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    SLC39A12 solute carrier family 39 member 12 [ Homo sapiens (human) ]

    Gene ID: 221074, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SLC39A12provided by HGNC
    Official Full Name
    solute carrier family 39 member 12provided by HGNC
    Primary source
    HGNC:HGNC:20860
    See related
    Ensembl:ENSG00000148482 MIM:608734; AllianceGenome:HGNC:20860
    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
    ZIP12; ZIP-12; LZT-Hs8; bA570F3.1
    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. SLC39A12 belongs to a subfamily of proteins that show structural characteristics of zinc transporters (Taylor and Nicholson, 2003 [PubMed 12659941]).[supplied by OMIM, Aug 2008]
    Expression
    Restricted expression toward brain (RPKM 9.2) See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC39A12 in Genome Data Viewer
    Location:
    10p12.33
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (17951918..18043285)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (17971349..18062603)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (18240847..18332214)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene mannose receptor C-type 1 Neighboring gene uncharacterized LOC124902600 Neighboring gene microRNA 511 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:18270087-18271286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3111 Neighboring gene SLC39A12 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:18324740-18325329 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:18325330-18325918 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:18355421-18356620 Neighboring gene MPRA-validated peak890 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr10:18424852-18425818 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_11486 Neighboring gene calcium voltage-gated channel auxiliary subunit beta 2 Neighboring gene uncharacterized LOC107984213 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:18629448-18629653 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3112 Neighboring gene uncharacterized LOC124902386 Neighboring gene uncharacterized LOC124902387

    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. Role of zinc transporter ZIP12 in susceptibility-weighted brain magnetic resonance imaging (MRI) phenotypes and mitochondrial function. Strong MD, et al. FASEB J, 2020 Sep. PMID 32716562
    2. Examination of the zinc transporter gene, SLC39A12. Bly M. Schizophr Res, 2006 Jan 31. PMID 16311021
    3. Neurulation and neurite extension require the zinc transporter ZIP12 (slc39a12). Chowanadisai W, et al. Proc Natl Acad Sci U S A, 2013 Jun 11. PMID 23716681, Free PMC Article
    4. The LZT proteins; the LIV-1 subfamily of zinc transporters. Taylor KM, et al. Biochim Biophys Acta, 2003 Apr 1. PMID 12659941
    5. Polymorphisms in mitochondrial genes and prostate cancer risk. Wang L, et al. Cancer Epidemiol Biomarkers Prev, 2008 Dec. PMID 19064571, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Role of zinc transporter ZIP12 in susceptibility-weighted brain magnetic resonance imaging (MRI) phenotypes and mitochondrial function.
      Title: Role of zinc transporter ZIP12 in susceptibility-weighted brain magnetic resonance imaging (MRI) phenotypes and mitochondrial function.
    2. Data indicate that the zinc transporter ZIP12 (slc39a12) is highly expressed in brain.
      Title: Neurulation and neurite extension require the zinc transporter ZIP12 (slc39a12).
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Polymorphisms in mitochondrial genes and prostate cancer risk.
    5. Examination of the zinc transporter gene, SLC39A12.
      Title: Examination of the zinc transporter gene, SLC39A12.
    Submit: New GeneRIF Correction

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Clone Names

    • FLJ30499, MGC43205, MGC51099

    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 zinc ion transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion transmembrane transporter activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in bicarbonate transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intracellular monoatomic cation homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neural tube formation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neuron projection extension ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of sprouting angiogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of microtubule polymerization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of neuron projection development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to decreased oxygen levels IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in zinc ion import across plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in zinc ion import across plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular vesicle HDA PubMed 
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    zinc transporter ZIP12
    Names
    LIV-1 subfamily of ZIP zinc transporter 8
    ZRT/IRT-like protein 12
    solute carrier family 39 (metal ion transporter), member 12
    solute carrier family 39 (zinc transporter), member 12
    zinc transporter 12
    zrt- and Irt-like protein 12

    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_001145195.2 → NP_001138667.1  zinc transporter ZIP12 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001138667.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AL360231, BC094700, DB469365
      Consensus CDS
      CCDS44362.1
      UniProtKB/Swiss-Prot
      B7Z2Y9, B7ZL35, C9JJL4, F5GX72, Q49AN8, Q4G0L3, Q504Y0, Q5VWV8, Q5VWV9, Q6NZY5, Q96NN4
      UniProtKB/TrEMBL
      B7Z8P9
      Related
      ENSP00000366586.2, ENST00000377369.7
      Conserved Domains (1) summary
      pfam02535
      Location:369 → 671
      Zip; ZIP Zinc transporter

    2. NM_001282733.2 → NP_001269662.1  zinc transporter ZIP12 isoform 3 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the coding region compared to variant 1. The encoded isoform (3) is shorter but has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      BC035118, BC094700, BF963263, DB540352, DB545916
      Consensus CDS
      CCDS60493.1
      UniProtKB/TrEMBL
      B7Z8P9
      Related
      ENSP00000366588.3, ENST00000377371.3
      Conserved Domains (1) summary
      pfam02535
      Location:369 → 670
      Zip; ZIP Zinc transporter

    3. NM_001282734.2 → NP_001269663.1  zinc transporter ZIP12 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two exons and initiates translation at a downstream start codon, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AK295294, BC143551, BF963263, DB469365, DB540352, DB545916
      Consensus CDS
      CCDS60494.1
      UniProtKB/TrEMBL
      B7Z8P9
      Related
      ENSP00000440445.1, ENST00000539911.5
      Conserved Domains (1) summary
      pfam02535
      Location:235 → 537
      Zip; ZIP Zinc transporter

    4. NM_152725.4 → NP_689938.2  zinc transporter ZIP12 isoform 2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the coding region compared to variant 1. The encoded isoform (2) is shorter but has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      AK055061, AL360231, BC094700, DB469365
      Consensus CDS
      CCDS7124.1
      UniProtKB/TrEMBL
      B7Z8P9
      Related
      ENSP00000366591.4, ENST00000377374.8
      Conserved Domains (1) summary
      pfam02535
      Location:369 → 634
      Zip; ZIP Zinc transporter

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      17951918..18043285
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      17971349..18062603
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q504Y0.3 GenPept UniProtKB/Swiss-Prot:Q504Y0

    Gene LinkOut

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

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