Human Gene CACNA2D4 (ENST00000382722.10_7) from GENCODE V47lift37
  Description: calcium voltage-gated channel auxiliary subunit alpha2delta 4 (from RefSeq NM_172364.5)
Gencode Transcript: ENST00000382722.10_7
Gencode Gene: ENSG00000151062.15_18
Transcript (Including UTRs)
   Position: hg19 chr12:1,901,129-2,027,818 Size: 126,690 Total Exon Count: 38 Strand: -
Coding Region
   Position: hg19 chr12:1,902,821-2,027,639 Size: 124,819 Coding Exon Count: 38 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:1,901,129-2,027,818)mRNA (may differ from genome)Protein (1137 aa)
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-  Comments and Description Text from UniProtKB
  ID: CA2D4_HUMAN
DESCRIPTION: RecName: Full=Voltage-dependent calcium channel subunit alpha-2/delta-4; AltName: Full=Voltage-gated calcium channel subunit alpha-2/delta-4; Contains: RecName: Full=Voltage-dependent calcium channel subunit alpha-2-4; Contains: RecName: Full=Voltage-dependent calcium channel subunit delta-4; Flags: Precursor;
FUNCTION: The alpha-2/delta subunit of voltage-dependent calcium channels regulates calcium current density and activation/inactivation kinetics of the calcium channel.
SUBUNIT: Dimer formed of alpha-2-2 and delta-2 chains; disulfide- linked. Voltage-dependent calcium channels are multisubunit complexes, consisting of alpha-1 (CACNA1), alpha-2 (CACNA2D), beta (CACNB) and delta (CACNA2D) subunits in a 1:1:1:1 ratio (Probable). Interacts with CACNA1C and CACNB3.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (Potential).
TISSUE SPECIFICITY: Predominantly expressed in certain types of endocrine cells. Present in the Paneth cells of the small intestine. Also present in the erythroblasts in the fetal liver, in the cells of the zona reticularis of the adrenal gland and in the basophils of the pituitary. Present at low level in some brain regions such as the cerebellum (at protein level).
DOMAIN: The MIDAS-like motif in the VWFA domain binds divalent metal cations and is required to promote trafficking of the alpha- 1 (CACNA1) subunit to the plasma membrane by an integrin-like switch (By similarity).
PTM: May be proteolytically processed into subunits alpha-2-4 and delta-4 that are disulfide-linked. It is however unclear whether such cleavage really takes place in vivo and has a functional role (By similarity).
DISEASE: Defects in CACNA2D4 are the cause of retinal cone dystrophy 4 (RCD4) [MIM:610478]. RCD4 is characterized by minimal symptoms except for slowly progressive reduction in visual acuity.
MISCELLANEOUS: In contrast to CACNA2D1 and CACNA2D2, it does not bind gabapentin, an antiepileptic drug.
SIMILARITY: Belongs to the calcium channel subunit alpha-2/delta family.
SIMILARITY: Contains 1 cache domain.
SIMILARITY: Contains 1 VWFA domain.
SEQUENCE CAUTION: Sequence=AAH48288.1; Type=Erroneous translation; Note=Wrong choice of frame; Sequence=AAN06672.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CACNA2D4
Diseases sorted by gene-association score: retinal cone dystrophy 4* (1019), retinitis pigmentosa* (37), cone dystrophy 4 (13), cone dystrophy (10), congenital stationary night blindness* (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.35 RPKM in Testis
Total median expression: 33.21 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -82.70179-0.462 Picture PostScript Text
3' UTR -536.401692-0.317 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004010 - Cache_domain
IPR013608 - VWA_N
IPR002035 - VWF_A

Pfam Domains:
PF00092 - von Willebrand factor type A domain
PF08399 - VWA N-terminal
PF08473 - Neuronal voltage-dependent calcium channel alpha 2acd
PF13519 - von Willebrand factor type A domain
PF13768 - von Willebrand factor type A domain

SCOP Domains:
53300 - vWA-like
103107 - Hypothetical protein c14orf129, hspc210

ModBase Predicted Comparative 3D Structure on Q7Z3S7
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005244 voltage-gated ion channel activity
GO:0005245 voltage-gated calcium channel activity
GO:0005262 calcium channel activity
GO:0046872 metal ion binding

Biological Process:
GO:0006811 ion transport
GO:0006816 calcium ion transport
GO:0034765 regulation of ion transmembrane transport
GO:0050908 detection of light stimulus involved in visual perception
GO:0070588 calcium ion transmembrane transport

