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    SLC30A6 solute carrier family 30 member 6 [ Homo sapiens (human) ]

    Gene ID: 55676, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SLC30A6provided by HGNC
    Official Full Name
    solute carrier family 30 member 6provided by HGNC
    Primary source
    HGNC:HGNC:19305
    See related
    Ensembl:ENSG00000152683 MIM:611148; AllianceGenome:HGNC:19305
    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
    ZNT6; MST103; MSTP103
    Summary
    This gene encodes a member of a family of proteins that function as zinc transporters. This protein can regulate subcellular levels of zinc in the Golgi and vesicles. Expression of this gene is altered in the Alzheimer's disease brain plaques. [provided by RefSeq, Aug 2016]
    Expression
    Ubiquitous expression in thyroid (RPKM 4.9), urinary bladder (RPKM 4.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    2p22.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (32165864..32224379)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (32214423..32272885)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (32390933..32449448)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:32288537-32289337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11339 Neighboring gene spastin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:32392253-32392769 Neighboring gene SLC30A6 divergent transcript Neighboring gene MPRA-validated peak3647 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15558 Neighboring gene DEAD-box helicase 50 pseudogene 1 Neighboring gene RNA, U6 small nuclear 647, pseudogene Neighboring gene NLR family CARD domain containing 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:32502088-32502833 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11340 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:32518022-32518694 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:32521211-32521404 Neighboring gene Yip1 domain family member 4

    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. A genetic variant within SLC30A6 has a protective role in the severity of rheumatoid arthritis. Adelino JE, et al. Scand J Rheumatol, 2017 Jul. PMID 27758124
    2. Identification of the Zn2+ binding site and mode of operation of a mammalian Zn2+ transporter. Ohana E, et al. J Biol Chem, 2009 Jun 26. PMID 19366695, Free PMC Article
    3. Zinc transporters ZnT3 and ZnT6 are downregulated in the spinal cords of patients with sporadic amyotrophic lateral sclerosis. Kaneko M, et al. J Neurosci Res, 2015 Feb. PMID 25284286
    4. Demonstration and characterization of the heterodimerization of ZnT5 and ZnT6 in the early secretory pathway. Fukunaka A, et al. J Biol Chem, 2009 Nov 6. PMID 19759014, Free PMC Article
    5. Altered expression of zinc transporters-4 and -6 in mild cognitive impairment, early and late Alzheimer's disease brain. Smith JL, et al. Neuroscience, 2006 Jul 7. PMID 16580781

    See all (48) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Increased expression of zinc transporter ZIP4, ZIP11, ZnT1, and ZnT6 predicts poor prognosis in pancreatic cancer.
      Title: Increased expression of zinc transporter ZIP4, ZIP11, ZnT1, and ZnT6 predicts poor prognosis in pancreatic cancer.
    2. There was a significant increase in protein levels of ZnT6 in the prefrontal cortex in Major depression disorder, relative to control subjects.
      Title: Zinc transporters protein level in postmortem brain of depressed subjects and suicide victims.
    3. A genetic variant within SLC30A6 has a protective role in the severity of Rheumatoid Arthritis.
      Title: A genetic variant within SLC30A6 has a protective role in the severity of rheumatoid arthritis.
    4. results of this study suggested that ZnT6 protein levels are decreased in the spinal cords of sporadic ALS patients.
      Title: Zinc transporters ZnT3 and ZnT6 are downregulated in the spinal cords of patients with sporadic amyotrophic lateral sclerosis.
    5. 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.
    6. our results suggest that alterations in Zn transport proteins ZnT-1, ZnT-4 and ZnT-6 may contribute to the pathology observed in preclinical Alzheimer's disease subjects before onset of clinical symptoms
      Title: Alterations of zinc transporter proteins ZnT-1, ZnT-4 and ZnT-6 in preclinical Alzheimer's disease brain.
    7. The cytosolic C-terminal tail of ZnT5 is important for its interaction with ZnT6 as a heterodimer.
      Title: Demonstration and characterization of the heterodimerization of ZnT5 and ZnT6 in the early secretory pathway.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    9. Data show that ZNT6 is extensively present in the Abeta-positive plaques in the cortex of human AD brains.
      Title: Abundant expression of zinc transporters in the amyloid plaques of Alzheimer's disease brain.
    10. hZnT-6 is up-regulated in response to cellular zinc depletion in Raji & THP-1 cells.
      Title: Intracellular zinc homeostasis in leukocyte subsets is regulated by different expression of zinc exporters ZnT-1 to ZnT-9.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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
    Novel gene variants predict serum levels of the cytokines IL-18 and IL-1ra in older adults.
    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

