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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
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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

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