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CACNA1A

Synonyms
APCA, BI, CACNL1A4, CAV2.1, DEE42, EA2, EIEE42, FHM, HPCA, MHP, MHP1, SCA6
External resources
Summary
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.

Variant counts

The variants found in rare patients tested by 3billion are classified and counted according to ACMG guidelines. The variants with over 5% variant frequency in population genome databases ( gnomAD, dbSNP, etc) are excluded.

Pathogenic
96
Likely pathogenic
5
VUS
22,028
Likely benign
17,186
Benign
1,547

Patient phenotypes

Proportions of phenotypes among 34 patients carrying pathogenic or likely pathogenic variants on CACNA1A gene are displayed below.

Phenotype class
Patients in 3billion (%)
Abnormality of the nervous system
58.8%
Abnormality of head or neck
20.6%
Abnormality of the eye
14.7%
Abnormality of the musculoskeletal system
14.7%
Growth abnormality
14.7%
Abnormality of the integument
11.8%
Abnormality of blood and blood-forming tissues
5.9%
Abnormality of the endocrine system
5.9%
Abnormality of the genitourinary system
5.9%
Abnormality of the immune system
5.9%
Abnormal cellular phenotype
2.9%
Abnormality of limbs
2.9%
Abnormality of prenatal development or birth
2.9%
Abnormality of the digestive system
2.9%
Abnormality of the ear
2.9%
Abnormality of the respiratory system
2.9%
Abnormality of metabolism homeostasis
0%
Abnormality of the breast
0%
Abnormality of the cardiovascular system
0%
Abnormality of the thoracic cavity
0%
Abnormality of the voice
0%
Constitutional symptom
0%
Neoplasm
0%

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