150-kb deletion on chromosome 16q24.1. This patient also had obesity with hyperinsulinism, which may have been caused by deletion of the CD36 gene (173510). The third patient had a 2.72-Mb deletion on 7q21.11 containing 5 genes; the deletion was inherited from her mother who had mild intellectual disability and was illiterate. The smallest region of overlap in the 2 patients with deletions encompassed 5 genes, including CACNA2D1.
Developmental and Epileptic Encephalopathy 110
In 2 unrelated boys with developmental and epileptic encephalopathy-110 (DEE110; 620149), Dahimene et al. (2022) identified homozygous or compound heterozygous mutations in the CACNA2D1 gene (114204.0001-114204.0003). The mutations, which were found by trio-based exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in both families. Patient 1 was homozygous for a frameshift allele, and patient 2 was compound heterozygous for a frameshift and a missense allele. Studies of patient fibroblasts and in vitro functional studies of cells transfected with the missense variant (G209D; 114204.0003) indicated that the variants resulted in a loss-of-function effect on calcium channel function.
Associations Pending Confirmation
A close association is formed at the skeletal muscle triadic junctions between the ryanodine receptor (RYR1; 180901) and the L-type voltage-dependent calcium channel, also referred to as the dihydropyridine receptor (DHPR), and the 2 channel complexes appear to function together in excitation-contraction coupling (Iles et al., 1994). Because of the association with the ryanodine receptor, other subunits of the L-type voltage-dependent calcium channel have been considered as possible sites of a mutation causing malignant hyperthermia susceptibility (MHS). In 6 families with susceptibility to malignant hyperthermia (MHS3; 154276) that were not linked to the RYR1 locus on chromosome 19, Iles et al. (1994) found linkage to D7S849. No recombination was observed between MHS and D7S849 and 2 other markers through 11 meioses in 1 well-characterized 3-generation pedigree. In affected members of a family linked to the MHS3 locus by Iles et al. (1994), Schleithoff et al. (1999) did not identify any pathogenic mutations in the coding region of the CACNA2D1 gene.
Templin et al. (2011) reported a single patient, a 17-year-old Caucasian girl, with short QT syndrome, which they designated SQTS6, manifesting as ventricular fibrillation and QTc of 329 ms, with a missense variant (c.2264G-C, ser755 to thr, S755T) in CACNA2D1. Her father and paternal grandmother also carried the variant, but her father had borderline short QTc interval (362 ms) and the grandmother's QTc interval was normal. Neither had any symptoms. Expression studies comparing wildtype and variant CACNA2D1 with other L-type calcium channel subunits in HEK293 cells showed that the mutant protein was expressed at levels comparable to wildtype protein, but that barium ion currents were reduced by 70% when the mutant channel was introduced, compared with wildtype CACNA2D1. Hamosh (2023) reported that the S755T variant was present in 1% of Ashkenazi Jews in gnomad (109/10,324, MAF of 0.01056), present in homozygosity in 2 individuals, and reported as benign by 4 independent clinical laboratories in ClinVar; it was present in a total of 241 of 281,304 individuals in gnomAD for an overall MAF of 8.57 x 10(-4) (February 8, 2023).
In porcine brain, Wang et al. (1999) identified putative gabapentin-bindings sites within the alpha-2/delta subunit and showed that an arg217-to-ala (R217A) substitution within the Cacna2d1 gene disrupted gabapentin binding.
In a mutant mouse line with the Cacna2d1 R217A substitution, Field et al. (2006) found significantly decreased binding of the analgesic pregabalin in multiple brain areas, including cortex, hippocampus, caudate putamen, lumbar dorsal horn, and cerebellum compared to wildtype controls. Pregabalin had no effect against chemically induced tonic pain or nerve injury-induced chronic pain in the mutant mice, whereas wildtype mice showed dose-dependent analgesia.
