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

Summary

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

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SLC30A3_7909 (e-PCR)
- UniSTS:466446

STS-U76010 (e-PCR)
- UniSTS:36629

RH102490 (e-PCR)
- UniSTS:96824

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)

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
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
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
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

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

27253684..27275817 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
XM_047445785.1 → XP_047301741.1 probable proton-coupled zinc antiporter SLC30A3 isoform X2
XM_047445786.1 → XP_047301742.1 probable proton-coupled zinc antiporter SLC30A3 isoform X5
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
XM_047445787.1 → XP_047301743.1 probable proton-coupled zinc antiporter SLC30A3 isoform X6

Related

ENSP00000388219.1, ENST00000445870.5
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
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
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

NC_060926.1 Alternate T2T-CHM13v2.0

Range

27295330..27317459 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054343814.1 → XP_054199789.1 probable proton-coupled zinc antiporter SLC30A3 isoform X3
XM_054343818.1 → XP_054199793.1 probable proton-coupled zinc antiporter SLC30A3 isoform X6
XM_054343813.1 → XP_054199788.1 probable proton-coupled zinc antiporter SLC30A3 isoform X2
XM_054343816.1 → XP_054199791.1 probable proton-coupled zinc antiporter SLC30A3 isoform X5
XM_054343815.1 → XP_054199790.1 probable proton-coupled zinc antiporter SLC30A3 isoform X3
XM_054343817.1 → XP_054199792.1 probable proton-coupled zinc antiporter SLC30A3 isoform X6
XM_054343812.1 → XP_054199787.1 probable proton-coupled zinc antiporter SLC30A3 isoform X2
XM_054343811.1 → XP_054199786.1 probable proton-coupled zinc antiporter SLC30A3 isoform X1