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    SLC1A4 solute carrier family 1 member 4 [ Homo sapiens (human) ]

    Gene ID: 6509, updated on 27-Nov-2024

    Summary

    Official Symbol
    SLC1A4provided by HGNC
    Official Full Name
    solute carrier family 1 member 4provided by HGNC
    Primary source
    HGNC:HGNC:10942
    See related
    Ensembl:ENSG00000115902 MIM:600229; AllianceGenome:HGNC:10942
    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
    SATT; ASCT1; SPATCCM
    Summary
    The protein encoded by this gene is a sodium-dependent neutral amino acid transporter for alanine, serine, cysteine, and threonine. Defects in this gene have been associated with developmental delay, microcephaly, and intellectual disability. [provided by RefSeq, Jan 2017]
    Expression
    Broad expression in brain (RPKM 33.8), adrenal (RPKM 12.8) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC1A4 in Genome Data Viewer
    Location:
    2p14
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (64988479..65023865)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (64998100..65033490)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (65215613..65250999)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15912 Neighboring gene long intergenic non-protein coding RNA 2245 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15915 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15917 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:65165275-65165830 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15920 Neighboring gene ribosomal protein L11 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15922 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:65216535-65217119 Neighboring gene RNA, U6 small nuclear 548, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15923 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:65258211-65259074 Neighboring gene long intergenic non-protein coding RNA 2576 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15924 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:65277603-65277775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15925 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11573 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11572 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11574 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:65288315-65288816 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:65294702-65295470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:65295471-65296237 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:65297006-65297772 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr2:65304333-65305043 Neighboring gene centrosomal protein 68 Neighboring gene RAB1A, member RAS oncogene family

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Spastic tetraplegia-thin corpus callosum-progressive postnatal microcephaly syndrome
    MedGen: C4225254 OMIM: 616657 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    An atlas of genetic influences on human blood metabolites.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple loci influencing human serum metabolite levels.
    EBI GWAS Catalog
    Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables L-alanine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables L-alanine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables L-alanine transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables L-aspartate transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables L-aspartate transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT enables L-cystine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables L-cystine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables L-glutamine transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables L-hydroxyproline transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables L-proline transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables L-serine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables L-serine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables L-serine transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables L-threonine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables L-threonine transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables amino acid transmembrane transporter activity TAS
    Traceable Author Statement
    more info
     
    enables chloride channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables symporter activity IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in L-alanine import across plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in L-alanine transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in L-aspartate import across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT involved_in L-cystine transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in L-cystine transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in L-glutamate transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in L-serine import across plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in L-serine transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in L-serine transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in amino acid transport TAS
    Traceable Author Statement
    more info
     
    involved_in chloride transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cognition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in glutamine transport TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in hydroxyproline transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in proline transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in proline transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in synaptic transmission, glutamatergic NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in threonine transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in transport across blood-brain barrier NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cell surface HDA PubMed 
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
     
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in intermediate filament ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in melanosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane HDA PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IC
    Inferred by Curator
    more info
    PubMed 
    is_active_in plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    neutral amino acid transporter A
    Names
    alanine/serine/cysteine/threonine transporter 1
    glutamate/neutral amino acid transporter
    solute carrier family 1 (glutamate/neutral amino acid transporter), member 4

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_053002.1 RefSeqGene

      Range
      5955..40421
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001193493.2NP_001180422.1  neutral amino acid transporter A isoform 2

      See identical proteins and their annotated locations for NP_001180422.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AK295687, BC026216, BC072423, DA218921
      Consensus CDS
      CCDS54362.1
      UniProtKB/Swiss-Prot
      P43007
      Related
      ENSP00000431942.1, ENST00000531327.5
      Conserved Domains (1) summary
      cl00573
      Location:2179
      SDF; Sodium:dicarboxylate symporter family
    2. NM_001348406.2NP_001335335.1  neutral amino acid transporter A isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1. Variants 3 and 4 both encode the same isoform (3).
      Source sequence(s)
      AC007386
      Conserved Domains (1) summary
      pfam00375
      Location:2257
      SDF; Sodium:dicarboxylate symporter family
    3. NM_001348407.2NP_001335336.1  neutral amino acid transporter A isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1. Variants 3 and 4 both encode the same isoform (3).
      Source sequence(s)
      AC007386
      Conserved Domains (1) summary
      pfam00375
      Location:2257
      SDF; Sodium:dicarboxylate symporter family
    4. NM_003038.5NP_003029.2  neutral amino acid transporter A isoform 1

      See identical proteins and their annotated locations for NP_003029.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC026216, BC072423, CR990382, L19444
      Consensus CDS
      CCDS1879.1
      UniProtKB/Swiss-Prot
      B7Z3C0, D6W5F0, P43007
      UniProtKB/TrEMBL
      B2R7N6
      Related
      ENSP00000234256.3, ENST00000234256.4
      Conserved Domains (1) summary
      pfam00375
      Location:72477
      SDF; Sodium:dicarboxylate symporter family

    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
      64988479..65023865
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      64998100..65033490
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001135581.1: Suppressed sequence

      Description
      NM_001135581.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.