Cellular Component:
GO:0005886 plasma membrane
GO:0005891 voltage-gated calcium channel complex
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BX537436 - Homo sapiens mRNA; cDNA DKFZp686A1395 (from clone DKFZp686A1395).
BX537437 - Homo sapiens mRNA; cDNA DKFZp686O0495 (from clone DKFZp686O0495); complete cds.
BC150186 - Homo sapiens calcium channel, voltage-dependent, alpha 2/delta subunit 4, mRNA (cDNA clone MGC:164965 IMAGE:40148321), complete cds.
AF516695 - Homo sapiens voltage-gated calcium channel alpha(2)delta-4 subunit mRNA, complete cds.
EU832150 - Synthetic construct Homo sapiens clone HAIB:100067179; DKFZo008F0425 calcium channel, voltage-dependent, alpha 2/delta subunit 4 protein (CACNA2D4) gene, encodes complete protein.
EU832243 - Synthetic construct Homo sapiens clone HAIB:100067272; DKFZo004F0426 calcium channel, voltage-dependent, alpha 2/delta subunit 4 protein (CACNA2D4) gene, encodes complete protein.
AL137658 - Homo sapiens mRNA; cDNA DKFZp434I1216 (from clone DKFZp434I1216).
JD370361 - Sequence 351385 from Patent EP1572962.
JD521223 - Sequence 502247 from Patent EP1572962.
JD091018 - Sequence 72042 from Patent EP1572962.
JD312624 - Sequence 293648 from Patent EP1572962.
JD389274 - Sequence 370298 from Patent EP1572962.
JD124634 - Sequence 105658 from Patent EP1572962.
BC048288 - Homo sapiens calcium channel, voltage-dependent, alpha 2/delta subunit 4, mRNA (cDNA clone IMAGE:5211689), complete cds.
JD073486 - Sequence 54510 from Patent EP1572962.
JD423456 - Sequence 404480 from Patent EP1572962.
JD251707 - Sequence 232731 from Patent EP1572962.
JD234758 - Sequence 215782 from Patent EP1572962.
JD485934 - Sequence 466958 from Patent EP1572962.
AK301234 - Homo sapiens cDNA FLJ50030 complete cds, highly similar to Homo sapiens calcium channel, voltage-dependent, alpha 2/delta subunit 4, transcript variant 3, mRNA.
JD303913 - Sequence 284937 from Patent EP1572962.
JD550980 - Sequence 532004 from Patent EP1572962.
JD045733 - Sequence 26757 from Patent EP1572962.
JD240799 - Sequence 221823 from Patent EP1572962.
JD514703 - Sequence 495727 from Patent EP1572962.
JD264468 - Sequence 245492 from Patent EP1572962.
JD274182 - Sequence 255206 from Patent EP1572962.
JD171928 - Sequence 152952 from Patent EP1572962.
JD208847 - Sequence 189871 from Patent EP1572962.
JD059909 - Sequence 40933 from Patent EP1572962.
JD267559 - Sequence 248583 from Patent EP1572962.
JD193609 - Sequence 174633 from Patent EP1572962.
JD364258 - Sequence 345282 from Patent EP1572962.
JD451421 - Sequence 432445 from Patent EP1572962.
JD387623 - Sequence 368647 from Patent EP1572962.
KJ903604 - Synthetic construct Homo sapiens clone ccsbBroadEn_12998 CACNA2D4 gene, encodes complete protein.
JD121561 - Sequence 102585 from Patent EP1572962.
JD151369 - Sequence 132393 from Patent EP1572962.
JD419363 - Sequence 400387 from Patent EP1572962.
JD196328 - Sequence 177352 from Patent EP1572962.
JD044990 - Sequence 26014 from Patent EP1572962.
JD445205 - Sequence 426229 from Patent EP1572962.
JD252947 - Sequence 233971 from Patent EP1572962.
JD326112 - Sequence 307136 from Patent EP1572962.
JD525667 - Sequence 506691 from Patent EP1572962.
JD105197 - Sequence 86221 from Patent EP1572962.
JD269376 - Sequence 250400 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q7Z3S7 (Reactome details) participates in the following event(s):

R-HSA-5577213 LTCC heteropentamer (open) transports Ca2+ from extracellular region to cytosol
R-HSA-5576892 Phase 0 - rapid depolarisation
R-HSA-5576893 Phase 2 - plateau phase
R-HSA-5576891 Cardiac conduction
R-HSA-397014 Muscle contraction

-  Other Names for This Gene
  Alternate Gene Symbols: CA2D4_HUMAN, ENST00000382722.1, ENST00000382722.2, ENST00000382722.3, ENST00000382722.4, ENST00000382722.5, ENST00000382722.6, ENST00000382722.7, ENST00000382722.8, ENST00000382722.9, NM_172364, Q7Z3S7, Q7Z3S8, Q86XZ5, Q8IZS9, uc318qyw.1, uc318qyw.2
UCSC ID: ENST00000382722.10_7
RefSeq Accession: NM_172364.5
Protein: Q7Z3S7 (aka CA2D4_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.