Aliases for SLC46A2 Gene

Aliases for SLC46A2 Gene

  • Solute Carrier Family 46 Member 2 2 3 4 5
  • Thymic Stromal Cotransporter Homolog 3 4
  • Thymic Stromal Co-Transporter 2 3
  • Ly110 2 3
  • TSCOT 3 4
  • Solute Carrier Family 46, Member 2 2
  • SLC46A2 5

External Ids for SLC46A2 Gene

Previous HGNC Symbols for SLC46A2 Gene


Previous GeneCards Identifiers for SLC46A2 Gene

  • GC09M114683
  • GC09M115641
  • GC09M085239

Summaries for SLC46A2 Gene

GeneCards Summary for SLC46A2 Gene

SLC46A2 (Solute Carrier Family 46 Member 2) is a Protein Coding gene. Diseases associated with SLC46A2 include Folate Malabsorption, Hereditary. Gene Ontology (GO) annotations related to this gene include symporter activity. An important paralog of this gene is SLC46A3.

UniProtKB/Swiss-Prot Summary for SLC46A2 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLC46A2 Gene

Genomics for SLC46A2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SLC46A2 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
GH09J112890 Promoter/Enhancer 1.1 EPDnew Ensembl dbSUPER 261.4 +4.7 4737 1.6 CTCF GLIS1 EZH2 MTA1 USF2 USF1 SLC46A2 HSALNG0073797 SNX30 ENSG00000226609 ENSG00000271631
GH09J112893 Promoter/Enhancer 1.1 FANTOM5 Ensembl ENCODE dbSUPER 257.8 +0.9 888 1.8 BATF MAFK MYC SLC46A2 SNX30 SLC31A2 FKBP15 HSALNG0073797
GH09J112866 Promoter/Enhancer 1.4 Ensembl ENCODE dbSUPER 22.8 +27.1 27115 4.5 IKZF1 ZNF217 HOMEZ ARNT FOXA2 VEZF1 NBN SMAD4 SAP130 ZEB2 HSALNG0073791 SLC46A2 ENSG00000226609 SNX30 SLC31A2 INIP piR-55804 lnc-SLC46A2-1
GH09J112860 Promoter/Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 19.3 +32.6 32575 3.5 GABPA SPI1 POLR2A MYC MAX EGR1 MTA3 KDM1A GABPB1 CEBPB SLC46A2 SNX30 SLC31A2 ENSG00000226609 ENSG00000271631 FKBP15 HSALNG0073791 HG984071
GH09J112749 Promoter/Enhancer 2 Ensembl ENCODE CraniofacialAtlas dbSUPER 9.7 +142.1 142076 8.1 TBP MXD4 MNT SMAD5 ETS1 IRF2 HES1 MBD2 ZNF217 POLR2A INIP SLC46A2 SNX30 ENSG00000226609 ENSG00000271631 piR-57134-114
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC46A2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLC46A2

Top Transcription factor binding sites by QIAGEN in the SLC46A2 gene promoter:
  • CREB
  • deltaCREB
  • FAC1
  • GATA-2
  • Ik-2
  • POU2F1
  • POU2F1a
  • Roaz
  • USF-1
  • USF1

Genomic Locations for SLC46A2 Gene

Latest Assembly
16,619 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
11,957 bases
Minus strand

(GRCh37/hg19 by Ensembl)
11,994 bases
Minus strand

Genomic View for SLC46A2 Gene

Genes around SLC46A2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC46A2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC46A2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC46A2 Gene

Proteins for SLC46A2 Gene

  • Protein details for SLC46A2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Thymic stromal cotransporter homolog
    Protein Accession:
    Secondary Accessions:
    • B1ALK1
    • Q86VT0
    • Q96NE2

    Protein attributes for SLC46A2 Gene

    475 amino acids
    Molecular mass:
    51067 Da
    Quaternary structure:
    No Data Available

neXtProt entry for SLC46A2 Gene

Post-translational modifications for SLC46A2 Gene

Other Protein References for SLC46A2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SLC46A2 Gene

