UCSF Pharmacogenetics of Membrane Transporters
Gene View
Common Name:EAAT4
HGNC Symbol:SLC1A6
HGNC Description:solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6
HGNC ID:10944
Superfamily:SLC
Chromosome:Chr.19(-): 15060845-15121455 GRCh37
Location:19p13.12
OMIM:600637
OMIM Phenotype:None
Accessions:NM_005071
Nucleotide RefSeq:NM_005071
Protein RefSeq:NP_005062
Entrez:6511
Ensembl:ENSG00000105143
Isoforms:3
Evidence:Substrate In Vitro Evidence: Glutamate Aspartate - Xenopus oocytes expressing EAAT4. Fairman WA, et al. Nature. 1995; 375: 599-603. Substrate In Vivo Evidence: Neurotransmitters - RNA interference in rats develop ataxia. Maragakis N, et al. 1997. Neurosci. Meeting Abstr. 23, 585.2. Tissue Distribution Evidence: Brain (mouse and cat) - RT-PCR, Immunocytochem., Western Blot. Massie A, et al. Neuroreport. 2001; 12: 393-7. Brain (cerebellum) - Furuta A, et al. Neuroscience. 1997 Dec;81(4):1031-42.
Tissues:Brain
Type:protein-coding
Sets:V
PharmGKB ID:PA35831
HPRD ID:09005
Substrates:Glutamate, Asparate, Neurotransmitters
Trivial Names:EAAT4
Transcripts:NM_005071.2 [Chr.19(-): 15060845-15083730 GRCh37]
NM_001272088.1 [Chr.19(-): 15072125-15090547 GRCh37]
NM_001272087.1 [Chr.19(-): 15072125-15090547 GRCh37]
ENST00000221742 [Chr.19(-): 15060991-15083730 GRCh37]
ENST00000430939 [Chr.19(-): 15060846-15121432 GRCh37]
ENST00000544886 [Chr.19(-): 15072122-15091110 GRCh37]
ENST00000594383 [Chr.19(-): 15083617-15090500 GRCh37]
ENST00000595863 [Chr.19(-): 15082562-15133802 GRCh37]
ENST00000596697 [Chr.19(-): 15074821-15086085 GRCh37]
ENST00000597262 [Chr.19(-): 15079181-15090534 GRCh37]
ENST00000598504 [Chr.19(-): 15072122-15090505 GRCh37]
ENST00000599636 [Chr.19(-): 15079237-15121455 GRCh37]
ENST00000600144 [Chr.19(-): 15061007-15087839 GRCh37]
ENST00000601761 [Chr.19(-): 15083501-15088958 GRCh37]
Annotation History:View Events (22)

GTEx Expression by Gene and Transcript

The heat map summarizes relative expression by tissue type at two levels of tissue detail, e.g., 'Brain' and 'Brain - Amygdala'. Choose among four calculated expression values, including mean and median RPKM values, and quantile normalized (QN) distributions of these values. (Note that differences between some distributions are subtle.) The coloring is relative to the mean of all displayed values. All values are log base 2. (See also PMT GTEx Expression Plotting.) Click on a transcript or tissue to resort the data.

Tissues:
Expression values:
No expression data exists for SLC1A6.

Variant Data

View all PMT variants for SLC1A6 on UCSC Genome Browser
Showing SNP features for transcript:   
1000 Genomes  

20141104 phase 3 variant call set of the 20130502 sequence freeze and alignments for SNPs and short indels (indels > 255 and structural variants are not included here). This variant set contains 2504 individuals from 26 populations (mouse over population column heading for population sizes).
Showing gene variants in regions defined by NCBI RefSeq exons, putative promoter, and PMT resequencing assays.
Note: Frequencies are calculated directly from reported genotypes and may vary from consensus frequencies reported by the 1000 Genomes project, which relied on additional data and the GATK tool Variant Quality Score Recalibrator.
dbSNP build 142.
Array availability: I - found on Illumina Human1M-Duo BeadChip (2011-04-21)  A - found on Affymetrix Genome-Wide SNP Array 6.0 (2011-06-21)  
Download the SNP table data as a tab-delimited file.

Transmembrane prediction:

Non-synonymous amino acid changes shown in red, indels (insertions and deletions) in blue, and synonymous changes in green. Exon(s) indicated by black outlines.