SLC1A6
Basic information
Region (hg38): 19:14950033-15022990
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (42 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLC1A6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005071.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 41 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 41 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SLC1A6 | protein_coding | protein_coding | ENST00000221742 | 9 | 72957 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.762 | 0.238 | 125479 | 0 | 3 | 125482 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.67 | 229 | 374 | 0.612 | 0.0000242 | 3635 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000180 | 0.0000177 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000329 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- 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;Transport of small molecules;Neuronal System;Histidine metabolism;Glutamate Neurotransmitter Release Cycle;Neurotransmitter release cycle;Transmission across Chemical Synapses
(Consensus)
Intolerance Scores
- loftool
- 0.200
- rvis_EVS
- -0.8
- rvis_percentile_EVS
- 12.33
Haploinsufficiency Scores
- pHI
- 0.261
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.625
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.759
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Slc1a6
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- neurotransmitter uptake;ion transport;chemical synaptic transmission;glutamate secretion;aspartate transmembrane transport;L-glutamate transmembrane transport;regulation of membrane potential;L-aspartate transmembrane transport;L-glutamate import across plasma membrane
- Cellular component
- Golgi apparatus;plasma membrane;integral component of plasma membrane;membrane;intermediate filament cytoskeleton;glutamatergic synapse;integral component of presynaptic membrane
- Molecular function
- high-affinity glutamate transmembrane transporter activity;amino acid transmembrane transporter activity;L-aspartate transmembrane transporter activity;metal ion binding