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

Gene ID: 27173, updated on 3-Apr-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
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Genomic context

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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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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

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
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NY26.1 GenPept UniProtKB/Swiss-Prot:Q9NY26

Gene LinkOut

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