SLC17A6
protein-codingsolute carrier family 17 member 6, the group of Solute carrier family 17
Gene summary
Enables L-glutamate uniporter activity. Involved in L-glutamate import and phosphate ion homeostasis. Located in synaptic vesicle membrane. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~41.1 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 SLC17A6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_020346.3. 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 | 2 | 2 | ||||
| missense | 56 | 1 | 57 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 56 | 0 | 3 | 59 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_065079.1 | 12 | MANE Select | |
| Ensembl | ENSP00000263160.3 | 12 | MANE Select | |
| Ensembl | ENSP00000803415.1 | 12 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| slc17a6b | Danio rerio | Structure: retinal ganglion cell Quality: structure abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Synaptic vesicle cycle - Homo sapiens (human)
- Retrograde endocannabinoid signaling - Homo sapiens (human)
- Glutamatergic synapse - Homo sapiens (human)
- Nicotine addiction - Homo sapiens (human)
- Synaptic Vesicle Pathway
Biological Process
- ion transport
- sodium ion transport
- L-glutamate transmembrane transport
- synaptic transmission, glutamatergic
- regulation of synapse structure or activity
Molecular Function
- L-glutamate transmembrane transporter activity
- neurotransmitter transporter activity
- symporter activity
Cellular Component
- integral component of membrane
- cell junction
- integral component of synaptic vesicle membrane
- synaptic vesicle membrane
- neuron projection
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000263160
- Coding exons
- 12
- Length
- 41407
- Individuals with no LoFs
- 125733
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 15
- Defined
- 125748
- p
- 0.0000596
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.54 | 246 | 324 | 0.760 | 0.0000155 | 3790 |
| Missense (PolyPhen) | 32 | 74.079 | 0.43197 | 837 | ||
| Synonymous | -0.127 | 117 | 115 | 1.01 | 0.00000566 | 1124 |
| Loss of Function | 3.68 | 7 | 28.0 | 0.250 | 0.00000118 | 355 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000089 | 0.000088 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Mediates the uptake of glutamate into synaptic vesicles at presynaptic nerve terminals of excitatory neural cells. May also mediate the transport of inorganic phosphate. {ECO:0000269|PubMed:10820226, ECO:0000269|PubMed:11698620}.;
Recessive Scores
- pRec
- 0.286
Intolerance Scores
- LoFtool
- 0.590
- RVIS EVS
- -0.22
- RVIS percentile EVS
- 37.43
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.650
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |