Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A6 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied... See more...

Aliases for SLC39A6 Gene

Aliases for SLC39A6 Gene

  • Solute Carrier Family 39 Member 6 2 3 4 5
  • Solute Carrier Family 39 (Metal Ion Transporter), Member 6 2 3
  • Solute Carrier Family 39 (Zinc Transporter), Member 6 2 3
  • Estrogen-Regulated Protein LIV-1 3 4
  • Zrt- And Irt-Like Protein 6 3 4
  • Zinc Transporter ZIP6 3 4
  • ZIP-6 3 4
  • ZIP6 3 4
  • LIV-1 Protein, Estrogen Regulated 3
  • LIV-1 3
  • LIV1 4

External Ids for SLC39A6 Gene

Previous GeneCards Identifiers for SLC39A6 Gene

  • GC18M033576
  • GC18M031941
  • GC18M031940
  • GC18M031943
  • GC18M033688
  • GC18M030547

Summaries for SLC39A6 Gene

Entrez Gene Summary for SLC39A6 Gene

  • Zinc is an essential cofactor for hundreds of enzymes. It is involved in protein, nucleic acid, carbohydrate, and lipid metabolism, as well as in the control of gene transcription, growth, development, and differentiation. SLC39A6 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Mar 2008]

GeneCards Summary for SLC39A6 Gene

SLC39A6 (Solute Carrier Family 39 Member 6) is a Protein Coding gene. Diseases associated with SLC39A6 include Acrodermatitis Enteropathica, Zinc-Deficiency Type and Breast Cancer. Among its related pathways are Metal ion SLC transporters and NRF2 pathway. Gene Ontology (GO) annotations related to this gene include metal ion transmembrane transporter activity and zinc ion transmembrane transporter activity. An important paralog of this gene is SLC39A10.

UniProtKB/Swiss-Prot Summary for SLC39A6 Gene

Gene Wiki entry for SLC39A6 Gene

Additional gene information for SLC39A6 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SLC39A6 Gene

Genomics for SLC39A6 Gene

GeneHancer (GH) Regulatory Elements for SLC39A6 Gene

Promoters and enhancers for SLC39A6 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18J036127 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.7 -0.7 -653 5.3 HNRNPK ZBTB40 ZNF217 EP300 SIN3A MYC NRF1 POLR2G SP1 GTF2E2 ELP2 SLC39A6 ENSG00000268573 KIAA1328 ZNF397 ENSG00000260552 MOCOS ENSG00000267404 HSALNG0120935
GH18J035610 Enhancer 1.3 Ensembl ENCODE CraniofacialAtlas 4.9 +512.5 512513 15.8 ZBTB40 ZSCAN5C SP1 FOS ZNF10 EP300 TRIM28 KLF7 TRIM22 ATF2 ENSG00000268573 GALNT1 ZNF397 SLC39A6 piR-57176-304 ENSG00000266965 lnc-GALNT1-2
GH18J035153 Enhancer 0.8 Ensembl ENCODE 4.1 +975.2 975176 3.3 MXI1 FOXA2 CBFB GATA3 SAP130 SPI1 FOXP1 GABPA SMAD4 RCOR1 lnc-ZSCAN30-4 lnc-MAPRE2-1 ZSCAN30 SLC39A6 lnc-ZSCAN30-3
GH18J035526 Enhancer 0.6 ENCODE dbSUPER 5.2 +602.9 602882 0.2 CEBPG CEBPB SPI1 ZNF384 GLIS1 CEBPA SLC39A6 INO80C lnc-GALNT1-2
GH18J035732 Enhancer 0.7 Ensembl ENCODE 4.3 +397.0 396955 1.1 ZNF316 NFE2 NFE2L1 MAFK MAFG NFE2L2 MAFF BACH1 EMSY GALNT1 SLC39A6 piR-56133-100 ENSG00000267397
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SLC39A6 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SLC39A6

Top Transcription factor binding sites by QIAGEN in the SLC39A6 gene promoter:
  • CP2
  • FOXO3
  • FOXO3a
  • FOXO3b
  • FOXO4
  • GATA-1
  • POU2F1
  • POU2F1a
  • Roaz
  • STAT3

