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    SLC30A3 solute carrier family 30 member 3 [ Homo sapiens (human) ]

    Gene ID: 7781, updated on 10-Dec-2024

    Summary

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    Official Symbol
    SLC30A3provided by HGNC
    Official Full Name
    solute carrier family 30 member 3provided by HGNC
    Primary source
    HGNC:HGNC:11014
    See related
    Ensembl:ENSG00000115194 MIM:602878; AllianceGenome:HGNC:11014
    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
    ZNT3
    Summary
    Enables zinc ion transmembrane transporter activity. Involved in zinc ion import into lysosome. Located in late endosome and synaptic vesicle. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in testis (RPKM 9.2), brain (RPKM 7.3) and 1 other tissue See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC30A3 in Genome Data Viewer
    Location:
    2p23.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (27253684..27275817, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (27295330..27317459, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (27476552..27498685, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 5 member 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11290 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11291 Neighboring gene all-trans retinoic acid induced differentiation factor Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:27454350-27455549 Neighboring gene carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:27465505-27466704 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:27472326-27473120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:27473121-27473914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11292 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11293 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11294 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11295 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11296 Neighboring gene DnaJ heat shock protein family (Hsp40) member C5 gamma Neighboring gene tripartite motif containing 54 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:27524348-27524553 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:27543343-27543946 Neighboring gene Sharpr-MPRA regulatory regions 9483 and 12628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15496 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15497 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15498 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:27545801-27546773 Neighboring gene mitochondrial inner membrane protein MPV17 Neighboring gene urocortin

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Depression and synaptic zinc regulation in Alzheimer disease, dementia with lewy bodies, and Parkinson disease dementia. Whitfield DR, et al. Am J Geriatr Psychiatry, 2015 Feb. PMID 24953873
    2. Increased Cerebrospinal Fluid Concentration of ZnT3 Is Associated with Cognitive Impairment in Alzheimer's Disease. Enache D, et al. J Alzheimers Dis, 2020. PMID 32925049
    3. The zinc transporter ZNT3 co-localizes with insulin in INS-1E pancreatic beta cells and influences cell survival, insulin secretion capacity, and ZNT8 expression. Smidt K, et al. Biometals, 2016 Apr. PMID 26867900
    4. Allelic variants in the zinc transporter-3 gene, SLC30A3, a candidate gene identified from gene expression studies, show gender-specific association with schizophrenia. Perez-Becerril C, et al. Eur Psychiatry, 2014 Mar. PMID 23849395
    5. Common variants in the chromosome 2p23 region containing the SLC30A3 (ZnT3) gene are associated with schizophrenia in female but not male individuals in a large collection of European samples. Perez-Becerril C, et al. Psychiatry Res, 2016 Dec 30. PMID 27750116

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Epigenetic targeting of SLC30A3 by HDAC1 is related to the malignant phenotype of glioblastoma.
      Title: Epigenetic targeting of SLC30A3 by HDAC1 is related to the malignant phenotype of glioblastoma.
    2. Increased Cerebrospinal Fluid Concentration of ZnT3 Is Associated with Cognitive Impairment in Alzheimer's Disease.
      Title: Increased Cerebrospinal Fluid Concentration of ZnT3 Is Associated with Cognitive Impairment in Alzheimer's Disease.
    3. ZNT3 was only detected in human beta-cells, but not in mouse beta-cells.
      Title: SLC30A family expression in the pancreatic islets of humans and mice: cellular localization in the β-cells.
    4. SNPs in the SLC30A3 gene and adjacent region are associated with schizophrenia in female but not male cases.
      Title: Common variants in the chromosome 2p23 region containing the SLC30A3 (ZnT3) gene are associated with schizophrenia in female but not male individuals in a large collection of European samples.
    5. There was a significant decreased in protein levels of ZnT3 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.
    6. The level of ERK1/2 phosphorylation was significantly increased by tunicamycin treatment in control cells, not in SLC30A3 knockdown cells. The ERK1/2 pathway is thought to have an association with defensive effects of SLC30A3 on cellular stress such as ER stress.
      Title: Protective roles of SLC30A3 against endoplasmic reticulum stress via ERK1/2 activation.
    7. ZNT3 and ZNT8 (known to regulate insulin secretion) have opposite effects on insulin synthesis and secretion possibly by a transcriptional co-regulation since mRNA expression of ZNT3 was inversely correlated to ZNT8 and ZNT3 over-expression reduced insulin synthesis and secretion.
      Title: The zinc transporter ZNT3 co-localizes with insulin in INS-1E pancreatic beta cells and influences cell survival, insulin secretion capacity, and ZNT8 expression.
    8. An association was found between reduced ZnT3 in the prefrontal cortex and cognitive impairment in patients with either dementia with Lewy bodies or Parkinson's disease dementia.
      Title: Assessment of ZnT3 and PSD95 protein levels in Lewy body dementias and Alzheimer's disease: association with cognitive impairment.
    9. SNPs in SLC30A3 show a gender-specific association with schizophrenia in an East UK cohort.
      Title: Allelic variants in the zinc transporter-3 gene, SLC30A3, a candidate gene identified from gene expression studies, show gender-specific association with schizophrenia.
    10. this study provides the first evidence of a role for zinc in depression in people with dementia.
      Title: Depression and synaptic zinc regulation in Alzheimer disease, dementia with lewy bodies, and Parkinson disease dementia.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables antiporter activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    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
    		  
    enables zinc ion transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to zinc ion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in zinc ion import into lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in zinc ion import into synaptic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in zinc ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in zinc ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in zinc ion transmembrane transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in hippocampal mossy fiber IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in hippocampal mossy fiber to CA3 synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in microvesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in neuron projection ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synaptic vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in synaptic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    probable proton-coupled zinc antiporter SLC30A3
    Names
    solute carrier family 30 (zinc transporter), member 3
    zinc transporter 3
    zinc transporter ZnT-3
    znT-3

