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Aliases for SLC46A3 Gene

Aliases for SLC46A3 Gene

  • Solute Carrier Family 46 Member 3 2 3 3 5
  • Solute Carrier Family 46, Member 3 2
  • FKSG16 3

External Ids for SLC46A3 Gene

Previous GeneCards Identifiers for SLC46A3 Gene

  • GC13M028173
  • GC13M029274
  • GC13M010095

Summaries for SLC46A3 Gene

Entrez Gene Summary for SLC46A3 Gene

  • 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]

GeneCards Summary for SLC46A3 Gene

SLC46A3 (Solute Carrier Family 46 Member 3) is a Protein Coding gene. An important paralog of this gene is SLC46A1.

Additional gene information for SLC46A3 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC46A3 Gene

Genomics for SLC46A3 Gene

GeneHancer (GH) Regulatory Elements for SLC46A3 Gene

Promoters and enhancers for SLC46A3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH13J028715 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 673.8 +1.0 970 5.8 PKNOX1 ATF1 SIN3A FEZF1 ZNF2 YY1 GLIS2 ELK1 ZNF207 ZNF143 SLC46A3 POMP CYP51A1P2 GC13M028704 RNU6-53P
GH13J028749 Enhancer 1.4 FANTOM5 Ensembl ENCODE 23.4 -33.8 -33801 6.3 PKNOX1 FOXA2 NEUROD1 SIN3A YY1 ZNF766 FOS RXRA JUNB REST SLC46A3 CYP51A1P2 RNU6-53P URAD MTUS2 ENSG00000277227
GH13J028693 Enhancer 1 Ensembl ENCODE dbSUPER 11.8 +25.1 25119 1 SOX13 FOXA2 SP5 FOXA3 SIN3A CBFA2T3 MNT FOXA1 TEAD3 NFIL3 SLC46A3 CYP51A1P2 GC13M028704 RNU6-53P GC13P028679 PIR58876
GH13J028707 Enhancer 1.2 Ensembl ENCODE dbSUPER 8.9 +10.7 10688 1.4 PKNOX1 SMAD1 STAT5A BATF IRF4 ZNF207 ATF7 FOS ETV6 BCLAF1 SLC46A3 GC13M028704 RNU6-53P
GH13J028794 Enhancer 0.6 ENCODE 17.8 -75.7 -75693 1.2 SP1 JUND ATF4 RXRA CEBPA MAX CEBPG HNF4A GABPA SLC46A3 POMP POM121L13P MTUS2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC46A3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC46A3 gene promoter:
  • PPAR-gamma1
  • PPAR-gamma2
  • Cart-1
  • FOXF2
  • POU2F1
  • POU2F1a
  • CUTL1
  • Meis-1
  • Meis-1a
  • Meis-1b

Genomic Locations for SLC46A3 Gene

Genomic Locations for SLC46A3 Gene
18,950 bases
Minus strand
18,950 bases
Minus strand

Genomic View for SLC46A3 Gene

Genes around SLC46A3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC46A3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC46A3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC46A3 Gene

Proteins for SLC46A3 Gene

  • Protein details for SLC46A3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Solute carrier family 46 member 3
    Protein Accession:
    Secondary Accessions:
    • Q3ZCV8
    • Q6NUK5
    • Q6P9B3
    • Q6ZVG5
    • Q96QA1

    Protein attributes for SLC46A3 Gene

    461 amino acids
    Molecular mass:
    51519 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAC85896.1; Type=Frameshift; Positions=353; Evidence={ECO:0000305};

    Alternative splice isoforms for SLC46A3 Gene


neXtProt entry for SLC46A3 Gene

Post-translational modifications for SLC46A3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SLC46A3 Gene

Antibody Products

  • Abcam antibodies for SLC46A3
  • Boster Bio Antibodies for SLC46A3

No data available for DME Specific Peptides for SLC46A3 Gene

Domains & Families for SLC46A3 Gene

Gene Families for SLC46A3 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC46A3 Gene


Suggested Antigen Peptide Sequences for SLC46A3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the major facilitator superfamily. SLC46A family.
  • Belongs to the major facilitator superfamily. SLC46A family.
genes like me logo Genes that share domains with SLC46A3: view

Function for SLC46A3 Gene

Phenotypes From GWAS Catalog for SLC46A3 Gene

Gene Ontology (GO) - Molecular Function for SLC46A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with SLC46A3: view
genes like me logo Genes that share phenotypes with SLC46A3: view

Animal Models for SLC46A3 Gene

MGI Knock Outs for SLC46A3:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC46A3

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLC46A3 Gene

Localization for SLC46A3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC46A3 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC46A3 gene
Compartment Confidence
extracellular 5
plasma membrane 4
cytoskeleton 2
cytosol 2
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (2)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SLC46A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome HDA 19056867
genes like me logo Genes that share ontologies with SLC46A3: view

Pathways & Interactions for SLC46A3 Gene

SuperPathways for SLC46A3 Gene

No Data Available

Interacting Proteins for SLC46A3 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
Selected Interacting proteins: Q7Z3Q1-S46A3_HUMAN ENSP00000370192 for SLC46A3 Gene via IID STRING

Gene Ontology (GO) - Biological Process for SLC46A3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008150 biological_process ND --
GO:0055085 transmembrane transport IEA --
genes like me logo Genes that share ontologies with SLC46A3: view

No data available for Pathways by source and SIGNOR curated interactions for SLC46A3 Gene

Drugs & Compounds for SLC46A3 Gene

No Compound Related Data Available

Transcripts for SLC46A3 Gene

mRNA/cDNA for SLC46A3 Gene

Unigene Clusters for SLC46A3 Gene

Solute carrier family 46, member 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC46A3

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC46A3 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7
SP1: - - -
SP2: - -
SP3: -

Relevant External Links for SLC46A3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SLC46A3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC46A3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC46A3 Gene

This gene is overexpressed in Liver (x5.0).

