GENE REFERENCE / HGNC:18865

KCNT1

potassium sodium-activated channel subfamily T member 1

protein-coding gene9q34.3Gene information

What does this gene do?

The KCNT1 gene belongs to a large family of genes that provide instructions for making potassium channels. These channels, which transport positively charged atoms (ions) of potassium into and out of cells, play a key role in a cell's ability to generate and transmit electrical signals.

Potassium channels are made up of several protein components (subunits). Each channel contains four alpha subunits that form the hole (pore) through which potassium ions move. Potassium channels can be made from four alpha subunits produced from the KCNT1 gene, or they can be made from subunits produced from both the KCNT1 gene and another gene called the KCNT2 gene.

The specific function of a potassium channel depends on its protein components and its location in the body. Channels that are made with the KCNT1 protein are active in nerve cells (neurons) in the brain, where they transport potassium ions out of cells. This flow of ions helps generate currents that activate (excite) neurons and send signals in the brain.

Researchers have determined that a molecule called PKC can increase the activity of channels that are made with the KCNT1 protein. While these channels can generate electrical currents without PKC, the currents are stronger when PKC attaches to the channel and increases the channel's activity.

Source: MedlinePlus, National Library of Medicine. Source publication: 2025-08-04. Source review: 2025-07.

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
childhood-onset epilepsy syndromeMONDO:0020072 · Evaluated 2022-08-16	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: 2,727
Submissions for variants in or overlapping this gene: 5,347
Submissions explicitly reporting this gene: 5,215
Alleles reported pathogenic / likely pathogenic: 80
VariationIDs with uncertain significance: 1,033
VariationIDs with conflicting classifications: 184

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 KCNT1?

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 80 alleles in KCNT1 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 KCNT1.

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

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