UCSF Pharmacogenetics of Membrane Transporters
Gene View
Common Name:ATA3
HGNC Symbol:SLC38A4
HGNC Description:solute carrier family 38, member 4
HGNC ID:14679
Superfamily:SLC
Chromosome:Chr.12(-): 47158544-47226205 GRCh37
Location:12q13
OMIM:608065
OMIM Phenotype:None
Accessions:AF305814
Nucleotide RefSeq:NM_018018
Protein RefSeq:NP_060488
Entrez:55089
Ensembl:ENSG00000139209
Isoforms:4
Evidence:Substrate In Vitro Evidence: L-alanine, L-glutamine, L-histidine, and L-lysine (but not L-glutamate) were found to be substrates of hNAT3 as determined by uptake of radiolabeled compounds in hNAT3-injected X. laevis oocytes (Gu S, Adan-Rice D, Leach RJ, Jiang JX. A novel human amino acid transporter, hNAT3: cDNA cloning, chromosomal mapping, genomic structure, expression, and functional characterization. Genomics 74(3):262-72, 2001). L-glycine, L-arginine, and (-(methylamino)isobutyric acid (MeAIB), a model substrate for system A amino acid transporters, were found to also be substrates of ATA3 using a human retinal pigment epithelial (HRPE) cell line and the vaccinia virus expression system (Hatanaka T, Huang W, Ling R, Prasad PD, Sugawara M, Leibach FH, Ganapathy V. Evidence for the transport of neutral as well as cationic amino acids by ATA3, a novel and liver-specific subtype of amino acid transport system A. Biochimica et Biophysica Acta 1510(1-2):10-7, 2001). These authors suggested that ATA3 is functionally distinct from previously cloned ATA family members by its higher affinity for cationic amino acids. Tissue Distribution Evidence: NAT3 mRNA was detected by RT-PCR in human adult and embryonic liver (high expression); moderate expression was detected in skeletal muscle, kidney, and pancreas; and low levels of mRNA were detected in heart and placenta (Gu S, Adan-Rice D, Leach RJ, Jiang JX. A novel human amino acid transporter, hNAT3: cDNA cloning, chromosomal mapping, genomic structure, expression, and functional characterization. Genomics 74(3):262-72, 2001). Nothern blot analysis showed ATA3 expression almost exclusively in adult liver, with very low expression in kidney (Hatanaka T, Huang W, Ling R, Prasad PD, Sugawara M, Leibach FH, Ganapathy V. Evidence for the transport of neutral as well as cationic amino acids by ATA3, a novel and liver-specific subtype of amino acid transport system A. Biochimica et Biophysica Acta 1510(1-2):10-7, 2001).
Tissues:Adult and embryonic liver (high); skeletal muscle, kidney, pancreas (moderate); heart, placenta (low)
Type:protein-coding
Sets:0
PharmGKB ID:PA37908
HPRD ID:12159
Substrates:L-alanine, L-glutamine, L-histidine, L-lysine, MeAIB, glycine, arginine
Trivial Names:ATA3, NAT3, PAAT
Transcripts:NM_018018.4 [Chr.12(-): 47158544-47219780 GRCh37]
NM_001143824.1 [Chr.12(-): 47158544-47219780 GRCh37]
XM_005268997.1 [Chr.12(-): 47158544-47226205 GRCh37]
XM_005268996.1 [Chr.12(-): 47158544-47197465 GRCh37]
ENST00000266579 [Chr.12(-): 47159799-47219780 GRCh37]
ENST00000447411 [Chr.12(-): 47158546-47219780 GRCh37]
ENST00000546940 [Chr.12(-): 47173732-47226191 GRCh37]
ENST00000547477 [Chr.12(-): 47173563-47219768 GRCh37]
ENST00000550670 [Chr.12(-): 47160086-47163087 GRCh37]
Annotation History:View Events (18)

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 SLC38A4.

Variant Data

View all PMT variants for SLC38A4 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.