    Clone Names

    • FLJ31101, MGC45055

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT enables zinc:proton antiporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of zinc ion transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in zinc ion import into Golgi lumen IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in zinc ion transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in trans-Golgi network membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    zinc transporter 6
    Names
    solute carrier family 30 (zinc transporter), member 6

    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_001193513.3 → NP_001180442.1  zinc transporter 6 isoform 1

      See identical proteins and their annotated locations for NP_001180442.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AA594503, AK055663, BC032525, BC066903, BG527678, DB469378
      Consensus CDS
      CCDS54341.1
      UniProtKB/Swiss-Prot
      Q6NXT4
      Related
      ENSP00000368648.2, ENST00000379343.6
      Conserved Domains (2) summary
      COG1230
      Location:113 → 371
      CzcD; Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]
      pfam01545
      Location:113 → 295
      Cation_efflux; Cation efflux family

    2. NM_001193514.3 → NP_001180443.1  zinc transporter 6 isoform 3

      See identical proteins and their annotated locations for NP_001180443.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks two alternate in-frame exons compared to variant 1. The resulting protein (isoform 3) is shorter than isoform 1.
      Source sequence(s)
      AA594503, AK055663, BC032525, BG527678, EF560719
      Consensus CDS
      CCDS54342.1
      UniProtKB/Swiss-Prot
      Q6NXT4
      Related
      ENSP00000399005.1, ENST00000435660.5
      Conserved Domains (1) summary
      pfam01545
      Location:43 → 255
      Cation_efflux; Cation efflux family

    3. NM_001193515.3 → NP_001180444.1  zinc transporter 6 isoform 4

      See identical proteins and their annotated locations for NP_001180444.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two alternate in-frame exons compared to variant 1. The resulting protein (isoform 4) is shorter than isoform 1.
      Source sequence(s)
      AA594503, AK304225, AL121653
      Consensus CDS
      CCDS54343.1
      UniProtKB/Swiss-Prot
      Q6NXT4
      Related
      ENSP00000349563.4, ENST00000357055.7
      Conserved Domains (2) summary
      COG1230
      Location:26 → 302
      CzcD; Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]
      pfam01545
      Location:14 → 226
      Cation_efflux; Cation efflux family

    4. NM_001330476.2 → NP_001317405.1  zinc transporter 6 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AA594503, AL121653, AL832755, DB469378
      Consensus CDS
      CCDS82434.1
      UniProtKB/TrEMBL
      B5MCR8
      Related
      ENSP00000384041.1, ENST00000406369.2
      Conserved Domains (1) summary
      COG1230
      Location:4 → 257
      CzcD; Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]

    5. NM_001330477.2 → NP_001317406.1  zinc transporter 6 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AA594503, AK096672, AL121653
      UniProtKB/TrEMBL
      B3KU87, B7WP49, D6W579
      Conserved Domains (1) summary
      cl25570
      Location:5 → 134
      Cation_efflux; Cation efflux family

    6. NM_001330478.2 → NP_001317407.1  zinc transporter 6 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AA594503, AK127716, AL121653
      UniProtKB/TrEMBL
      B3KU87, B7WP49, D6W579
      Conserved Domains (1) summary
      cl25570
      Location:5 → 134
      Cation_efflux; Cation efflux family

