SLC6A13
protein-codingsolute carrier family 6 member 13, the group of Solute carrier family 6
Gene summary
Enables gamma-aminobutyric acid:sodium:chloride symporter activity. Involved in amino acid import across plasma membrane and monocarboxylic acid transport. Located in mitochondrion and 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 ~42.3 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 SLC6A13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016615.5. 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 | 4 | 6 | ||
| missense | 81 | 2 | 1 | 84 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 3 | 4 | |||
| Total | 0 | 1 | 85 | 3 | 5 | 94 |
Highest pathogenic variant AF is 6.851117e-7
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057699.2 | 14 | MANE Select | |
| Ensembl | ENSP00000339260.4 | 14 | MANE Select | |
| RefSeq | NP_001177926.1 | 12 | Standard | |
| RefSeq | NP_001230321.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Benzodiazepine Pathway, Pharmacodynamics
- GABAergic synapse - Homo sapiens (human)
- Nuclear Receptors Meta-Pathway
- NRF2 pathway
- Amine compound SLC transporters
Biological Process
- gamma-aminobutyric acid transport
- transmembrane transport
Molecular Function
- gamma-aminobutyric acid:sodium symporter activity
- neurotransmitter binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- neuron projection
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000343164
- Coding exons
- 14
- Length
- 42251
- Individuals with no LoFs
- 125659
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 88
- Defined
- 125748
- p
- 0.000354
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0232 | 342 | 343 | 0.996 | 0.0000192 | 3889 |
| Missense (PolyPhen) | 144 | 155.75 | 0.92458 | 1790 | ||
| Synonymous | -0.961 | 161 | 146 | 1.10 | 0.00000902 | 1200 |
| Loss of Function | 1.65 | 22 | 32.1 | 0.685 | 0.00000144 | 358 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00017 | 0.00017 | rare |
| Ashkenazi Jewish | 0.00040 | 0.00040 | rare |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00030 | 0.00030 | rare |
| South Asian | 0.0012 | 0.0011 | notable |
| Other | 0.00019 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Sodium-dependent GABA and taurine transporter. In presynaptic terminals, regulates GABA signaling termination through GABA uptake. May also be involved in beta-alanine transport. {ECO:0000269|PubMed:17502375, ECO:0000269|PubMed:22932902}.;
Recessive Scores
- pRec
- 0.143
Intolerance Scores
- LoFtool
- 0.724
- RVIS EVS
- -0.53
- RVIS percentile EVS
- 20.89
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.173
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |