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    SLC3A1 solute carrier family 3 member 1 [ Homo sapiens (human) ]

    Gene ID: 6519, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SLC3A1provided by HGNC
    Official Full Name
    solute carrier family 3 member 1provided by HGNC
    Primary source
    HGNC:HGNC:11025
    See related
    Ensembl:ENSG00000138079 MIM:104614; AllianceGenome:HGNC:11025
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    D2H; ATR1; NBAT; RBAT; CSNU1
    Summary
    This gene encodes a type II membrane glycoprotein which is one of the components of the renal amino acid transporter which transports neutral and basic amino acids in the renal tubule and intestinal tract. Mutations and deletions in this gene are associated with cystinuria. Alternatively spliced transcript variants have been described, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in kidney (RPKM 175.5), small intestine (RPKM 50.6) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC3A1 in Genome Data Viewer
    Location:
    2p21
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (44275480..44322437)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (44280847..44327754)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (44502619..44548633)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene protein phosphatase, Mg2+/Mn2+ dependent 1B Neighboring gene uncharacterized LOC124906174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:44513823-44514378 Neighboring gene ribosomal protein L12 pseudogene 19 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:44558969-44559142 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:44588276-44589475 Neighboring gene prolyl endopeptidase like Neighboring gene MPRA-validated peak3688 silencer Neighboring gene uncharacterized LOC124905998 Neighboring gene uncharacterized LOC124907759 Neighboring gene calmodulin-lysine N-methyltransferase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Identification of 12 novel mutations in the SLC3A1 gene in Swedish cystinuria patients. Harnevik L, et al. Hum Mutat, 2001 Dec. PMID 11748844
    2. Role of rBAT gene products in cystinuria. Miyamoto K, et al. Int J Urol, 1996 Jan. PMID 24449952
    3. [ATR1 gene polymorphism in patients with hypertrophic cardiomyopathy and hypertensive heart]. Smirnova MD, et al. Kardiologiia, 2010. PMID 20146678
    4. Distinct classes of trafficking rBAT mutants cause the type I cystinuria phenotype. Bartoccioni P, et al. Hum Mol Genet, 2008 Jun 15. PMID 18332091
    5. Gene symbol: SLC3A1. Disease: cystinuria. Nunes V, et al. Hum Genet, 2005 Feb. PMID 15818802

    See all (77) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel compound heterozygous pathogenic variants in the SLC3A1 gene in a Chinese family with cystinuria.
      Title: Novel compound heterozygous pathogenic variants in the SLC3A1 gene in a Chinese family with cystinuria.
    2. Interpretation of SLC3A1 and SLC7A9 variants in cystinuria patients: The significance of the PM3 criterion and protein stability.
      Title: Interpretation of SLC3A1 and SLC7A9 variants in cystinuria patients: The significance of the PM3 criterion and protein stability.
    3. Population genetics analysis of SLC3A1 and SLC7A9 revealed the etiology of cystine stone may be more than what our current genetic knowledge can explain.
      Title: Population genetics analysis of SLC3A1 and SLC7A9 revealed the etiology of cystine stone may be more than what our current genetic knowledge can explain.
    4. Clinical profile of a Polish cohort of children and young adults with cystinuria.
      Title: Clinical profile of a Polish cohort of children and young adults with cystinuria.
    5. Structural basis for amino acid exchange by a human heteromeric amino acid transporter.
      Title: Structural basis for amino acid exchange by a human heteromeric amino acid transporter.
    6. A homozygous c.325G>A mutation in cationic amino cid transport proteins (SLC7A9) was identified in two patients, and six neutral and basic amino acid transporter protein (SLC3A1) mutations were found in five patients.
      Title: Clinical, Biochemical, and Genetic Findings of Cystinuria in Chinese Children.
    7. Study shows that various computational tools were able to distinguish cystinuria-causing mutations from benign polymorphisms. Four deleterious mutation (R362C, T216M, M467K/T) in the coding region of SLC3A1 were identified. The intron variant c.1136+2/3delT in SLC3A1 gene probably affected the splicing process.
      Title: In silico analysis of SLC3A1 and SLC7A9 mutations in Iranian patients with Cystinuria.
    8. Thirteen pediatric patients with cystine stones were evaluated in our clinic between 2012 and 2015. Gene mutations in SLC3A1 and SLC7A9 were investigated
      Title: Clinical and genetic characterization of Chinese pediatric cystine stone patients.
    9. Spectrum of SLC3A1 and SLC7A9 mutations in cystinuria patients presenting with prenatal hyperechoic colon has been described.
      Title: Spectrum of mutations in cystinuria patients presenting with prenatal hyperechoic colon.
    10. Analysis showing how different mutations in SLC3A1 and SLC7A9 affect severity of cystinuria.
      Title: Associating mutations causing cystinuria with disease severity with the aim of providing precision medicine.
    Submit: New GeneRIF Correction See all GeneRIFs (47)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Cystinuria
    MedGen: C0010691 OMIM: 220100 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34681

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables L-cystine transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables amino acid transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables basic amino acid transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein heterodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein-containing complex binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in L-cystine transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in L-glutamate transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in amino acid transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in aspartate transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in basic amino acid transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in basic amino acid transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in carbohydrate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in apical plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in brush border membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in vacuolar membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    amino acid transporter heavy chain SLC3A1
    Names
    B(0,+)-type amino acid transport protein
    amino acid transporter 1
    b(0,+)-type amino acid transporter-related heavy chain
    neutral and basic amino acid transport protein rBAT
    solute carrier family 3 (amino acid transporter heavy chain), member 1
    solute carrier family 3 (cystine, dibasic and neutral amino acid transporters), member 1
    solute carrier family 3 (cystine, dibasic and neutral amino acid transporters, activator of cystine, dibasic and neutral amino acid transport), member 1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008233.1 RefSeqGene

      Range
      5023..51037
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000341.4 → NP_000332.2  amino acid transporter heavy chain SLC3A1

      See identical proteins and their annotated locations for NP_000332.2

      Status: REVIEWED

      Source sequence(s)
      AC013717, AK223146, BC093626
      Consensus CDS
      CCDS1819.1
      UniProtKB/Swiss-Prot
      A8K0S1, O00658, Q07837, Q15295, Q4J6B4, Q4J6B5, Q4J6B6, Q4J6B7, Q4J6B8, Q4J6B9, Q52M92, Q52M94
      UniProtKB/TrEMBL
      A0A0S2Z4E1, B2R7X8
      Related
      ENSP00000260649.6, ENST00000260649.11
      Conserved Domains (1) summary
      cd11359
      Location:116 → 569
      AmyAc_SLC3A1; Alpha amylase catalytic domain found in Solute Carrier family 3 member 1 proteins

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      44275480..44322437
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011533047.4 → XP_011531349.1  amino acid transporter heavy chain SLC3A1 isoform X1

      UniProtKB/TrEMBL
      A0A087X0R9, B8ZZK1
      Related
      ENSP00000387308.1, ENST00000409387.5
      Conserved Domains (3) summary
      cd11359
      Location:116 → 539
      AmyAc_SLC3A1; Alpha amylase catalytic domain found in Solute Carrier family 3 member 1 proteins
      pfam00128
      Location:140 → 488
      Alpha-amylase; Alpha amylase, catalytic domain
      pfam13900
      Location:543 → 564
      GVQW; Putative domain of unknown function

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      44280847..44327754
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343470.1 → XP_054199445.1  amino acid transporter heavy chain SLC3A1 isoform X1

      UniProtKB/TrEMBL
      A0A087X0R9, B8ZZK1
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q07837.2 GenPept UniProtKB/Swiss-Prot:Q07837

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