GENE REFERENCE / HGNC:10914

SLC12A6

solute carrier family 12 member 6

protein-coding gene15q14Gene information

What does this gene do?

The SLC12A6 gene provides instructions for making a protein called KCC3, a K-Cl co-transporter present in several organs. This protein is involved in moving charged atoms (ions) of potassium (K) and chlorine (Cl) across the cell membrane. The positively charged potassium ions and negatively charged chlorine ions are moved together (co-transported), so that the charges inside and outside the cell membrane are unchanged (electroneutral).

Electroneutral co-transport of ions across cell membranes is involved in many functions of the body. While the specific function of the KCC3 protein is unknown, it seems to be critical for the development and maintenance of nerve tissue and axons, which are specialized extensions of neurons that transmit nerve impulses throughout the nervous system. KCC3 may be involved in regulating the amounts of potassium, chlorine, or water in cells and intercellular spaces. The KCC3 protein may also help regulate the activity of other proteins that are sensitive to ion concentrations.

Source: MedlinePlus, National Library of Medicine. Source publication: 2025-04-03. Source review: 2022-09.

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: 1,858
Submissions for variants in or overlapping this gene: 2,724
Submissions explicitly reporting this gene: 2,673
Alleles reported pathogenic / likely pathogenic: 269
VariationIDs with uncertain significance: 621
VariationIDs with conflicting classifications: 33

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 SLC12A6?

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 269 alleles in SLC12A6 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 SLC12A6.

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

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