Gene
CACNA1S
calcium voltage-gated channel subunit alpha1 S
- HGNC 1397(opens in a new tab)
- Ensembl gene ENSG00000081248(opens in a new tab)
- NCBI Gene 779(opens in a new tab)
Summary
- Cytogenetic location
- 1q32.1
- Coordinates
- Chromosome 1: 201,039,512–201,112,426 (GRCh38)
- Exons
- 44 exons across 72.9 kb
- Protein
- 1,873 amino acids
- Inheritance
- Autosomal dominant
- Also known as
- Cav1.1, hypoPP
- Previous symbols
- HOKPP, MHS5, CACNL1A3
- MANE Select transcript
- ENST00000362061.4NM_000069.3
- Locus type
- gene with protein product
- Very high
- Confident
- Low
- Very low
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
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Familial Periodic Paralysis
- Periodic ParalysisAutosomal dominant
Editor note: classified as genetic in ORDO but we treat as neutral here
- 3 GenCC submitters rate it definitive or strong
Malignant Hyperthermia Susceptibility
- Autosomal dominant
An inherited muscle condition, mainly caused by changes in RYR1 or CACNA1S, in which volatile anaesthetic gases or suxamethonium can trigger a rapid rise in body temperature, muscle rigidity and muscle breakdown.
- ClinGen rates the link moderate
- 1 GenCC submitter rates it definitive or strong
What knowing changes
Telling the anaesthetist allows non-triggering anaesthesia to be used, which largely prevents reactions; relatives may also be at risk.
Inheritance
- Autosomal dominant
- One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.
How CACNA1S is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
- Variants with a page
Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.
Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).
Nearby genes from Ensembl release 116, on GRCh38.
Exons make up 6 kb of the gene's 72.9 kb; 5,622 of those bases code for the protein.
How a genome test reads CACNA1S
133
positions in CACNA1S where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 72.9 kb of CACNA1S, introns included, not only the 6 kb of exons.
Variants with a page (25)
The CACNA1S variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.
| Variant | HGVS c. | Exon or intron | Position (GRCh38) | ClinVar classification | Review status |
|---|---|---|---|---|---|
| c.258+2T>C | Intron 2 | 201,110,162 | Likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.1233-1G>A | Intron 9 | 201,083,323 | Likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.3414+3A>T | Intron 26 | 201,060,655 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.4113+1G>A | Intron 33 | 201,050,983 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.4113+1G>C | Intron 33 | 201,050,983 | Likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.4543+2T>C | Intron 37 | 201,047,523 | Likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| c.4798-2A>G | Intron 39 | 201,043,533 | Likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts | |
| D1650Ifs*73 | c.4947del | Exon 40 | 201,043,381 | Pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| E1348Rfs*76 | c.4038del | Exon 33 | 201,051,058 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts |
| L938Yfs*26 | c.2812del | Exon 22 | 201,065,878 | Pathogenic/likely pathogenic | 2 stars out of 4 criteria provided, multiple submitters, no conflicts |
Traits linked to CACNA1S
The Human Phenotype Ontology lists these as features of the rare conditions CACNA1S can cause. Each trait's page lists the other genes linked to it.
Abnormality of the musculoskeletal system
- Axial muscle weakness
- Episodic flaccid weakness
- Low muscle tone
- Abnormal muscle fiber morphology
- EMG abnormality
- Increased variability in muscle fiber diameter
- Breakdown of skeletal muscle
- Exercise-induced muscle fatigue
Show 17 more traits
- Increased endomysial connective tissue
- Intermittent painful muscle spasms
- Muscle spasm
- Muscle stiffness
- Scoliosis
- Acute rhabdomyolysis
- Centrally nucleated skeletal muscle fibers
- Decreased lung function due to weak breathing muscles
- Exercise-induced rhabdomyolysis
- Fatty replacement of skeletal muscle
- Late-onset proximal muscle weakness
- Muscle tissue disease
- Necrotizing myopathy
- Fatigable weakness of respiratory muscles
- Respiratory paralysis
- Muscle weakness
- Myotonia
Abnormality of the nervous system
- Motor delay
- Periodic hypokalemic paresis
- Periodic paralysis
- Paralysis
- Paralysis of all four limbs
- Decreased reflex response
- Diminished deep tendon reflex
- Tremor
Show 1 more trait
External links
Gene records
Transcript
Protein
Where this comes from
- HGNC: the gene's symbol, name, other symbols and location.
- MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
- GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
- The ACMG secondary findings list, SF v3.2.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.16-c6eea6bf.
Cite this page
Dante Labs. (n.d.). CACNA1S gene: calcium voltage-gated channel subunit alpha1 S. Retrieved 16 October 2026, from https://dantelabs.com/genes/cacna1s
Dante Labs. CACNA1S gene: calcium voltage-gated channel subunit alpha1 S [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/cacna1s
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