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CACNA2D3 calcium voltage-gated channel auxiliary subunit alpha2delta 3 [ Homo sapiens (human) ]

Gene ID: 55799, updated on 27-Nov-2024

Summary

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Official Symbol
CACNA2D3provided by HGNC
Official Full Name
calcium voltage-gated channel auxiliary subunit alpha2delta 3provided by HGNC
Primary source
HGNC:HGNC:15460
See related
Ensembl:ENSG00000157445 MIM:606399; AllianceGenome:HGNC:15460
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HSA272268
Summary
This gene encodes a member of the alpha-2/delta subunit family, a protein in the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization and consist of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. Various versions of each of these subunits exist, either expressed from similar genes or the result of alternative splicing. Research on a highly similar protein in rabbit suggests the protein described in this record is cleaved into alpha-2 and delta subunits. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized. [provided by RefSeq, Jul 2008]
Expression
Broad expression in brain (RPKM 3.0), adrenal (RPKM 1.8) and 16 other tissues See more
Orthologs
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Genomic context

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See CACNA2D3 in Genome Data Viewer
Location:
3p21.1-p14.3
Exon count:
38
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (54122552..55074557)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (54156427..55108831)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (54156579..55108584)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377095 Neighboring gene uncharacterized LOC124909381 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:54121379-54121902 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:54121903-54122425 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14470 Neighboring gene calcium binding tyrosine phosphorylation regulated pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 13251 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54237261-54237762 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:54246728-54247322 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54250734-54251234 Neighboring gene NANOG hESC enhancer GRCh37_chr3:54262808-54263341 Neighboring gene uncharacterized LOC124909382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54319420-54319921 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54497979-54498480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54498481-54498980 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:54520692-54520885 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54551370-54551870 Neighboring gene uncharacterized LOC107986088 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:54668358-54668860 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:54668861-54669361 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:54673489-54674415 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:54743647-54744366 Neighboring gene ribosomal protein S15 pseudogene 5 Neighboring gene embryonic stem cell related Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:54855004-54855707 Neighboring gene NANOG hESC enhancer GRCh37_chr3:54877384-54877885 Neighboring gene CACNA2D3 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54973116-54973616 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:54986884-54987876 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:54987877-54988869 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:54989863-54990854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:54992683-54993184 Neighboring gene VISTA enhancer hs1436 Neighboring gene leucine rich repeats and transmembrane domains 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:55096424-55097039 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:55113410-55113654 Neighboring gene uncharacterized LOC124906243 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:55183044-55183208 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:55194201-55195400 Neighboring gene long intergenic non-protein coding RNA 2017 Neighboring gene long intergenic non-protein coding RNA 2030

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A two-stage genome-wide association study identifies novel germline genetic variations in CACNA2D3 associated with radiotherapy response in nasopharyngeal carcinoma. Yu LL, et al. J Transl Med, 2023 Jan 9. PMID 36624463, Free PMC Article
  2. Cloning a calcium channel alpha2delta-3 subunit gene from a putative tumor suppressor gene region at chromosome 3p21.1 in conventional renal cell carcinoma. Hanke S, et al. Gene, 2001 Feb 7. PMID 11245980
  3. Methylation of the calcium channel-related gene, CACNA2D3, is frequent and a poor prognostic factor in gastric cancer. Wanajo A, et al. Gastroenterology, 2008 Aug. PMID 18588891
  4. Methylation of the calcium channel regulatory subunit α2δ-3 (CACNA2D3) predicts site-specific relapse in oestrogen receptor-positive primary breast carcinomas. Palmieri C, et al. Br J Cancer, 2012 Jul 10. PMID 22644305, Free PMC Article
  5. Identification of a novel quantitative trait nucleotype related to iron status in a calcium channel gene. Baeza-Richer C, et al. Dis Markers, 2013. PMID 23324578, Free PMC Article

