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    SLC39A1 solute carrier family 39 member 1 [ Homo sapiens (human) ]

    Gene ID: 27173, updated on 6-Jun-2024

    Summary

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    Official Symbol
    SLC39A1provided by HGNC
    Official Full Name
    solute carrier family 39 member 1provided by HGNC
    Primary source
    HGNC:HGNC:12876
    See related
    Ensembl:ENSG00000143570 MIM:604740; AllianceGenome:HGNC:12876
    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
    ZIP1; ZIRTL
    Summary
    This gene encodes a member of the zinc-iron permease family. The encoded protein is localized to the cell membrane and acts as a zinc uptake transporter. This gene has been linked to prostate cancer, breast cancer, and Alzheimer's disease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]
    Expression
    Ubiquitous expression in placenta (RPKM 41.2), lung (RPKM 24.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC39A1 in Genome Data Viewer
    Location:
    1q21.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (153959110..153968184, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (153096371..153105445, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (153931586..153940660, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928059 Neighboring gene DENN domain containing 4B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1757 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:153918384-153918884 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1758 Neighboring gene CREB regulated transcription coactivator 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1760 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1761 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1762 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:153935601-153936800 Neighboring gene microRNA 6737 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:153939664-153940520 Neighboring gene cAMP responsive element binding protein 3 like 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:153948322-153948971 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:153949621-153950269 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1770 Neighboring gene Sharpr-MPRA regulatory region 11874 Neighboring gene jumping translocation breakpoint Neighboring gene JTB divergent transcript

    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. Decreased SLC39A1 (Solute carrier family 39 member 1) expression predicts unfavorable prognosis in patients with early-stage hepatocellular carcinoma. Zhang Q, et al. Bioengineered, 2021 Dec. PMID 34615436, Free PMC Article
    2. Persistent low expression of hZip1 in mucinous carcinomas of the ovary, colon, stomach and lung. Desouki MM, et al. J Ovarian Res, 2015 Jun 17. PMID 26081940, Free PMC Article
    3. Zinc fortification decreases ZIP1 gene expression of some adolescent females with appropriate plasma zinc levels. Méndez RO, et al. Nutrients, 2014 Jun 11. PMID 24922175, Free PMC Article
    4. hZIP1 that is down-regulated in clear cell renal cell carcinoma is negatively associated with the malignant potential of the tumor. Dong X, et al. Urol Oncol, 2014 Aug. PMID 24878177
    5. Differential zinc accumulation and expression of human zinc transporter 1 (hZIP1) in prostate glands. Johnson LA, et al. Methods, 2010 Dec. PMID 20705137

    See all (51) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Decreased SLC39A1 (Solute carrier family 39 member 1) expression predicts unfavorable prognosis in patients with early-stage hepatocellular carcinoma.
      Title: Decreased SLC39A1 (Solute carrier family 39 member 1) expression predicts unfavorable prognosis in patients with early-stage hepatocellular carcinoma.
    2. Mitochondrial membrane potential is reduced focally at a fission site by the Drp1 recruitment, which is initiated by the interaction of Drp1 with mitochondrial zinc transporter Zip1 and Zn(2+) entry through the Zip1-MCU complex. After division, healthy mitochondria restore MMP levels and participate in the fusion-fission cycle again, but mitochondria that fail to restore MMP undergo mitophagy.
      Title: Drp1-Zip1 Interaction Regulates Mitochondrial Quality Surveillance System.
    3. Despite the fact that these preliminary findings are unlikely to be of much diagnostic significance, these findings suggest that hZip1 plays a fundamental role in the carcinogenesis of mucinous tumors.
      Title: Persistent low expression of hZip1 in mucinous carcinomas of the ovary, colon, stomach and lung.
    4. Data indicate that zinc transporters ZnT1 and Zip1 were the most abundantly expressed zinc transporters in leukocytes.
      Title: The alteration of zinc transporter gene expression is associated with inflammatory markers in obese women.
    5. Data suggest that high zrt- and Irt-like protein 1 (hZIP1) expression may be an indicator of good prognosis in clear cell renal cell carcinoma (ccRCC).
      Title: hZIP1 that is down-regulated in clear cell renal cell carcinoma is negatively associated with the malignant potential of the tumor.
    6. The effect of zinc administered for 27 days on the expression of ZIP1 in peripheral white blood cells is reported.
      Title: Zinc fortification decreases ZIP1 gene expression of some adolescent females with appropriate plasma zinc levels.
    7. RREB-1 overexpression results in down-regulation of hZIP1 and contributes to the loss of hZIP1 expression and zinc in prostate cancer.
      Title: hZIP1 zinc transporter down-regulation in prostate cancer involves the overexpression of ras responsive element binding protein-1 (RREB-1).
    8. Data indicate that the average expression level of zinc transporter Zip2 was significantly higher and zinc transporters Zip6, Zip8 mRNA levels were significantly lower in short stature children than in health controls.
      Title: Zip1, Zip2, and Zip8 mRNA expressions were associated with growth hormone level during the growth hormone provocation test in children with short stature.
    9. Data indicate that the expression levels of ZnT and ZIP families in the three cell lines, when treated with high concentration of ZnSO4, increased and decreased corresponding to their functions, respectively.
      Title: Effects of exogenous zinc on cell cycle, apoptosis and viability of MDAMB231, HepG2 and 293 T cells.
    10. The results of this study showed that signi fi cant positive correlations between ZIP1,ZnT1, and ZnT6 in most brain in patient with Alzheimer's disease.
      Title: Zinc transporter mRNA levels in Alzheimer's disease postmortem brain.
    Submit: New GeneRIF Correction See all GeneRIFs (24)