Protein differential expression in normal tissues from HIPED for SLC46A3 Gene

This gene is overexpressed in Heart (33.9), Liver (23.2), and Testis (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SLC46A3 Gene

Protein tissue co-expression partners for SLC46A3 Gene

NURSA nuclear receptor signaling pathways regulating expression of SLC46A3 Gene:


SOURCE GeneReport for Unigene cluster for SLC46A3 Gene:


Evidence on tissue expression from TISSUES for SLC46A3 Gene

  • Nervous system(4.4)
  • Lung(3.3)
genes like me logo Genes that share expression patterns with SLC46A3: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC46A3 Gene

Orthologs for SLC46A3 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC46A3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC46A3 34 33
  • 99.64 (n)
(Canis familiaris)
Mammalia SLC46A3 34 33
  • 88.29 (n)
(Bos Taurus)
Mammalia SLC46A3 34 33
  • 83.22 (n)
(Mus musculus)
Mammalia Slc46a3 16 34 33
  • 76.52 (n)
(Rattus norvegicus)
Mammalia Slc46a3 33
  • 75.72 (n)
(Monodelphis domestica)
Mammalia SLC46A3 34
  • 72 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 67 (a)
-- 34
  • 67 (a)
(Gallus gallus)
Aves SLC46A3 34 33
  • 61.44 (n)
(Anolis carolinensis)
Reptilia SLC46A3 34
  • 43 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia slc46a3 33
  • 54.75 (n)
(Danio rerio)
Actinopterygii si:dkey-5g14.1 33
  • 52.7 (n)
SLC46A3 (2 of 2) 34
  • 43 (a)
slc46a3 34
  • 38 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004562 33
  • 41.89 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG15890 34 33
  • 39.94 (n)
CG42514 34
  • 17 (a)
CG30345 34
  • 17 (a)
CG8046 34
  • 16 (a)
CG15553 34
  • 16 (a)
CG30344 34
  • 16 (a)
CG31321 34
  • 15 (a)
CG8008 34
  • 15 (a)
(Caenorhabditis elegans)
Secernentea Y4C6B.5 34
  • 22 (a)
Y43F8A.5 34
  • 16 (a)
Species where no ortholog for SLC46A3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC46A3 Gene

Gene Tree for SLC46A3 (if available)
Gene Tree for SLC46A3 (if available)
Evolutionary constrained regions (ECRs) for SLC46A3: view image

Paralogs for SLC46A3 Gene

Paralogs for SLC46A3 Gene

(1) SIMAP similar genes for SLC46A3 Gene using alignment to 1 proteins:

  • S46A3_HUMAN
genes like me logo Genes that share paralogs with SLC46A3: view

Variants for SLC46A3 Gene

Sequence variations from dbSNP and Humsavar for SLC46A3 Gene

SNP ID Clin Chr 13 pos Variation AA Info Type
rs193920747 uncertain-significance, Malignant tumor of prostate 28,704,055(-) C/T coding_sequence_variant, missense_variant
rs1000007679 -- 28,704,488(-) C/T intron_variant
rs1000212230 -- 28,714,915(-) A/G intron_variant
rs1000304951 -- 28,717,458(-) C/T intron_variant
rs1000337639 -- 28,707,120(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC46A3 Gene

Variant ID Type Subtype PubMed ID
nsv832571 CNV loss 17160897
nsv974 CNV insertion 18451855

Variation tolerance for SLC46A3 Gene

Residual Variation Intolerance Score: 70.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.99; 36.82% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC46A3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC46A3 Gene

Disorders for SLC46A3 Gene

Additional Disease Information for SLC46A3

No disorders were found for SLC46A3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SLC46A3 Gene

Publications for SLC46A3 Gene

  1. Genome-wide association study identifies variants associated with histologic features of nonalcoholic Fatty liver disease. (PMID: 20708005) Chalasani N … Nonalcoholic Steatohepatitis Clinical Research Network (Gastroenterology 2010) 3 44 58
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  3. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin EL … Gygi SP (Cell 2015) 3 58
  4. SLC46A3 Is Required to Transport Catabolites of Noncleavable Antibody Maytansine Conjugates from the Lysosome to the Cytoplasm. (PMID: 26631267) Hamblett KJ … Fanslow WC (Cancer research 2015) 3 58
  5. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PMID: 23251661) Comuzzie AG … Butte NF (PloS one 2012) 3 58

Products for SLC46A3 Gene

Sources for SLC46A3 Gene

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