GENE REFERENCE / HGNC:13211

ATP2C1

ATPase secretory pathway Ca2+ transporting 1

protein-coding gene3q22.1Gene information

What does this gene do?

The ATP2C1 gene provides instructions for making a protein called hSPCA1. This protein is an adenosine triphosphate (ATP)-powered calcium pump, which uses energy from ATP molecules to pump charged calcium atoms (calcium ions) across cell membranes. Specifically, the hSPCA1 protein transports calcium ions into a cell structure called the Golgi apparatus, where they are stored until needed. The appropriate storage and release of calcium is essential for many cell activities, including cell growth and division (proliferation), cell movement (migration), and attachment of cells to one another (cell adhesion).

The hSPCA1 protein also transports manganese ions into the Golgi apparatus. Manganese works with a variety of enzymes and is involved in processing newly formed proteins.

The hSPCA1 protein is present in cells throughout the body. It appears to be particularly important for the normal function of cells called keratinocytes, which are found in the outer layer of the skin (the epidermis). In addition to proliferation and adhesion, calcium regulation in these cells appears to play an important role in maintaining the skin's barrier function, helping to keep foreign invaders such as bacteria out of the body.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2013-05.

ClinGen reviews

We found no matching ClinGen review in the data used here. This does not rule out a link between the gene and a condition.

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 412
Submissions for variants in or overlapping this gene: 570
Submissions explicitly reporting this gene: 454
Alleles reported pathogenic / likely pathogenic: 72
VariationIDs with uncertain significance: 166
VariationIDs with conflicting classifications: 6

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about ATP2C1?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 72 alleles in ATP2C1 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in ATP2C1.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

Buy BioDecode See a sample report →Check file compatibility →