GENE REFERENCE / HGNC:10941

SLC1A3

solute carrier family 1 member 3

protein-coding gene5p13.2Gene information

What does this gene do?

The SLC1A3 gene provides instructions for making a protein called excitatory amino acid transporter 1 (EAAT1). The EAAT1 protein is primarily found in nervous system cells called glia (or glial cells), which protect and maintain nerve cells (neurons). While the protein is found in cells throughout the brain, it is most abundant in the part of the brain that is connected to the spinal cord (the brainstem) and the region of the brain involved in coordinating movements (the cerebellum).

The EAAT1 protein transports a molecule called glutamate in the brain. Glutamate is one of several brain chemicals called neurotransmitters, which allow neurons to communicate with one another. EAAT1 also transports negatively charged chlorine atoms (chloride ions).

Neurotransmitters (such as glutamate) are released from neurons and relay signals to other cells by attaching to receptor proteins on neighboring neurons. After the neurotransmitters have had their effect, they detach from their receptors and must be cleared from the spaces between neurons. Researchers have determined that EAAT1 is one of several glutamate transporters that clear excess glutamate from these spaces. This process is carefully regulated to ensure that signals are transmitted accurately throughout the nervous system. The timely removal of glutamate is also necessary to prevent a buildup of this neurotransmitter between cells, which would be toxic to neurons.

The EAAT1 protein also transports chloride ions in and out of cells. This function of the protein may help regulate the size (volume) of glia by playing a role in their intake and release of water. EAAT1 may also help maintain a normal balance of charged molecules (ions) in cells.

Source: MedlinePlus, National Library of Medicine. Source publication: 2023-05-04. Source review: 2023-05.

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
episodic ataxia type 6MONDO:0012982 · Evaluated 2020-10-09	Autosomal dominant	DefinitiveAminoacidopathy 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: 389
Submissions for variants in or overlapping this gene: 618
Submissions explicitly reporting this gene: 568
Alleles reported pathogenic / likely pathogenic: 2
VariationIDs with uncertain significance: 200
VariationIDs with conflicting classifications: 17

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 SLC1A3?

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 2 alleles in SLC1A3 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 SLC1A3.

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

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