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    SLC30A10 solute carrier family 30 member 10 [ Homo sapiens (human) ]

    Gene ID: 55532, updated on 11-Apr-2024

    Summary

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    Official Symbol
    SLC30A10provided by HGNC
    Official Full Name
    solute carrier family 30 member 10provided by HGNC
    Primary source
    HGNC:HGNC:25355
    See related
    Ensembl:ENSG00000196660 MIM:611146; AllianceGenome:HGNC:25355
    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
    ZNT8; ZRC1; HMDPC; ZNT10; ZnT-10; HMNDYT1
    Summary
    This gene is highly expressed in the liver and is inducible by manganese. Its protein product appears to be critical in maintaining manganese levels, and has higher specificity for manganese than zinc. Loss of function mutations appear to result in a pleomorphic phenotype, including dystonia and adult-onset parkinsonism. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Mar 2012]
    Expression
    Biased expression in duodenum (RPKM 12.8), liver (RPKM 7.9) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1q41
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (219910445..219959098, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (219148333..219196857, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (220083787..220132440, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene zinc finger CCCH-type containing 11B Neighboring gene Sharpr-MPRA regulatory region 297 Neighboring gene uncharacterized LOC105372926 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:219883505-219884704 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_4814 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2549 Neighboring gene RNA, 5S ribosomal pseudogene 76 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2550 Neighboring gene NANOG hESC enhancer GRCh37_chr1:219999577-220000141 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:220006336-220007281 Neighboring gene MPRA-validated peak704 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:220012377-220013120 Neighboring gene Sharpr-MPRA regulatory region 9893 Neighboring gene uncharacterized LOC107985281 Neighboring gene small nucleolar RNA U3 Neighboring gene small nucleolar RNA U13 Neighboring gene glutamyl-prolyl-tRNA synthetase 1

    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. Manganese efflux transporter SLC30A10 missense polymorphism T95I associated with liver injury retains manganese efflux activity. Gurol KC, et al. Am J Physiol Gastrointest Liver Physiol, 2023 Jan 1. PMID 36414535, Free PMC Article
    2. A rare genetic variant in the manganese transporter SLC30A10 and elevated liver enzymes in the general population. Seidelin AS, et al. Hepatol Int, 2022 Jun. PMID 35397106
    3. Characterization of in vitro models of SLC30A10 deficiency. Prajapati M, et al. Biometals, 2021 Jun. PMID 33713241, Free PMC Article
    4. Long noncoding RNA SLC30A10 promotes colorectal tumor proliferation and migration via miR-21c/APC axis. Hou L, et al. Eur Rev Med Pharmacol Sci, 2020 Jun. PMID 32633358
    5. A case of dystonia with polycythemia and hypermanganesemia caused by SLC30A10 mutation: a treatable inborn error of manganese metabolism. Tavasoli A, et al. BMC Pediatr, 2019 Jul 9. PMID 31288771, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Cell-free SLC30A10 messenger ribonucleic acid (mRNA) expression and their association with vitamin-D level among non-small cell lung cancer (NSCLC) patients.
      Title: Cell-free SLC30A10 messenger ribonucleic acid (mRNA) expression and their association with vitamin-D level among non-small cell lung cancer (NSCLC) patients.
    2. Manganese efflux transporter SLC30A10 missense polymorphism T95I associated with liver injury retains manganese efflux activity.
      Title: Manganese efflux transporter SLC30A10 missense polymorphism T95I associated with liver injury retains manganese efflux activity.
    3. A rare genetic variant in the manganese transporter SLC30A10 and elevated liver enzymes in the general population.
      Title: A rare genetic variant in the manganese transporter SLC30A10 and elevated liver enzymes in the general population.
    4. Manganese transport in mammals by zinc transporter family proteins, ZNT and ZIP.
      Title: Manganese transport in mammals by zinc transporter family proteins, ZNT and ZIP.
    5. Characterization of in vitro models of SLC30A10 deficiency.
      Title: Characterization of in vitro models of SLC30A10 deficiency.
    6. Genome-wide and Mendelian randomisation studies of liver MRI yield insights into the pathogenesis of steatohepatitis.
      Title: Genome-wide and Mendelian randomisation studies of liver MRI yield insights into the pathogenesis of steatohepatitis.
    7. GWAS of serum ALT and AST reveals an association of SLC30A10 Thr95Ile with hypermanganesemia symptoms.
      Title: GWAS of serum ALT and AST reveals an association of SLC30A10 Thr95Ile with hypermanganesemia symptoms.
    8. Long noncoding RNA SLC30A10 promotes colorectal tumor proliferation and migration via miR-21c/APC axis.
      Title: Long noncoding RNA SLC30A10 promotes colorectal tumor proliferation and migration via miR-21c/APC axis.
    9. The Functions of ZIP8, ZIP14, and ZnT10 in the Regulation of Systemic Manganese Homeostasis.
      Title: The Functions of ZIP8, ZIP14, and ZnT10 in the Regulation of Systemic Manganese Homeostasis.
    10. A case of dystonia with polycythemia and hypermanganesemia caused by SLC30A10 mutation: a treatable inborn error of manganese metabolism.
      Title: A case of dystonia with polycythemia and hypermanganesemia caused by SLC30A10 mutation: a treatable inborn error of manganese metabolism.
    Submit: New GeneRIF Correction See all GeneRIFs (32)