    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_001318949.2 → NP_001305878.1  probable proton-coupled zinc antiporter SLC30A3 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a.
      Source sequence(s)
      AC013413, AK302174, BC028358, DB034101
      UniProtKB/TrEMBL
      B4DXX8
      Conserved Domains (1) summary
      TIGR01297
      Location:80 → 367
      CDF; cation diffusion facilitator family transporter

    2. NM_001318950.2 → NP_001305879.1  probable proton-coupled zinc antiporter SLC30A3 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (c) has a shorter and distinct N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (c).
      Source sequence(s)
      AC013413, BC028358, BM554028
      UniProtKB/TrEMBL
      B4DXX8
      Conserved Domains (1) summary
      TIGR01297
      Location:72 → 359
      CDF; cation diffusion facilitator family transporter

    3. NM_001318951.2 → NP_001305880.1  probable proton-coupled zinc antiporter SLC30A3 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (c) has a shorter and distinct N-terminus compared to isoform a. Variants 3 and 4 both encode the same isoform (c).
      Source sequence(s)
      AC013413, BC028358, DB034101
      UniProtKB/TrEMBL
      B4DXX8
      Conserved Domains (1) summary
      TIGR01297
      Location:72 → 359
      CDF; cation diffusion facilitator family transporter

    4. NM_003459.5 → NP_003450.2  probable proton-coupled zinc antiporter SLC30A3 isoform a

      See identical proteins and their annotated locations for NP_003450.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AC013413, BC028358
      Consensus CDS
      CCDS1743.1
      UniProtKB/Swiss-Prot
      Q8TC03, Q99726
      UniProtKB/TrEMBL
      B4DXX8
      Related
      ENSP00000233535.4, ENST00000233535.9
      Conserved Domains (1) summary
      TIGR01297
      Location:85 → 372
      CDF; cation diffusion facilitator family 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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      27253684..27275817 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004874.2 → XP_016860363.1  probable proton-coupled zinc antiporter SLC30A3 isoform X3

      Conserved Domains (1) summary
      TIGR01297
      Location:72 → 129
      CDF; cation diffusion facilitator family transporter

    2. XM_011533102.3 → XP_011531404.1  probable proton-coupled zinc antiporter SLC30A3 isoform X6

      Conserved Domains (2) summary
      TIGR01297
      Location:154 → 299
      CDF; cation diffusion facilitator family transporter
      pfam01545
      Location:154 → 220
      Cation_efflux; Cation efflux family

    3. XM_047445785.1 → XP_047301741.1  probable proton-coupled zinc antiporter SLC30A3 isoform X2

    4. XM_047445786.1 → XP_047301742.1  probable proton-coupled zinc antiporter SLC30A3 isoform X5

      UniProtKB/TrEMBL
      B4DXX8

    5. XM_017004873.2 → XP_016860362.1  probable proton-coupled zinc antiporter SLC30A3 isoform X3

      Conserved Domains (1) summary
      TIGR01297
      Location:72 → 129
      CDF; cation diffusion facilitator family transporter

    6. XM_047445787.1 → XP_047301743.1  probable proton-coupled zinc antiporter SLC30A3 isoform X6

      Related
      ENSP00000388219.1, ENST00000445870.5

    7. XM_005264548.4 → XP_005264605.1  probable proton-coupled zinc antiporter SLC30A3 isoform X2

      Conserved Domains (1) summary
      pfam01545
      Location:80 → 137
      Cation_efflux; Cation efflux family

    8. XM_017004875.3 → XP_016860364.1  probable proton-coupled zinc antiporter SLC30A3 isoform X4

      Conserved Domains (1) summary
      pfam01545
      Location:63 → 120
      Cation_efflux; Cation efflux family

    9. XM_005264547.3 → XP_005264604.1  probable proton-coupled zinc antiporter SLC30A3 isoform X1

      Conserved Domains (1) summary
      pfam01545
      Location:85 → 142
      Cation_efflux; Cation efflux family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      27295330..27317459 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054343814.1 → XP_054199789.1  probable proton-coupled zinc antiporter SLC30A3 isoform X3

    2. XM_054343818.1 → XP_054199793.1  probable proton-coupled zinc antiporter SLC30A3 isoform X6

    3. XM_054343813.1 → XP_054199788.1  probable proton-coupled zinc antiporter SLC30A3 isoform X2

    4. XM_054343816.1 → XP_054199791.1  probable proton-coupled zinc antiporter SLC30A3 isoform X5

      UniProtKB/TrEMBL
      B4DXX8

    5. XM_054343815.1 → XP_054199790.1  probable proton-coupled zinc antiporter SLC30A3 isoform X3

    6. XM_054343817.1 → XP_054199792.1  probable proton-coupled zinc antiporter SLC30A3 isoform X6

    7. XM_054343812.1 → XP_054199787.1  probable proton-coupled zinc antiporter SLC30A3 isoform X2

    8. XM_054343811.1 → XP_054199786.1  probable proton-coupled zinc antiporter SLC30A3 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99726.2 GenPept UniProtKB/Swiss-Prot:Q99726

    Gene LinkOut

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