See all (32) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Remote ischemic preconditioning reduces mitochondrial apoptosis mediated by calpain 1 activation in myocardial ischemia-reperfusion injury through calcium channel subunit Cacna2d3.
    Title: Remote ischemic preconditioning reduces mitochondrial apoptosis mediated by calpain 1 activation in myocardial ischemia-reperfusion injury through calcium channel subunit Cacna2d3.
  2. A two-stage genome-wide association study identifies novel germline genetic variations in CACNA2D3 associated with radiotherapy response in nasopharyngeal carcinoma.
    Title: A two-stage genome-wide association study identifies novel germline genetic variations in CACNA2D3 associated with radiotherapy response in nasopharyngeal carcinoma.
  3. CNS sensitisation was associated with a common genetic variant near the calcium channel gene CACNA2D3 at genome-wide significance.
    Title: Genes, biomarkers, and clinical features associated with the course of bipolar disorder.
  4. The authors show that ventricular alpha2delta3 expression is low in healthy mice and humans, but significantly elevated in ventricular muscles from DM1 patients with conduction defects.
    Title: Straightjacket/α2δ3 deregulation is associated with cardiac conduction defects in myotonic dystrophy type 1.
  5. Nine of the 32 (28.1%) iCCA patients had gene mutations at chromosome 3p, totaling 11 mutations across five genes. Those included five (15.6%) BAP1 mutations, two each (6.3%) of CACNA2D3 and RASSF1 mutations, and one each (3.1%) of ATG7 and PLCD1 mutations. Six (18.8%) cases had concurrent loss of chromosome 3p and gene mutations.
    Title: Mutations of candidate tumor suppressor genes at chromosome 3p in intrahepatic cholangiocarcinoma.
  6. Findings demonstrate the tumor suppressive role of CACNA2D3 in gliomas. CACNA2D3 operates via Ca 2thorn signaling and the activation of non-canonical Wnt signaling to inhibit cell proliferation and motility and induce apoptosis.
    Title: CACNA2D3 is downregulated in gliomas and functions as a tumor suppressor.
  7. The risk of developing anaemia is increased in reproductive age women carriers of A allele of rs1868505 (CACNA2D3) and/or T allele of rs13194491 (HIST1H2BJ).
    Title: Genetic contribution to iron status: SNPs related to iron deficiency anaemia and fine mapping of CACNA2D3 calcium channel subunit.
  8. CACNA2D3-mediated increase in intracellular calcium (Ca2+) can induce mitochondrial-mediated apoptosis.
    Title: Characterization of CACNA2D3 as a putative tumor suppressor gene in the development and progression of nasopharyngeal carcinoma.
  9. CACNA2D3 is a novel tumor suppressor gene responsible for the 3p21 deletion event that plays a critical suppressing role in the development and progression of esophageal squamous cell carcinoma.
    Title: Investigation of tumor suppressing function of CACNA2D3 in esophageal squamous cell carcinoma.
  10. CACNA2D3 polymorphism rs1375515 plays important role in iron status and is associated with the levels of iron-related biomarkers, as well as with iron clinical phenotypes (normal, iron de fi cient and anaemic).
    Title: Identification of a novel quantitative trait nucleotype related to iron status in a calcium channel gene.
Submit: New GeneRIF Correction See all GeneRIFs (19)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
EBI GWAS Catalog
Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants.
EBI GWAS Catalog
Genetics of coronary artery calcification among African Americans, a meta-analysis.
EBI GWAS Catalog
Genome-wide association study in musician's dystonia: a risk variant at the arylsulfatase G locus?
EBI GWAS Catalog
Genome-wide association study of antibody response to smallpox vaccine.
EBI GWAS Catalog
Genome-wide association study of endometrial cancer in E2C2.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables voltage-gated calcium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in calcium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of presynapse organization IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in presynaptic active zone membrane IEA
Inferred from Electronic Annotation
more info
  
part_of voltage-gated calcium channel complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
voltage-dependent calcium channel subunit alpha-2/delta-3
Names
alpha2delta-3
calcium channel alpha2-delta3 subunit
calcium channel, voltage-dependent, alpha 2/delta 3 subunit
calcium channel, voltage-dependent, alpha 2/delta subunit 3
voltage-gated calcium channel subunit alpha-2/delta-3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_018398.3 → NP_060868.2  voltage-dependent calcium channel subunit alpha-2/delta-3 precursor

    See identical proteins and their annotated locations for NP_060868.2

    Status: REVIEWED

    Source sequence(s)
    AC092057, AC092797, AC104298, AC109584, AC115282, AC133010, AC137673, AC138059
    Consensus CDS
    CCDS54598.1
    UniProtKB/Swiss-Prot
    B2RPL6, Q8IZS8, Q9NY16, Q9NY18
    Related
    ENSP00000419101.1, ENST00000474759.6
    Conserved Domains (5) summary
    cd01463
    Location:242 → 425
    vWA_VGCC_like; VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta. The alpha 2 and delta subunits result from proteolytic processing of a single gene product and carries at ...
    cd12912
    Location:508 → 622
    PDC2_MCP_like; second PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins and similar domains
    pfam08399
    Location:113 → 229
    VWA_N; VWA N-terminal
    pfam08473
    Location:655 → 1068
    VGCC_alpha2; Neuronal voltage-dependent calcium channel alpha 2acd
    pfam02743
    Location:442 → 552
    dCache_1; Cache domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    54122552..55074557
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    54156427..55108831
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IZS8.1 GenPept UniProtKB/Swiss-Prot:Q8IZS8

Gene LinkOut

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