Genomic Locations for SLC39A6 Gene

Genomic Locations for SLC39A6 Gene
chr18:36,108,531-36,129,814
(GRCh38/hg38)
Size:
21,284 bases
Orientation:
Minus strand
chr18:33,688,494-33,709,357
(GRCh37/hg19)
Size:
20,864 bases
Orientation:
Minus strand

Genomic View for SLC39A6 Gene

Genes around SLC39A6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC39A6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC39A6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC39A6 Gene

Proteins for SLC39A6 Gene

  • Protein details for SLC39A6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13433-S39A6_HUMAN
    Recommended name:
    Zinc transporter ZIP6
    Protein Accession:
    Q13433
    Secondary Accessions:
    • B4DR49
    • B4E224
    • Q8IXR3
    • Q96HP5

    Protein attributes for SLC39A6 Gene

    Size:
    755 amino acids
    Molecular mass:
    85047 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAG61161.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for SLC39A6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC39A6 Gene

Post-translational modifications for SLC39A6 Gene

  • N-glycosylated.
  • Glycosylation at Asn283, Asn67, Ser196, Ser219, Ser221, Thr222, Ser225, Thr227, Ser228, Asn241, Asn266, and Asn684
  • Ubiquitination at Lys77
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • S39A6_HUMAN (1908)

Other Protein References for SLC39A6 Gene

No data available for DME Specific Peptides for SLC39A6 Gene

Domains & Families for SLC39A6 Gene

Gene Families for SLC39A6 Gene

Protein Domains for SLC39A6 Gene

Blocks:
  • Zinc transporter ZIP
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SLC39A6 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ50261, highly similar to Zinc transporter SLC39A6 (B4DWH6_HUMAN)
  • Zrt- and Irt-like protein 6 (S39A6_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13433

UniProtKB/Swiss-Prot:

S39A6_HUMAN :
  • Belongs to the ZIP transporter (TC 2.A.5) family.
Family:
  • Belongs to the ZIP transporter (TC 2.A.5) family.
genes like me logo Genes that share domains with SLC39A6: view

Function for SLC39A6 Gene

Molecular function for SLC39A6 Gene

UniProtKB/Swiss-Prot Function:
May act as a zinc-influx transporter.
UniProtKB/Swiss-Prot Induction:
Up-regulated by estrogen in breast cancer cells lines.

Phenotypes From GWAS Catalog for SLC39A6 Gene

Gene Ontology (GO) - Molecular Function for SLC39A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005385 zinc ion transmembrane transporter activity IDA 15642354
GO:0046873 metal ion transmembrane transporter activity IEA --
genes like me logo Genes that share ontologies with SLC39A6: view
genes like me logo Genes that share phenotypes with SLC39A6: view

Animal Models for SLC39A6 Gene

MGI Knock Outs for SLC39A6:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC39A6

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLC39A6 Gene

Localization for SLC39A6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC39A6 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
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 SLC39A6 gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 3
extracellular 2
nucleus 2
cytosol 2
lysosome 2
golgi apparatus 2
cytoskeleton 1
mitochondrion 1
endosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
  • Cytosol (1)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SLC39A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005623 cell IEA --
GO:0005783 endoplasmic reticulum IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane IDA 15642354
GO:0009986 cell surface HDA 19581412
genes like me logo Genes that share ontologies with SLC39A6: view

Pathways & Interactions for SLC39A6 Gene

genes like me logo Genes that share pathways with SLC39A6: view

Gene Ontology (GO) - Biological Process for SLC39A6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006829 zinc ion transport IEA --
GO:0006882 cellular zinc ion homeostasis IDA 15642354
GO:0030001 metal ion transport IEA --
GO:0055085 transmembrane transport IEA --
genes like me logo Genes that share ontologies with SLC39A6: view

No data available for SIGNOR curated interactions for SLC39A6 Gene

Drugs & Compounds for SLC39A6 Gene

No Compound Related Data Available

Transcripts for SLC39A6 Gene

mRNA/cDNA for SLC39A6 Gene

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

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC39A6 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11
SP1: - - - -
SP2:
SP3: -
SP4:
SP5: -

Relevant External Links for SLC39A6 Gene

GeneLoc Exon Structure for
SLC39A6

Expression for SLC39A6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SLC39A6 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SLC39A6 Gene