In a 4-year-old boy (patient 1), born of consanguineous Afghan parents, with developmental and epileptic encephalopathy-110 (DEE110; 620149), Dahimene et al. (2022) identified a homozygous 4-bp duplication (c.818_821dupGAAC, NM_000722.3) in the CACNA2D1 gene, resulting in a frameshift and premature termination (Ser275AsnfsTer13). The mutation, which was found by trio-based exome sequencing and confirmed by Sanger sequencing, was present in each unaffected parent in the heterozygous state. It was not present in the gnomAD database. Patient fibroblasts showed reduced levels of CACNA2D1 mRNA (6 to 9% compared to controls) and decreased levels of the full-length protein (10 to 12% compared to controls). These findings were consistent with nonsense-mediated mRNA decay and a loss-of-function effect of the mutation.
In a 4-year-old boy (patient 2), born of unrelated parents, with developmental and epileptic encephalopathy-110 (DEE110; 620149), Dahimene et al. (2022) identified compound heterozygous mutations in the CACNA2D1 gene: an 11-bp duplication (c.13_23dupTGCCTGCTGGC, NM_000722.3), predicted to result in a frameshift and premature termination (Leu9AlafsTer5), and a c.626G-A transition in exon 7, resulting in a gly209-to-asp (G209D; 114204.0003) substitution at a highly conserved residue that is important for protein structure. The mutations, which were found by trio-based exome sequencing and confirmed by Sanger sequencing, showed parental segregation. The 11-bp duplication was present at a low frequency in the gnomAD database (0.003%), whereas G209D was absent from gnomAD. Patient fibroblasts showed normal levels of CACNA2D1 mRNA, but mildly decreased amounts of the full-length protein (31 to 38% compared to controls), suggesting that the frameshift allele resulted in a loss of function. In vitro cellular studies showed that the G209D mutation disrupted plasma expression of the protein, as it was reduced by about 80% at the cell membrane compared to controls. The G209D variant abolished the ability of CACNA2D1 to promote calcium currents in cells transfected with the mutation. The mutation also disrupted trafficking of calcium channels into hippocampal neurites and reduced complex formation with Ca(V)2.2 (see CACNA1B, 601012). The G209D mutant protein remained largely in the uncleaved immature form, suggesting it is likely retained in the endoplasmic reticulum. These data indicated that G209D is a loss-of-function allele.
For discussion of the c.626G-A transition (c.626G-A, NM_000722.3) in exon 7 in the CACNA2D1 gene, resulting in gly209-to-asp (G209D) substitution, that was found in compound heterozygous state in a patient with developmental and epileptic encephalopathy-110 (DEE110; 620149) by Dahimene et al. (2022), see 114204.0002.
Dahimene, S., von Elsner, L., Holling, T., Mattas, L. S., Pickard, J., Lessel, D., Pilch, K. S., Kadurin, I., Pratt, W. S., Zhulin, I. B., Dai, H., Hempel, M., Ruzhnikov, M. R. Z., Kutsche, K., Dolphin, A. C. Biallelic CACNA2D1 loss-of-function variants cause early-onset developmental epileptic encephalopathy. Brain 145: 2721-2729, 2022. [PubMed: 35293990] [Full Text: https://doi.org/10.1093/brain/awac081]
Field, M. J., Cox, P. J., Stott, E., Melrose, H., Offord, J., Su, T.-Z., Bramwell, S., Corradini, L., England, S., Winks, J., Kinloch, R. A., Hendrich, J., Dolphin, A. C., Webb, T., Williams, D. Identification of the alpha-2-delta-1 subunit of voltage-dependent calcium channels as a molecular target for pain mediating the analgesic actions of pregabalin. Proc. Nat. Acad. Sci. 103: 17537-17542, 2006. [PubMed: 17088553] [Full Text: https://doi.org/10.1073/pnas.0409066103]
Hamosh, A. Personal Communication. Baltimore, Md. 02/08/2023.