Domains & Families for SLC46A2 Gene

Gene Families for SLC46A2 Gene

Protein Domains for SLC46A2 Gene

Suggested Antigen Peptide Sequences for SLC46A2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ95197, Homo sapiens thymic stromal co-transporter (TSCOT), mRNA (B1ALK1_HUMAN)
  • Solute carrier family 46 member 2 (TSCOT_HUMAN)

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 SLC46A2: view

Function for SLC46A2 Gene

Molecular function for SLC46A2 Gene

UniProtKB/Swiss-Prot Function:
May act as a transporter.

Phenotypes From GWAS Catalog for SLC46A2 Gene

Gene Ontology (GO) - Molecular Function for SLC46A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015293 symporter activity NAS 10978518
GO:0022857 transmembrane transporter activity IEA --
genes like me logo Genes that share ontologies with SLC46A2: view
genes like me logo Genes that share phenotypes with SLC46A2: view

Animal Models for SLC46A2 Gene

MGI Knock Outs for SLC46A2:

Animal Models for research

  • Taconic Biosciences Mouse Models for SLC46A2

miRNA for SLC46A2 Gene

miRTarBase miRNAs that target SLC46A2

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC46A2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLC46A2 Gene

Localization for SLC46A2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC46A2 Gene

Cell 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 SLC46A2 gene
Compartment Confidence
plasma membrane 4
extracellular 1
endoplasmic reticulum 1
endosome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for SLC46A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0009986 cell surface IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,NAS 10978518
genes like me logo Genes that share ontologies with SLC46A2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SLC46A2 Gene

Pathways & Interactions for SLC46A2 Gene

PathCards logo

SuperPathways for SLC46A2 Gene

No Data Available

Interacting Proteins for SLC46A2 Gene

Gene Ontology (GO) - Biological Process for SLC46A2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0043029 T cell homeostasis IEA --
GO:0045580 regulation of T cell differentiation IEA --
GO:0048538 thymus development IEA --
GO:0055085 transmembrane transport IEA --
GO:0070233 negative regulation of T cell apoptotic process IEA --
genes like me logo Genes that share ontologies with SLC46A2: view

No data available for Pathways by source and SIGNOR curated interactions for SLC46A2 Gene

Drugs & Compounds for SLC46A2 Gene

No Compound Related Data Available

Transcripts for SLC46A2 Gene

mRNA/cDNA for SLC46A2 Gene

5 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SLC46A2

Alternative Splicing Database (ASD) splice patterns (SP) for SLC46A2 Gene

No ASD Table

Relevant External Links for SLC46A2 Gene

GeneLoc Exon Structure for

Expression for SLC46A2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SLC46A2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC46A2 Gene

This gene is overexpressed in Skin - Sun Exposed (Lower leg) (x16.7), Skin - Not Sun Exposed (Suprapubic) (x12.3), Whole Blood (x6.2), Lung (x4.4), and Bladder (x4.3).

Protein differential expression in normal tissues from HIPED for SLC46A2 Gene

This gene is overexpressed in Breast (47.4) and Heart (21.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SLC46A2 Gene

Protein tissue co-expression partners for SLC46A2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLC46A2

SOURCE GeneReport for Unigene cluster for SLC46A2 Gene:


mRNA Expression by UniProt/SwissProt for SLC46A2 Gene:

Tissue specificity: Strongly expressed in the adult thymus. Expressed in spleen, lymph nodes, thymus, PBL, bone marrow and fetal liver.

