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

Gene ID: 7781, updated on 2-Nov-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, Nov 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

Expression

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  • Project title: HPA RNA-seq normal tissues 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. 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)

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

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

  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

  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

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