UCSF Pharmacogenetics of Membrane Transporters
Gene View
Common Name:ATR1
HGNC Symbol:SLC3A1
HGNC Description:solute carrier family 3 (amino acid transporter heavy chain), member 1
HGNC ID:11025
Superfamily:SLC
Chromosome:Chr.2(+): 44502597-44547963 GRCh37
Location:2p16.3
OMIM:104614
OMIM Phenotype:Cystinuria
Accessions:NM_000341
Nucleotide RefSeq:NM_000341
Protein RefSeq:NP_000332
Entrez:6519
Ensembl:ENSG00000138079
Isoforms:1
Evidence:Substrate In Vitro Evidence: SLC3A1 (rBAT) is called an "activator" of cationic and neutral amino acid transport: it is a subunit that forms a covalent heterodimer with SLC7A9 (b0,+ AT) and possibly other members of the SLC7 family. The SLC3 transporters are called the "heavy" subunits of the heteromeric amino acid transporters (HATs), and appear to be necessary for trafficking of the "light" subunits (which are probably the "catalytic" domains of the protein complexes); members of the SLC7 family (SLC7A5-11) make up the "light" subunits (Palacin M, Kanai Y. The ancillary proteins of HATs: SLC3 family of amino acid transporters. Pflugers Archives, May 6, 2003 [Epub ahead of print]; Verrey F, Closs EI, Wagner CA, Palacin M, Endou H, Kanai Y. CATs and HATs: the SLC7 family of amino acid transporters. Pflugers Archives Jun 11, 2003 [Epub ahead of print]). Uptake of L-arginine, L-cystine, and L-leucine was induced by injection of rBAT cRNA into X. laevis oocytes (Bertran J, Werner A, Chillaron J, Nunes V, Biber J, Testar X, Zorzano A, Estivill X, Murer H, Palacin M. Expression cloning of a human renal cDNA that induces high affinity transport of L-cystine shared with dibasic amino acids in Xenopus oocytes. J Biol Chem 268(20):14842-9, 1993). Substrate In Vivo Evidence: System b0,+ (i.e., the rBAT/b0,+AT heterodimer) is defective in cystinuria. This is the most common primary inherited aminoaciduria, characterized by hyperexcretion of dibasic amino acids and cystine in urine. The low solubility of cystine causes the formation of cystine calculi. Mutations in SLC3A1 cause cystinuria type I, whereas mutations in SLC7A9 cause cystinuria non-type I, and some cases of cystinuria type I (Palacin M, Kanai Y. The ancillary proteins of HATs: SLC3 family of amino acid transporters. Pflugers Archives, May 6, 2003 [Epub ahead of print]; Verrey F, Closs EI, Wagner CA, Palacin M, Endou H, Kanai Y. CATs and HATs: the SLC7 family of amino acid transporters. Pflugers Archives Jun 11, 2003 [Epub ahead of print]). At present, >60 cystinuria-specific mutations (>30 missense mutations) in SLC3A1 have been identified (reviewed in: Verrey F, Closs EI, Wagner CA, Palacin M, Endou H, Kanai Y. CATs and HATs: the SLC7 family of amino acid transporters. Pflugers Archives Jun 11, 2003 [Epub ahead of print]). Tissue Distribution Evidence: rBAT mRNA was found in kidney, small intestine, liver and pancreas by Northern blot (Bertran J, Werner A, Chillaron J, Nunes V, Biber J, Testar X, Zorzano A, Estivill X, Murer H, Palacin M. Expression cloning of a human renal cDNA that induces high affinity transport of L-cystine shared with dibasic amino acids in Xenopus oocytes. J Biol Chem 268(20):14842-9, 1993).
Tissues:kidney, small intestine, liver, pancreas
Type:protein-coding
Sets:V
PharmGKB ID:PA35893
HPRD ID:00090
Substrates:L-arginine, L-cystine, L-leucine
Trivial Names:D2H, ATR1, NBAT, RBAT, CSNU1
Transcripts:NM_000341.3 [Chr.2(+): 44502597-44547963 GRCh37]
ENST00000260649 [Chr.2(+): 44502599-44548633 GRCh37]
ENST00000409229 [Chr.2(+): 44502675-44542382 GRCh37]
ENST00000409294 [Chr.2(+): 44527166-44541337 GRCh37]
ENST00000409380 [Chr.2(+): 44512222-44547960 GRCh37]
ENST00000409387 [Chr.2(+): 44502603-44545894 GRCh37]
ENST00000409740 [Chr.2(+): 44530945-44547937 GRCh37]
ENST00000409741 [Chr.2(+): 44502675-44539929 GRCh37]
ENST00000410056 [Chr.2(+): 44502675-44528556 GRCh37]
ENST00000427285 [Chr.2(+): 44512634-44528225 GRCh37]
Annotation History:View Events (2)

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 SLC3A1.

Variant Data

View all PMT variants for SLC3A1 on UCSC Genome Browser
Showing SNP features for transcript: NM_000341  
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.