Human Gene CACNA1A (ENST00000637736.1) Description and Page Index
  Description: calcium voltage-gated channel subunit alpha1 A (from HGNC CACNA1A)
RefSeq Summary (NM_001127221): Voltage-dependent calcium channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, and gene expression. Calcium channels are multisubunit complexes composed of alpha-1, beta, alpha-2/delta, and gamma subunits. The channel activity is directed by the pore-forming alpha-1 subunit, whereas, the others act as auxiliary subunits regulating this activity. The distinctive properties of the calcium channel types are related primarily to the expression of a variety of alpha-1 isoforms, alpha-1A, B, C, D, E, and S. This gene encodes the alpha-1A subunit, which is predominantly expressed in neuronal tissue. Mutations in this gene are associated with 2 neurologic disorders, familial hemiplegic migraine and episodic ataxia 2. This gene also exhibits polymorphic variation due to (CAG)n-repeats. Multiple transcript variants encoding different isoforms have been found for this gene. In one set of transcript variants, the (CAG)n-repeats occur in the 3' UTR, and are not associated with any disease. But in another set of variants, an insertion extends the coding region to include the (CAG)n-repeats which encode a polyglutamine tract. Expansion of the (CAG)n-repeats from the normal 4-18 to 21-33 in the coding region is associated with spinocerebellar ataxia 6. [provided by RefSeq, Jul 2016].
Gencode Transcript: ENST00000637736.1
Gencode Gene: ENSG00000141837.20
Transcript (Including UTRs)
   Position: hg38 chr19:13,206,591-13,506,459 Size: 299,869 Total Exon Count: 46 Strand: -
Coding Region
   Position: hg38 chr19:13,207,313-13,506,224 Size: 298,912 Coding Exon Count: 46 

Page IndexSequence and LinksMalaCardsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureOther SpeciesmRNA DescriptionsPathwaysOther NamesGeneReviews
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr19:13,206,591-13,506,459)mRNA (may differ from genome)Protein (2460 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
MGImyGene2PubMedStanford SOURCEUniProtKBWikipedia

-  MalaCards Disease Associations
  MalaCards Gene Search: CACNA1A
Diseases sorted by gene-association score: spinocerebellar ataxia 6* (1723), episodic ataxia, type 2* (1692), migraine, familial hemiplegic, 1* (1331), epileptic encephalopathy, early infantile, 42* (1230), sporadic hemiplegic migraine* (419), benign paroxysmal torticollis of infancy* (369), cerebellar ataxia* (311), familial or sporadic hemiplegic migraine* (202), ataxia-oculomotor apraxia 3* (200), undetermined early-onset epileptic encephalopathy* (101), autosomal dominant cerebellar ataxia (49), episodic ataxia (44), hemiplegic migraine (42), familial hemiplegic migraine (37), alternating hemiplegia of childhood* (28), cerebellar disease (27), migraine with aura (22), headache (20), episodic ataxia/myokymia syndrome (19), migraine with or without aura 1 (19), spinocerebellar ataxia 12 (17), machado-joseph disease (15), cluster headache (15), friedreich ataxia (14), cerebellar degeneration (13), hemiplegia (13), dentatorubro-pallidoluysian atrophy (12), benign paroxysmal positional nystagmus (11), vestibulocochlear nerve disease (11), vestibular neuronitis (11), spinocerebellar ataxia 1 (10), spinocerebellar ataxia 26 (9), episodic ataxia, type 7 (9), spinocerebellar ataxia type 19/22 (9), spinocerebellar ataxia 17 (9), episodic ataxia, type 6 (9), ataxia (8), paraneoplastic cerebellar degeneration (8), spinocerebellar ataxia 27 (7), hereditary ataxia (7), exfoliation syndrome (7), spinocerebellar ataxia 31 (7), lambert-eaton myasthenic syndrome (7), marshall-smith syndrome (5), childhood absence epilepsy (5), spinocerebellar ataxia 18 (5), meninges hemangiopericytoma (5), spinocerebellar ataxia 2 (5), epileptic encephalopathy, childhood-onset (5), idiopathic generalized epilepsy (3), diarrhea (3), congenital myasthenic syndrome (1), nervous system disease (1), central nervous system disease (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 130.80 RPKM in Brain - Cerebellum
Total median expression: 344.90 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 -117.30235-0.499 Picture PostScript Text
3' UTR -217.10722-0.301 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.

