Gene
ATP2C1
ATPase secretory pathway Ca2+ transporting 1
- HGNC 13211(opens in a new tab)
- Ensembl gene ENSG00000017260(opens in a new tab)
- NCBI Gene 27032(opens in a new tab)
Summary
- Cytogenetic location
- 3q22.1
- Coordinates
- Chromosome 3: 130,894,084–131,003,150 (GRCh38)
- Exons
- 28 exons across 109.1 kb
- Protein
- 919 amino acids
- Inheritance
- Autosomal dominant
- Also known as
- KIAA1347, ATP2C1A, PMR1, SPCA1
- Previous symbols
- BCPM
- MANE Select transcript
- ENST00000510168.6NM_001378687.1
- 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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Autoimmune Disease
A disorder resulting from loss of function or tissue destruction of an organ or multiple organs, arising from humoral or cellular immune responses of the individual to their own tissue constituents. It may be systemic (e.g., systemic lupus erythematosus), or organ specific, (e.g., thyroiditis).
- 5 GenCC submitters rate it definitive or strong
Darier and Hailey-Hailey Disease
- Hailey-Hailey diseaseAutosomal dominant
An ATP2C1 disorder causing recurrent painful blisters and erosions in skin folds such as the armpits and groin.
- 5 GenCC submitters rate it definitive or strong
What knowing changes
Keeping skin folds cool and dry and treating infection early help control flares.
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 ATP2C1 is laid out
- Coding sequence
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
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 5 kb of the gene's 109.1 kb; 2,760 of those bases code for the protein.
How a genome test reads ATP2C1
8
positions in ATP2C1 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 109.1 kb of ATP2C1, introns included, not only the 5 kb of exons.
Traits linked to ATP2C1
The Human Phenotype Ontology lists these as features of the rare conditions ATP2C1 can cause. Each trait's page lists the other genes linked to it.
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.). ATP2C1 gene: ATPase secretory pathway Ca2+ transporting 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/atp2c1
Dante Labs. ATP2C1 gene: ATPase secretory pathway Ca2+ transporting 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atp2c1
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