    7. NM_001330479.2 → NP_001317408.1  zinc transporter 6 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL121653, AL121658
      Conserved Domains (2) summary
      COG1230
      Location:6 → 282
      CzcD; Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]
      pfam01545
      Location:6 → 206
      Cation_efflux; Cation efflux family

    8. NM_017964.5 → NP_060434.2  zinc transporter 6 isoform 2

      See identical proteins and their annotated locations for NP_060434.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting protein (isoform 2) is shorter than isoform 1.
      Source sequence(s)
      AA594503, AK055663, BC032525, BG527678
      Consensus CDS
      CCDS1780.1
      UniProtKB/Swiss-Prot
      A5YM45, B7Z901, Q6NXT4, Q8N5C9, Q96NC3
      Related
      ENSP00000282587.5, ENST00000282587.9
      Conserved Domains (2) summary
      COG1230
      Location:55 → 331
      CzcD; Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]
      pfam01545
      Location:43 → 255
      Cation_efflux; Cation efflux family

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      32165864..32224379
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047444944.1 → XP_047300900.1  zinc transporter 6 isoform X2

    2. XM_011532962.4 → XP_011531264.1  zinc transporter 6 isoform X3

      See identical proteins and their annotated locations for XP_011531264.1

      UniProtKB/TrEMBL
      B5MCR8
      Conserved Domains (1) summary
      COG1230
      Location:4 → 257
      CzcD; Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]

    3. XM_011532963.4 → XP_011531265.1  zinc transporter 6 isoform X4

      Conserved Domains (2) summary
      COG1230
      Location:113 → 331
      CzcD; Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]
      pfam01545
      Location:113 → 295
      Cation_efflux; Cation efflux family

    4. XM_011532959.4 → XP_011531261.1  zinc transporter 6 isoform X1

      Conserved Domains (2) summary
      COG1230
      Location:113 → 348
      CzcD; Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]
      pfam01545
      Location:113 → 295
      Cation_efflux; Cation efflux family

    5. XM_017004465.3 → XP_016859954.1  zinc transporter 6 isoform X7

    6. XM_047444946.1 → XP_047300902.1  zinc transporter 6 isoform X5

    7. XM_047444947.1 → XP_047300903.1  zinc transporter 6 isoform X9

    8. XM_017004464.3 → XP_016859953.1  zinc transporter 6 isoform X6

    9. XM_017004466.3 → XP_016859955.1  zinc transporter 6 isoform X8

      UniProtKB/TrEMBL
      Q7Z4D6

    10. XM_047444945.1 → XP_047300901.1  zinc transporter 6 isoform X3

      UniProtKB/TrEMBL
      B5MCR8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      32214423..32272885
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054342880.1 → XP_054198855.1  zinc transporter 6 isoform X2

    2. XM_054342881.1 → XP_054198856.1  zinc transporter 6 isoform X3

      UniProtKB/TrEMBL
      B5MCR8

    3. XM_054342883.1 → XP_054198858.1  zinc transporter 6 isoform X4

    4. XM_054342879.1 → XP_054198854.1  zinc transporter 6 isoform X1

    5. XM_054342886.1 → XP_054198861.1  zinc transporter 6 isoform X7

    6. XM_054342884.1 → XP_054198859.1  zinc transporter 6 isoform X5

    7. XM_054342888.1 → XP_054198863.1  zinc transporter 6 isoform X9

    8. XM_054342885.1 → XP_054198860.1  zinc transporter 6 isoform X6

    9. XM_054342887.1 → XP_054198862.1  zinc transporter 6 isoform X8

    10. XM_054342882.1 → XP_054198857.1  zinc transporter 6 isoform X3

      UniProtKB/TrEMBL
      B5MCR8
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6NXT4.2 GenPept UniProtKB/Swiss-Prot:Q6NXT4

    Gene LinkOut

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