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

Gene ID: 283537, updated on 11-Apr-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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Location:
13q12.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (28700080..28718970, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (27923367..27942251, complement)
105.20220307 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)

Genotypes

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 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_2023_10

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

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

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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