GENE REFERENCE / HGNC:800

ATP1A2

ATPase Na+/K+ transporting subunit alpha 2

protein-coding gene1q23.2Gene information

What does this gene do?

The ATP1A2 gene provides instructions for making one part (the alpha-2 subunit) of a protein known as a Na+/K+ ATPase. This protein uses energy from a molecule called adenosine triphosphate (ATP) to transport charged atoms (ions) into and out of cells. Specifically, it pumps sodium ions (Na+) out of cells and potassium ions (K+) into cells.

Na+/K+ ATPases that include the alpha-2 subunit are primarily found in nervous system cells called glia, which protect and maintain nerve cells (neurons). Through its action in glia, the protein plays a critical role in the normal function of neurons. Communication between neurons depends on chemicals called neurotransmitters. To relay signals, a neuron releases neurotransmitters, which attach to receptor proteins on neighboring neurons. After the neurotransmitters have had their effect, they detach from their receptors and are removed from the spaces between neurons by glia. This process is carefully regulated to ensure that signals are transmitted accurately throughout the nervous system. The Na+/K+ ATPase helps regulate this process by stimulating glia to clear neurotransmitters from the spaces between neurons. This protein also removes excess potassium ions from these spaces.

Source: MedlinePlus, National Library of Medicine. Source publication: 2023-03-07. Source review: 2014-02.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
fetal akinesia, respiratory insufficiency, microcephaly, polymicrogyria, and dysmorphic faciesMONDO:0859204 · Evaluated 2025-07-01	Autosomal recessive	DefinitivePrenatal Gene Curation Expert Panel
hemiplegic migraine-developmental and epileptic encephalopathy spectrumMONDO:0100539 · Evaluated 2024-01-16	Autosomal dominant	DefinitiveEpilepsy Gene Curation Expert Panel

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: 1,613
Submissions for variants in or overlapping this gene: 3,080
Submissions explicitly reporting this gene: 3,030
Alleles reported pathogenic / likely pathogenic: 144
VariationIDs with uncertain significance: 695
VariationIDs with conflicting classifications: 90

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 ATP1A2?

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 144 alleles in ATP1A2 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 ATP1A2.

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

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