-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Descriptions from all associated GenBank mRNAs
  LF384412 - JP 2014500723-A/191915: Polycomb-Associated Non-Coding RNAs.
MA619989 - JP 2018138019-A/191915: Polycomb-Associated Non-Coding RNAs.
U79668 - Human alpha1A-voltage-dependent calcium channel mRNA, splice form BI-1-V2,V3, partial cds.
AF100774 - Homo sapiens voltage-dependent P/Q type calcium channel alpha 1A subunit (CACNA1A) mRNA, partial cds.
AF004883 - Homo sapiens neuronal calcium channel alpha 1A subunit isoform 1A-2 mRNA, complete cds.
AF004884 - Homo sapiens neuronal calcium channel alpha 1A subunit isoform A-1 mRNA, complete cds.
U79663 - Human alpha1A-voltage-dependent calcium channel mRNA, splice form BI-1, partial cds.
U79664 - Human alpha1A-voltage-dependent calcium channel mRNA, splice form BI-1 (V1), partial cds.
U79665 - Human alpha1A-voltage-sensitive calcium channel mRNA, splice form BI-1-GGCAG, partial cds.
U79667 - Human alpha1A-voltage-dependent calcium channel mRNA, splice form BI-1-V2-GGCAG, partial cds.
U79666 - Homo sapiens alpha1A-voltage-dependent calcium channel mRNA, complete cds.
AB035727 - Homo sapiens CACNA1A mRNA for alpha1A-voltage-dependent calcium channel, complete cds, isolate:TMDN-CNT-001.
AB035726 - Homo sapiens CACNA1A mRNA for alpha1A-voltage-dependent calcium channel, partial cds, isolate:TMDN-SCA6-001.
X99897 - H.sapiens mRNA for P/Q-type calcium channel alpha1 subunit.
FJ040507 - Homo sapiens neuronal calcium channel alpha 1a subunit Cav 2.1 (CACNA1A) mRNA, complete cds.
A22924 - H.sapiens mRNA fragment (p1247-
A22944 - H.sapiens mRNA fragment (p1247-
A22946 - H.sapiens mRNA fragment (pR5-6cort).
BC028611 - Homo sapiens cDNA clone IMAGE:4795326.
EU016197 - Homo sapiens fetal brain Ca2+ voltage-gated channel alpha1A pore-forming subunit (CACNA1A) mRNA, partial cds.
JD461098 - Sequence 442122 from Patent EP1572962.
JD395069 - Sequence 376093 from Patent EP1572962.
JD151859 - Sequence 132883 from Patent EP1572962.
JD399371 - Sequence 380395 from Patent EP1572962.
JD125237 - Sequence 106261 from Patent EP1572962.
JD058408 - Sequence 39432 from Patent EP1572962.
JD118591 - Sequence 99615 from Patent EP1572962.
JD458749 - Sequence 439773 from Patent EP1572962.
JD476202 - Sequence 457226 from Patent EP1572962.
JD141553 - Sequence 122577 from Patent EP1572962.
JD116597 - Sequence 97621 from Patent EP1572962.
JD186813 - Sequence 167837 from Patent EP1572962.
JD395118 - Sequence 376142 from Patent EP1572962.
JD458435 - Sequence 439459 from Patent EP1572962.
JD094902 - Sequence 75926 from Patent EP1572962.
JD131264 - Sequence 112288 from Patent EP1572962.
U06702 - Human clone CCA54 mRNA containing CCA trinucleotide repeat.
LF208178 - JP 2014500723-A/15681: Polycomb-Associated Non-Coding RNAs.
MA443755 - JP 2018138019-A/15681: Polycomb-Associated Non-Coding RNAs.
S76537 - P-type voltage-gated calcium channel alpha 1 subunit homolog [human, H146 small-cell lung carcinoma cells, mRNA Partial, 345 nt].
LF373289 - JP 2014500723-A/180792: Polycomb-Associated Non-Coding RNAs.
MA608866 - JP 2018138019-A/180792: Polycomb-Associated Non-Coding RNAs.
LF373287 - JP 2014500723-A/180790: Polycomb-Associated Non-Coding RNAs.
MA608864 - JP 2018138019-A/180790: Polycomb-Associated Non-Coding RNAs.
A22948 - H.sapiens mRNA fragment (pR5-4cort).
JD387456 - Sequence 368480 from Patent EP1572962.
JD225279 - Sequence 206303 from Patent EP1572962.
JD128964 - Sequence 109988 from Patent EP1572962.
JD402741 - Sequence 383765 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04010 - MAPK signaling pathway
hsa04020 - Calcium signaling pathway
hsa04730 - Long-term depression
hsa04742 - Taste transduction
hsa04930 - Type II diabetes mellitus

-  Other Names for This Gene
  Alternate Gene Symbols: A0A1B0GTW2, U79666, uc285pkg.1
UCSC ID: uc285pkg.1
RefSeq Accession: NM_001127221
CCDS: CCDS45998.1, CCDS82300.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CACNA1A:
ataxias (Hereditary Ataxia Overview)
ea2 (Episodic Ataxia Type 2)
fhm (Familial Hemiplegic Migraine)
sca6 (Spinocerebellar Ataxia Type 6)

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