SLC1A6
protein-codingsolute carrier family 1 member 6, the group of Solute carrier family 1
Gene summary
Enables L-aspartate transmembrane transporter activity; L-glutamate transmembrane transporter activity; and glutamate:sodium symporter activity. Involved in L-aspartate import across plasma membrane; L-glutamate import across plasma membrane; and neurotransmitter uptake. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~73.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLC1A6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005071.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 46 | 46 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 46 | 1 | 0 | 47 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005062.1 | 9 | MANE Select | |
| Ensembl | ENSP00000472133.2 | 9 | MANE Select | |
| RefSeq | NP_001259016.1 | 5 | Standard | |
| RefSeq | NP_001259017.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Glutamatergic synapse - Homo sapiens (human)
- Purine metabolism
- Amino acid and oligopeptide SLC transporters
- Transport of inorganic cations/anions and amino acids/oligopeptides
- SLC-mediated transmembrane transport
Biological Process
- neurotransmitter uptake
- ion transport
- chemical synaptic transmission
- glutamate secretion
- aspartate transmembrane transport
Molecular Function
- high-affinity glutamate transmembrane transporter activity
- amino acid transmembrane transporter activity
- L-aspartate transmembrane transporter activity
- metal ion binding
Cellular Component
- Golgi apparatus
- plasma membrane
- integral component of plasma membrane
- membrane
- intermediate filament cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000221742
- Coding exons
- 9
- Length
- 72957
- Individuals with no LoFs
- 125479
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125482
- p
- 0.0000120
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.67 | 229 | 374 | 0.612 | 0.0000242 | 3635 |
| Missense (PolyPhen) | 91 | 173.22 | 0.52533 | 1633 | ||
| Synonymous | 1.02 | 140 | 156 | 0.896 | 0.0000105 | 1236 |
| Loss of Function | 3.26 | 3 | 17.9 | 0.168 | 8.48e-7 | 198 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Sodium-dependent, high-affinity amino acid transporter that mediates the uptake of L-glutamate and also L-aspartate and D-aspartate (PubMed:7791878). Functions as a symporter that transports one amino acid molecule together with two or three Na(+) ions and one proton, in parallel with the counter-transport of one K(+) ion. Mediates Cl(-) flux that is not coupled to amino acid transport; this avoids the accumulation of negative charges due to aspartate and Na(+) symport (By similarity). Plays a redundant role in the rapid removal of released glutamate from the synaptic cleft, which is essential for terminating the postsynaptic action of glutamate (Probable). {ECO:0000250|UniProtKB:O35921, ECO:0000269|PubMed:7791878, ECO:0000305}.;
Intolerance Scores
- LoFtool
- 0.200
- RVIS EVS
- -0.8
- RVIS percentile EVS
- 12.33
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.759
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |