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    SLC46A3 solute carrier family 46 member 3 [ Homo sapiens (human) ]

    Gene ID: 283537, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SLC46A3provided by HGNC
    Official Full Name
    solute carrier family 46 member 3provided by HGNC
    Primary source
    HGNC:HGNC:27501
    See related
    Ensembl:ENSG00000139508 MIM:616764; AllianceGenome:HGNC:27501
    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
    FKSG16
    Summary
    The protein encoded by this gene is a member of a transmembrane protein family that transports small molecules across membranes. The encoded protein has been found in lysosomal membranes, where it can transport catabolites from the lysosomes to the cytoplasm. This protein has been shown to be an effective transporter of the cytotoxic drug maytansine, which is used in antibody-based targeting of cancer cells. [provided by RefSeq, Dec 2016]
    Expression
    Broad expression in small intestine (RPKM 41.0), duodenum (RPKM 24.5) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC46A3 in Genome Data Viewer
    Location:
    13q12.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (28700080..28718970, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (27923367..27942251, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (29274217..29293107, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene eukaryotic translation initiation factor 4A1 pseudogene 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5217 Neighboring gene proteasome maturation protein Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:29267612-29268144 Neighboring gene uncharacterized LOC124903143 Neighboring gene RNA, U6 small nuclear 53, pseudogene Neighboring gene cytochrome P450 family 51 subfamily A member 1 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5218 Neighboring gene Sharpr-MPRA regulatory region 8918 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr13:29327481-29328226 Neighboring gene POM121 transmembrane nucleoporin like 13, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. SLC46A3 Is Required to Transport Catabolites of Noncleavable Antibody Maytansine Conjugates from the Lysosome to the Cytoplasm. Hamblett KJ, et al. Cancer Res, 2015 Dec 15. PMID 26631267
    2. Identification of candidate genes for human pituitary development by EST analysis. Ma Y, et al. BMC Genomics, 2009 Mar 15. PMID 19284880, Free PMC Article
    3. Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. Chalasani N, et al. Gastroenterology, 2010 Nov. PMID 20708005, Free PMC Article
    4. The SARS-coronavirus-host interactome: identification of cyclophilins as target for pan-coronavirus inhibitors. Pfefferle S, et al. PLoS Pathog, 2011 Oct. PMID 22046132, Free PMC Article
    5. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. our results establish SLC46A3 as a direct transporter of maytansine-based catabolites from the lysosome to the cytoplasm
      Title: SLC46A3 Is Required to Transport Catabolites of Noncleavable Antibody Maytansine Conjugates from the Lysosome to the Cytoplasm.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ42613

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables copper ion transmembrane transporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables symporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to 2,3,7,8-tetrachlorodibenzodioxine IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in copper ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vacuolar transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vacuolar transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lysosomal membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3

    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_053189.2 RefSeqGene

      Range
      5000..23890
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001135919.2 → NP_001129391.1  lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform b precursor

      See identical proteins and their annotated locations for NP_001129391.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks a segment in the 3' coding region, which results in a frameshift, compared to variant 1. The resulting protein has a distinct and longer C-terminus when it is compared to isoform a.
      Source sequence(s)
      AL359454
      Consensus CDS
      CCDS45021.1
      UniProtKB/TrEMBL
      B3KSM7
      Related
      ENSP00000370192.4, ENST00000380814.4
      Conserved Domains (1) summary
      pfam07690
      Location:81 → 399
      MFS_1; Major Facilitator Superfamily

    2. NM_001347960.2 → NP_001334889.1  lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform a precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1 and 3 both encode the same isoform (a).
      Source sequence(s)
      AL359454
      Consensus CDS
      CCDS9332.1
      UniProtKB/Swiss-Prot
      Q3ZCV8, Q6NUK5, Q6P9B3, Q6ZVG5, Q7Z3Q1, Q96QA1
      UniProtKB/TrEMBL
      B3KSM7

    3. NM_181785.4 → NP_861450.1  lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform a precursor

      See identical proteins and their annotated locations for NP_861450.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript yet it encodes the shorter isoform (a). Variants 1 and 3 both encode the same isoform (a).
      Source sequence(s)
      AL359454
      Consensus CDS
      CCDS9332.1
      UniProtKB/Swiss-Prot
      Q3ZCV8, Q6NUK5, Q6P9B3, Q6ZVG5, Q7Z3Q1, Q96QA1
      UniProtKB/TrEMBL
      B3KSM7
      Related
      ENSP00000266943.7, ENST00000266943.11
      Conserved Domains (2) summary
      cd06174
      Location:81 → 409
      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:81 → 399
      MFS_1; Major Facilitator Superfamily

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      28700080..28718970 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005266361.3 → XP_005266418.1  lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform X1

      See identical proteins and their annotated locations for XP_005266418.1

      UniProtKB/TrEMBL
      B3KSM7
      Conserved Domains (1) summary
      pfam07690
      Location:81 → 399
      MFS_1; Major Facilitator Superfamily

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      27923367..27942251 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374476.1 → XP_054230451.1  lysosomal proton-coupled steroid conjugate and bile acid symporter SLC46A3 isoform X1

      UniProtKB/TrEMBL
      B3KSM7
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z3Q1.1 GenPept UniProtKB/Swiss-Prot:Q7Z3Q1

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