This gene is overexpressed in Fetal Brain (33.9) and Frontal cortex (25.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SLC39A6 Gene



Protein tissue co-expression partners for SLC39A6 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SLC39A6

SOURCE GeneReport for Unigene cluster for SLC39A6 Gene:

Hs.79136

mRNA Expression by UniProt/SwissProt for SLC39A6 Gene:

Q13433-S39A6_HUMAN
Tissue specificity: Highly expressed in the breast, prostate, placenta, kidney, pituitary and corpus callosum. Weakly expressed in heart and intestine. Also highly expressed in cells derived from an adenocarcinoma of the cervix and lung carcinoma.

Evidence on tissue expression from TISSUES for SLC39A6 Gene

  • Eye(4.2)
  • Nervous system(3)
genes like me logo Genes that share expression patterns with SLC39A6: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC39A6 Gene

Orthologs for SLC39A6 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC39A6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLC39A6 31 30
  • 99.43 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SLC39A6 31 30
  • 92.88 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SLC39A6 31 30
  • 91.97 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Slc39a6 30
  • 85.46 (n)
mouse
(Mus musculus)
Mammalia Slc39a6 17 31 30
  • 84.53 (n)
oppossum
(Monodelphis domestica)
Mammalia SLC39A6 31
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SLC39A6 31
  • 72 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLC39A6 31 30
  • 70.4 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SLC39A6 31
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487349 30
  • 67.12 (n)
zebrafish
(Danio rerio)
Actinopterygii slc39a6 31 30
  • 62.58 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta foi 31
  • 26 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 45 (a)
OneToMany
Species where no ortholog for SLC39A6 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)
  • worm (Caenorhabditis elegans)

Evolution for SLC39A6 Gene

ENSEMBL:
Gene Tree for SLC39A6 (if available)
TreeFam:
Gene Tree for SLC39A6 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SLC39A6: view image

Paralogs for SLC39A6 Gene

Paralogs for SLC39A6 Gene

(1) SIMAP similar genes for SLC39A6 Gene using alignment to 2 proteins:

  • S39A6_HUMAN
  • K7EQ91_HUMAN
genes like me logo Genes that share paralogs with SLC39A6: view

Variants for SLC39A6 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SLC39A6 Gene

SNP ID Clinical significance and condition Chr 18 pos Variation AA Info Type
rs1789528 - p.Glu119Asp

Additional dbSNP identifiers (rs#s) for SLC39A6 Gene

Structural Variations from Database of Genomic Variants (DGV) for SLC39A6 Gene

Variant ID Type Subtype PubMed ID
nsv576651 CNV loss 21841781
nsv576652 CNV loss 21841781

Variation tolerance for SLC39A6 Gene

Residual Variation Intolerance Score: 9.02% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.42; 27.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC39A6 Gene

Human Gene Mutation Database (HGMD)
SLC39A6
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC39A6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC39A6 Gene

Disorders for SLC39A6 Gene

MalaCards: The human disease database

(2) MalaCards diseases for SLC39A6 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
acrodermatitis enteropathica, zinc-deficiency type
  • aez
breast cancer
  • breast cancer, familial
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SLC39A6

genes like me logo Genes that share disorders with SLC39A6: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLC39A6 Gene

Publications for SLC39A6 Gene

  1. Structure-function analysis of LIV-1, the breast cancer-associated protein that belongs to a new subfamily of zinc transporters. (PMID: 12839489) Taylor KM … Nicholson RI (The Biochemical journal 2003) 2 3 4 23 54
  2. The LZT proteins; the LIV-1 subfamily of zinc transporters. (PMID: 12659941) Taylor KM … Nicholson RI (Biochimica et biophysica acta 2003) 2 3 23 54
  3. Concordant correlation of LIV-1 and E-cadherin expression in human breast cancer cell MCF-7. (PMID: 18330719) Shen H … Guo J (Molecular biology reports 2009) 3 23 54
  4. LIV-1 suppression inhibits HeLa cell invasion by targeting ERK1/2-Snail/Slug pathway. (PMID: 17825787) Zhao L … Li X (Biochemical and biophysical research communications 2007) 3 23 54
  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 54

Products for SLC39A6 Gene

Sources for SLC39A6 Gene