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SLC6A9
solute carrier family 6 member 9
SLC6A9 is located on the short (p) arm of chromosome 1, at band 1p34.1. Arm ratio per GRCh38 - banding schematic.
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Overview
SLC6A9 belongs to the solute carrier family 6, a group of membrane transport proteins that move small molecules across cell membranes. The protein encoded by this gene specifically transports glycine, an amino acid that functions as an inhibitory neurotransmitter in the brain and spinal cord. By clearing glycine from the synaptic cleft after neuronal signalling, this transporter helps maintain proper communication between nerve cells.
Variants in SLC6A9 can affect how efficiently the transporter removes glycine from synapses. When the transporter does not function optimally, glycine may accumulate in the synaptic space, potentially disrupting normal inhibitory signalling. Research into this gene has focused primarily on neurological conditions where glycine regulation appears compromised.
What the gene does
The SLC6A9 protein functions as a plasma membrane transporter that removes glycine from the extracellular space surrounding neurons. It operates by coupling the movement of glycine to the simultaneous transport of sodium and chloride ions, using the electrochemical gradient of these ions to drive glycine uptake into cells. This process is essential for terminating glycine-mediated inhibitory neurotransmission.
The transporter is expressed predominantly in the central nervous system, particularly in regions where glycine serves as a neurotransmitter, including the spinal cord, brainstem, and certain brain areas. By rapidly clearing glycine from synapses, the protein ensures that inhibitory signals are brief and precisely timed. This regulation is critical for motor control, sensory processing, and other neurological functions that depend on balanced excitatory and inhibitory neurotransmission.
When the transporter is absent or impaired, glycine concentrations at synapses may remain elevated for longer periods, potentially leading to excessive inhibition of postsynaptic neurons. The resulting disruption in neuronal signalling can affect various motor and sensory pathways.
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Chromosome location
SLC6A9 is located on chromosome 1 at position p34.1, within the short arm of the chromosome. This chromosomal region contains multiple genes involved in neurological and metabolic processes. The precise number of exons comprising the SLC6A9 coding sequence has not been specified in the available reference data.
Protein structure
Domain architecture has not been experimentally characterised in detail for this protein. The SLC6A9 protein is predicted to contain multiple transmembrane segments that span the cell membrane, consistent with its function as a membrane transporter. Like other members of the solute carrier family 6, the protein likely adopts a structure that creates a channel through which glycine and ions can pass, though specific domain annotations are not currently available in protein structure databases.
Key variants
Genetic variants in SLC6A9 range from single nucleotide changes to larger deletions that may affect protein production or function. Some variants alter amino acids in regions critical for glycine binding or ion coupling, potentially reducing transporter efficiency. The inheritance pattern for SLC6A9-related conditions can vary depending on the specific variant and its functional impact, with both recessive and dominant mechanisms reported in the literature.
No pathogenic or likely-pathogenic ClinVar variants recorded yet for this gene.
Associated conditions
Variants in SLC6A9 have been studied in relation to neurological conditions characterised by impaired motor control and muscle tone regulation. When glycine clearance from synapses is compromised, the resulting neurotransmitter imbalance may manifest as motor abnormalities. The clinical features associated with SLC6A9 variants can range in severity, reflecting the varied impact of different genetic changes on transporter function. Research continues to clarify the full spectrum of conditions linked to this gene.
No disease links recorded for this gene in our reference set.
UK clinical status
Sources: NHS GMS PanelApp · Genomics England PanelApp · NHS National Genomic Test Directory
Frequently asked questions
What does the SLC6A9 protein do in the nervous system?
The SLC6A9 protein transports glycine out of the synaptic space between neurons, helping to terminate inhibitory signals. This clearance process is essential for maintaining proper timing and balance in neuronal communication throughout the brain and spinal cord.
Where in the body is SLC6A9 most active?
SLC6A9 is most active in the central nervous system, particularly in the spinal cord and brainstem regions where glycine functions as an inhibitory neurotransmitter. The transporter is expressed on the surface of cells surrounding glycinergic synapses.
How are variants in SLC6A9 inherited?
The inheritance pattern for SLC6A9 variants varies depending on the specific genetic change and its effect on protein function. Both autosomal recessive and autosomal dominant patterns have been observed in different families, reflecting the diverse ways variants can impact transporter activity.