    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 identifies genetic variants associated with lentiform nucleus volume in N = 1345 young and elderly subjects.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables inorganic cation transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling receptor binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in embryonic cranial skeleton morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in limb development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in monoatomic cation transport TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in zinc ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in zinc ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in zinc ion transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in zinc ion transmembrane transport TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    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

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    Preferred Names
    zinc transporter ZIP1
    Names
    ZRT/IRT-like protein 1
    solute carrier family 39 (zinc transporter), member 1
    solute carrier family 39 (zinc transporter), member 3
    zinc transporter 1
    zrt- and Irt-like protein 1

    NCBI Reference Sequences (RefSeq)

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    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_001271957.2 → NP_001258886.1  zinc transporter ZIP1 isoform a

      See identical proteins and their annotated locations for NP_001258886.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AF132942, AK074943, AL358472, BG704399, DA354647
      Consensus CDS
      CCDS1055.1
      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8
      Related
      ENSP00000357610.1, ENST00000368621.5
      Conserved Domains (1) summary
      pfam02535
      Location:48 → 319
      Zip; ZIP Zinc transporter

    2. NM_001271958.2 → NP_001258887.1  zinc transporter ZIP1 isoform a

      See identical proteins and their annotated locations for NP_001258887.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AF132942, AK075257, BC014303
      Consensus CDS
      CCDS1055.1
      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8
      Related
      ENSP00000348535.4, ENST00000356205.9
      Conserved Domains (1) summary
      pfam02535
      Location:48 → 319
      Zip; ZIP Zinc transporter

    3. NM_001271959.2 → NP_001258888.1  zinc transporter ZIP1 isoform a

      See identical proteins and their annotated locations for NP_001258888.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AF151829, AL358472, DA711655, HY042960
      Consensus CDS
      CCDS1055.1
      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8
      Related
      ENSP00000484182.1, ENST00000621013.4
      Conserved Domains (1) summary
      pfam02535
      Location:48 → 319
      Zip; ZIP Zinc transporter

    4. NM_001271960.2 → NP_001258889.1  zinc transporter ZIP1 isoform a

      See identical proteins and their annotated locations for NP_001258889.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, 4 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AW571711, BC014303, DB001496
      Consensus CDS
      CCDS1055.1
      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8
      Related
      ENSP00000479421.1, ENST00000617697.4
      Conserved Domains (1) summary
      pfam02535
      Location:48 → 319
      Zip; ZIP Zinc transporter

    5. NM_001271961.2 → NP_001258890.1  zinc transporter ZIP1 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and lacks an exon in the 3' coding region which results in a frameshift, compared to variant 1. The encoded isoform (b) is shorter and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AK293389, BM807264
      Consensus CDS
      CCDS72920.1
      UniProtKB/TrEMBL
      A0A0A0MTL8
      Related
      ENSP00000443632.2, ENST00000537590.5

    6. NM_014437.5 → NP_055252.2  zinc transporter ZIP1 isoform a

      See identical proteins and their annotated locations for NP_055252.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a. Variants 1, 2, 3, 4 and 5 encode the same protein (isoform a).
      Source sequence(s)
      AL358472, AW571711, BC014303
      Consensus CDS
      CCDS1055.1
      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8
      Related
      ENSP00000309710.6, ENST00000310483.10
      Conserved Domains (1) summary
      pfam02535
      Location:48 → 319
      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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      153959110..153968184 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047418008.1 → XP_047273964.1  zinc transporter ZIP1 isoform X1

      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      153096371..153105445 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336011.1 → XP_054191986.1  zinc transporter ZIP1 isoform X1

      UniProtKB/Swiss-Prot
      B4DDY7, Q5T4K1, Q8N2H7, Q9BTV0, Q9NY26, Q9UBI7, Q9Y2Z7, Q9Y380
      UniProtKB/TrEMBL
      Q6IAD8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NY26.1 GenPept UniProtKB/Swiss-Prot:Q9NY26

    Gene LinkOut

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

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