Evidence on tissue expression from TISSUES for SLC46A2 Gene

  • Lung(4.3)
  • Blood(4.2)
genes like me logo Genes that share expression patterns with SLC46A2: view

Primer products for research

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC46A2 Gene

Orthologs for SLC46A2 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC46A2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SLC46A2 30 31
  • 99.51 (n)
(Canis familiaris)
Mammalia SLC46A2 30 31
  • 85.55 (n)
(Bos Taurus)
Mammalia SLC46A2 30
  • 85.55 (n)
  • 81 (a)
(Mus musculus)
Mammalia Slc46a2 30 17 31
  • 80.69 (n)
(Rattus norvegicus)
Mammalia Slc46a2 30
  • 80.1 (n)
(Monodelphis domestica)
Mammalia SLC46A2 31
  • 76 (a)
(Ornithorhynchus anatinus)
Mammalia SLC46A2 31
  • 73 (a)
(Gallus gallus)
Aves SLC46A2 30 31
  • 63.55 (n)
(Anolis carolinensis)
Reptilia SLC46A2 31
  • 56 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100487203 30
  • 54.91 (n)
(Danio rerio)
Actinopterygii LOC100002406 30
  • 55.13 (n)
SLC46A2 31
  • 45 (a)
Fruit Fly
(Drosophila melanogaster)
Insecta CG30344 31
  • 17 (a)
CG42514 31
  • 17 (a)
CG8046 31
  • 16 (a)
CG30345 31
  • 16 (a)
CG8008 31
  • 15 (a)
CG15553 31
  • 15 (a)
CG15890 31
  • 14 (a)
CG31321 31
  • 13 (a)
(Caenorhabditis elegans)
Secernentea Y4C6B.5 31
  • 21 (a)
Y43F8A.5 31
  • 14 (a)
Species where no ortholog for SLC46A2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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 Vase (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 SLC46A2 Gene

Gene Tree for SLC46A2 (if available)
Gene Tree for SLC46A2 (if available)
Evolutionary constrained regions (ECRs) for SLC46A2: view image

Paralogs for SLC46A2 Gene

Paralogs for SLC46A2 Gene

genes like me logo Genes that share paralogs with SLC46A2: view

Variants for SLC46A2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLC46A2 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs114822090 Benign: not provided 112,889,956(-) G/A
NM_033051.4(SLC46A2):c.726C>T (p.Ala242=)
rs16917454 Benign: not provided. - 112,889,585(-) G/Ap.Ala366Val
NM_033051.4(SLC46A2):c.1097C>T (p.Ala366Val)
rs7021942 Benign: not provided 112,889,905(-) A/G
NM_033051.4(SLC46A2):c.777T>C (p.Asp259=)
rs7022287 Benign: not provided 112,889,923(-) G/A
NM_033051.4(SLC46A2):c.759C>T (p.Tyr253=)

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SLC46A2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SLC46A2 Gene

Variant ID Type Subtype PubMed ID
esv2422302 CNV deletion 17116639
esv2759710 CNV gain 17122850
nsv529036 CNV loss 19592680

Variation tolerance for SLC46A2 Gene

Residual Variation Intolerance Score: 84.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.93; 67.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC46A2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC46A2 Gene

Disorders for SLC46A2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SLC46A2 Gene - From: COP

Disorder Aliases PubMed IDs
folate malabsorption, hereditary
  • hereditary folate malabsorption
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SLC46A2

Genetic Association Database
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with SLC46A2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLC46A2 Gene

Publications for SLC46A2 Gene

  1. Characterization of the mouse gene, human promoter and human cDNA of TSCOT reveals strong interspecies homology. (PMID: 10978518) Chen C … Flomerfelt FA (Biochimica et biophysica acta 2000) 2 3 4 23
  2. A putative 12-transmembrane domain cotransporter associated with apical membranes of the epididymal duct. (PMID: 12826694) Obermann H … Kirchhoff C (Journal of andrology 2003) 2 3 23
  3. Polymorphisms in 9q32 and TSCOT are linked to cervical cancer in affected sib-pairs with high mean age at diagnosis. (PMID: 18392855) Engelmark MT … Gyllensten UB (Human genetics 2008) 3 23
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4

Products for SLC46A2 Gene

  • Biorbyt antibodies for SLC46A2

Sources for SLC46A2 Gene