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    SLC46A1 solute carrier family 46 member 1 [ Homo sapiens (human) ]

    Gene ID: 113235, updated on 1-Mar-2024

    Summary

    Official Symbol
    SLC46A1provided by HGNC
    Official Full Name
    solute carrier family 46 member 1provided by HGNC
    Primary source
    HGNC:HGNC:30521
    See related
    Ensembl:ENSG00000076351 MIM:611672; AllianceGenome:HGNC:30521
    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
    G21; HCP1; PCFT; hPCFT; HsPCFT
    Summary
    This gene encodes a transmembrane proton-coupled folate transporter protein that facilitates the movement of folate and antifolate substrates across cell membranes, optimally in acidic pH environments. This protein is also expressed in the brain and choroid plexus where it transports folates into the central nervous system. This protein further functions as a heme transporter in duodenal enterocytes, and potentially in other tissues like liver and kidney. Its localization to the apical membrane or cytoplasm of intestinal cells is modulated by dietary iron levels. Mutations in this gene are associated with autosomal recessive hereditary folate malabsorption disease. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2013]
    Expression
    Ubiquitous expression in duodenum (RPKM 45.1), small intestine (RPKM 21.0) and 22 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SLC46A1 in Genome Data Viewer
    Location:
    17q11.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (28394642..28406592, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (29336494..29348065, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (26721661..26733230, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene transmembrane protein 199 Neighboring gene SEBOX homeobox Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8338 Neighboring gene vitronectin Neighboring gene sterile alpha and TIR motif containing 1 Neighboring gene MPRA-validated peak2778 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11925 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:26722700-26723383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:26724067-26724750 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11926 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:26729147-26729889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:26731519-26732244 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8340 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:26735385-26736225 Neighboring gene uncharacterized LOC124903964 Neighboring gene H3 histone pseudogene 41

    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
    Congenital defect of folate absorption Compare labs

    EBI GWAS Catalog

    Description
    Meta-analysis of genome-wide association studies identifies two loci associated with circulating osteoprotegerin levels.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of solute carrier family 46 (folate transporter), member 1 (SLC46A1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC9564, FLJ39875

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in folate import across plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in folate transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in folic acid metabolic process TAS
    Traceable Author Statement
    more info
     
    involved_in folic acid transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in folic acid transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in heme metabolic process TAS
    Traceable Author Statement
    more info
     
    involved_in heme transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intestinal folate absorption IC
    Inferred by Curator
    more info
    PubMed 
    involved_in intracellular iron ion homeostasis TAS
    Traceable Author Statement
    more info
     
    involved_in methotrexate transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in proton transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in apical plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in basolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in basolateral plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in brush border membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cell surface HDA PubMed 
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    proton-coupled folate transporter
    Names
    heme carrier protein 1
    solute carrier family 46 (folate transporter), member 1

    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_013306.1 RefSeqGene

      Range
      4999..16567
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_183

    mRNA and Protein(s)

    1. NM_001242366.3NP_001229295.1  proton-coupled folate transporter isoform 2

      See identical proteins and their annotated locations for NP_001229295.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2, also known as HCP-1B) lacks an in-frame coding exon compared to variant 1. This results in a shorter isoform (2) missing an internal protein segment (containing one of the transmembrane domains) compared to isoform 1. This isoform was shown to have a different subcellular localization compared to the longer isoform 1 (PMID:17947394).
      Source sequence(s)
      AK074161, BC010691, BC022100, BC065365, DA013269, DA188147, DA436636, DA527125
      Consensus CDS
      CCDS74019.1
      UniProtKB/TrEMBL
      B4DJ17
      Related
      ENSP00000483652.1, ENST00000618626.1
      Conserved Domains (2) summary
      cd06174
      Location:73230
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
      pfam07690
      Location:94291
      MFS_1; Major Facilitator Superfamily
    2. NM_080669.6NP_542400.2  proton-coupled folate transporter isoform 1

      See identical proteins and their annotated locations for NP_542400.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1, also known as HCP-1A) encodes the longer protein (isoform 1).
      Source sequence(s)
      AK054669, AK074161, BC022100, BC065365, DA013269, DA188147, DA436636, DA527125, DB121588
      Consensus CDS
      CCDS74020.1
      UniProtKB/Swiss-Prot
      Q1HE20, Q86T92, Q8TEG3, Q96FL0, Q96NT5
      Related
      ENSP00000480703.1, ENST00000612814.5
      Conserved Domains (2) summary
      cd06174
      Location:73443
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
      pfam07690
      Location:94407
      MFS_1; Major Facilitator Superfamily

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      28394642..28406592 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435280.1XP_047291236.1  proton-coupled folate transporter isoform X4

    2. XM_047435279.1XP_047291235.1  proton-coupled folate transporter isoform X3

    3. XM_017024110.2XP_016879599.1  proton-coupled folate transporter isoform X2

    4. XM_005277786.4XP_005277843.1  proton-coupled folate transporter isoform X1

      UniProtKB/TrEMBL
      B4DJ17
      Conserved Domains (2) summary
      cd06174
      Location:73230
      MFS; The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of ...
      pfam07690
      Location:94291
      MFS_1; Major Facilitator Superfamily

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      29336494..29348065 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314929.1XP_054170904.1  proton-coupled folate transporter isoform X1

      UniProtKB/TrEMBL
      B4DJ17