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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
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Genomic context

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See SLC30A10 in Genome Data Viewer
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.

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