U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SLC39A6 solute carrier family 39 member 6 [ Homo sapiens (human) ]

Gene ID: 25800, updated on 17-Jun-2024

Summary

Official Symbol
SLC39A6provided by HGNC
Official Full Name
solute carrier family 39 member 6provided by HGNC
Primary source
HGNC:HGNC:18607
See related
Ensembl:ENSG00000141424 MIM:608731; AllianceGenome:HGNC:18607
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LIV1; ZIP6; LIV-1
Summary
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]
Expression
Broad expression in prostate (RPKM 62.4), endometrium (RPKM 31.1) and 24 other tissues See more
Orthologs
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

See SLC39A6 in Genome Data Viewer
Location:
18q12.2
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (36108531..36129340, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (36300097..36320904, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (33688494..33709303, complement)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33552432-33553324 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr18:33564018-33565217 Neighboring gene chromosome 18 open reading frame 21 Neighboring gene regulation of nuclear pre-mRNA domain containing 1A Neighboring gene Sharpr-MPRA regulatory region 15530 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:33647245-33647760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:33664612-33665166 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:33666275-33666828 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:33678780-33678940 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33709607-33710112 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33709101-33709606 Neighboring gene elongator acetyltransferase complex subunit 2 Neighboring gene MPRA-validated peak3116 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:33765682-33766504 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:33767264-33767527 Neighboring gene uncharacterized LOC124904286 Neighboring gene cell fate and sterol metabolism associated divergent transcript of MOCOS Neighboring gene molybdenum cofactor sulfurase

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Genome-wide association study identifies common variants in SLC39A6 associated with length of survival in esophageal squamous-cell carcinoma.
EBI GWAS Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of SLC39A6 PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables monoatomic cation:bicarbonate symporter activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables zinc ion transmembrane transporter activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables zinc ion transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
enables zinc ion transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables zinc ion transmembrane transporter activity TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
located_in apical plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in cell surface HDA PubMed 
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
located_in lamellipodium membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in membrane raft IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
zinc transporter ZIP6
Names
LIV-1 protein, estrogen regulated
ZIP-6
ZRT/IRT-like protein 6
estrogen-regulated protein LIV-1
solute carrier family 39 (metal ion transporter), member 6
solute carrier family 39 (zinc transporter), member 6
zinc transporter 6
zrt- and Irt-like protein 6

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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.

mRNA and Protein(s)

  1. NM_001099406.2NP_001092876.1  zinc transporter ZIP6 isoform 2

    See identical proteins and their annotated locations for NP_001092876.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and 3' UTR, and lacks exons in the 5' and 3' coding regions (compared to variant 1), resulting in the use of a downstream translation initiation codon. The encoded protein (isoform 2) is shorter at both the N- and C-termini, compared to isoform 1.
    Source sequence(s)
    AC091060, BC039498, DC414741
    Consensus CDS
    CCDS45854.1
    UniProtKB/TrEMBL
    B4DWH6
    Related
    ENSP00000401139.1, ENST00000440549.6
    Conserved Domains (1) summary
    pfam02535
    Location:48431
    Zip; ZIP Zinc transporter
  2. NM_012319.4NP_036451.4  zinc transporter ZIP6 isoform 1 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC091060
    Consensus CDS
    CCDS42428.1
    UniProtKB/Swiss-Prot
    B4DR49, B4E224, Q13433, Q8IXR3, Q96HP5
    Related
    ENSP00000269187.4, ENST00000269187.10
    Conserved Domains (1) summary
    pfam02535
    Location:323742
    Zip; ZIP Zinc transporter

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_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    36108531..36129340 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    36300097..36320904 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)