Hoppa, M. B., Lana, B., Margas, W., Dolphin, A. C., Ryan, T. A. Alpha-2-delta expression sets presynaptic calcium channel abundance and release probability. Nature 486: 122-125, 2012. [PubMed: 22678293] [Full Text: https://doi.org/10.1038/nature11033]
Iles, D. E., Lehmann-Horn, F., Scherer, S. W., Tsui, L.-C., Olde Weghuis, D., Suijkerbuijk, R. F., Heytens, L., Mikala, G., Schwartz, A., Ellis, F. R., Stewart, A. D., Deufel, T., Wieringa, B. Localization of the gene encoding the alpha-2/delta-subunits of the L-type voltage-dependent calcium channel to chromosome 7q and analysis of the segregation of flanking markers in malignant hyperthermia susceptible families. Hum. Molec. Genet. 3: 969-975, 1994. [PubMed: 7951247] [Full Text: https://doi.org/10.1093/hmg/3.6.969]
Marais, E., Klugbauer, N., Hofmann, F. Calcium channel alpha(2)delta subunits: structure and gabapentin binding. Molec. Pharm. 59: 1243-1248, 2001. [PubMed: 11306709] [Full Text: https://doi.org/10.1124/mol.59.5.1243]
Powers, P. A., Scherer, S. W., Tsui, L.-C., Gregg, R. G., Hogan, K. Localization of the gene encoding the alpha-2/delta subunit (CACNL2A) of the human skeletal muscle voltage-dependent Ca(2+) channel to chromosome 7q21-q22 by somatic cell hybrid analysis. Genomics 19: 192-193, 1994. [PubMed: 8188232] [Full Text: https://doi.org/10.1006/geno.1994.1044]
Schleithoff, L., Mehrke, G., Reutlinger, B., Lehmann-Horn, F. Genomic structure and functional expression of a human alpha-2/delta calcium channel subunit gene (CACNA2). Genomics 61: 201-209, 1999. [PubMed: 10534405] [Full Text: https://doi.org/10.1006/geno.1999.5941]
Templin, C., Ghadri, J. R., Rougier, J. S., Baumer, A., Kaplan, V., Albesa, M., Sticht, H., Rauch, A., Puleo, C., Hu, D., Barajas-Martinez, H., Antzelevitch, C., Luscher, T. F., Abriel, H., Duru, F. Identification of a novel loss-of-function calcium channel gene mutation in short QT syndrome (SQTS6). Europ. Heart J. 32: 1077-1088, 2011. [PubMed: 21383000] [Full Text: https://doi.org/10.1093/eurheartj/ehr076]
Vergult, S., Dheedene, A., Meurs, A., Faes, F., Isidor, B., Janssens, S., Gautier, A., Le Caignec, C., Menten, B. Genomic aberrations of the CACNA2D1 gene in three patients with epilepsy and intellectual disability. Europ. J. Hum. Genet. 23: 628-632, 2015. [PubMed: 25074461] [Full Text: https://doi.org/10.1038/ejhg.2014.141]
Wang, M., Offord, J., Oxender, D. L., Su, T.-Z. Structural requirement of the calcium-channel subunit alpha-2-delta for gabapentin binding. Biochem. J. 342: 313-320, 1999. [PubMed: 10455017]
Williams, M. E., Feldman, D. H., McCue, A. F., Brenner, R., Velicelebi, G., Ellis, S. B., Harpold, M. M. Structure and functional expression of alpha-1, alpha-2, and beta subunits of a novel human neuronal calcium channel subtype. Neuron 8: 71-84, 1992. [PubMed: 1309651] [Full Text: https://doi.org/10.1016/0896-6273(92)90109-q]
Yamaguchi, H., Okuda, M., Mikala, G., Fukasawa, K., Varadi, G. Cloning of the beta-2a subunit of the voltage-dependent calcium channel from human heart: cooperative effect of alpha-2/delta and beta-2a on the membrane expression of the alpha-1c subunit. Biochem. Biophys. Res. Commun. 267: 156-163, 2000. [PubMed: 10623591] [Full Text: https://doi.org/10.1006/bbrc.1999.1926]