    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
    Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits.
    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

    • DKFZp547M236

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium:manganese antiporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables manganese ion transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables manganese ion transmembrane transporter activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables manganese ion transmembrane transporter activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    NOT enables zinc ion transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to angiotensin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in detoxification of zinc ion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within epidermal growth factor receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT involved_in intracellular copper ion homeostasis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in intracellular manganese ion homeostasis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in intracellular manganese ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular zinc ion homeostasis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    NOT involved_in intracellular zinc ion homeostasis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in intracellular zinc ion homeostasis IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT involved_in intracellular zinc ion homeostasis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in manganese ion export across plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in manganese ion export across plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in manganese ion transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in manganese ion transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of positive regulation of ERK1 and ERK2 cascade IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in zinc ion import into organelle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in zinc ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in early endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in 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
    		  
    located_in recycling endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in recycling endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT located_in synaptic vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    calcium/manganese antiporter SLC30A10
    Names
    manganese transporter SLC30A10
    zinc resistance conferring homolog
    zinc transporter 8

    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.

    Genomic

    1. NG_032153.3 RefSeqGene

      Range
      35541..53653
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001376929.1 → NP_001363858.1  calcium/manganese antiporter SLC30A10 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC093562, AC103590
      Consensus CDS
      CCDS91159.1
      UniProtKB/TrEMBL
      A0A8Q3WLF3
      Related
      ENSP00000512752.1, ENST00000696608.1
      Conserved Domains (1) summary
      COG1230
      Location:22 → 320
      CzcD; Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]

    2. NM_001416004.1 → NP_001402933.1  calcium/manganese antiporter SLC30A10 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC093562
      UniProtKB/TrEMBL
      B3KR19, D3DTA8

    3. NM_001416005.1 → NP_001402934.1  calcium/manganese antiporter SLC30A10 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC093562
      UniProtKB/TrEMBL
      B3KR19, D3DTA8

    4. NM_018713.3 → NP_061183.2  calcium/manganese antiporter SLC30A10 isoform 1

      See identical proteins and their annotated locations for NP_061183.2

      Status: VALIDATED

      Source sequence(s)
      AC093562
      Consensus CDS
      CCDS31026.1
      UniProtKB/Swiss-Prot
      Q49AL9, Q6XR72, Q9NPW0
      Related
      ENSP00000355893.4, ENST00000366926.4
      Conserved Domains (1) summary
      COG1230
      Location:10 → 383
      CzcD; Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]

    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
      219910445..219959098 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      219148333..219196857 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001004433.1: Suppressed sequence

      Description
      NM_001004433.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6XR72.2 GenPept UniProtKB/Swiss-Prot:Q6XR72

    Gene LinkOut

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

    Chemical Information
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