SLC30A2 solute carrier family 30 member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC30A2provided by HGNC
Official Full Name: solute carrier family 30 member 2provided by HGNC
Primary source: HGNC:HGNC:11013
See related: Ensembl:ENSG00000158014 MIM:609617; AllianceGenome:HGNC:11013
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: TNZD; ZNT2; ZnT-2; PP12488
Summary: The protein encoded by this gene is a zinc transporter that acts as a homodimer. The encoded protein plays a role in secreting zinc into breast milk. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]
Expression: Biased expression in thyroid (RPKM 19.5), kidney (RPKM 11.8) and 4 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.11

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (26037252..26046118, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (25874654..25883519, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (26363743..26372609, complement)

Chromosome 1 - NC_000001.11 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
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?

Loss-of-function SLC30A2 mutants are associated with gut dysbiosis and alterations in intestinal gene expression in preterm infants.
Title: Loss-of-function SLC30A2 mutants are associated with gut dysbiosis and alterations in intestinal gene expression in preterm infants.
A novel homozygous mutation p.E88K in maternal SLC30A2 gene as a cause of transient neonatal zinc deficiency.
Title: A novel homozygous mutation p.E88K in maternal SLC30A2 gene as a cause of transient neonatal zinc deficiency.
Milk-derived miRNA profiles elucidate molecular pathways that underlie breast dysfunction in women with common genetic variants in SLC30A2.
Title: Milk-derived miRNA profiles elucidate molecular pathways that underlie breast dysfunction in women with common genetic variants in SLC30A2.
Thr288Ser mutation in SLC30A2/ZnT2 impairs critical functions of mammary epithelial cells, resulting in milk volume and altering lysosome function and cell energetics.
Title: A common genetic variant in zinc transporter ZnT2 (Thr288Ser) is present in women with low milk volume and alters lysosome function and cell energetics.
High proportion of alleles was found in the general population due to loss of function mutations in the zinc transporter ZnT2, which result in impaired zinc secretion into breast milk consequently causing transient neonatal zinc deficiency in exclusively breastfed infants.
Title: High proportion of transient neonatal zinc deficiency causing alleles in the general population.
This study confirms that ZnT2 is important for normal breast function in women during lactation, and suggests that women who harbor defective variants in ZnT2 may be at-risk for poor lactation performance.
Title: A genetic variant in SLC30A2 causes breast dysfunction during lactation by inducing ER stress, oxidative stress and epithelial barrier defects.
ZNT2 was localized on the cell surface of both human and mouse beta-cells, suggesting a role of ZNT2 in direct export of zinc out of the beta-cell
Title: SLC30A family expression in the pancreatic islets of humans and mice: cellular localization in the β-cells.
Article highlights the importance of early diagnosis of SLC30A2/ZnT2 variants in order to supplement zinc-deficient infants in real-time, thus preventing TNZD morbidity and enhancing newborn health. [Review]
Title: The role of the zinc transporter SLC30A2/ZnT2 in transient neonatal zinc deficiency.
many SLC30A2/ZnT2 mutations cause or potentially cause transient neonatal zinc deficiency, as shown in three cases of Japanese infants
Title: Novel mutations in SLC30A2 involved in the pathogenesis of transient neonatal zinc deficiency.
findings establish that some heterozygous loss of function ZnT2 mutations disrupt zinc binding and zinc permeation, thereby suggesting a haploinsufficiency state for the unaffected WT ZnT2 allele in Transient Neonatal Zinc Deficiency
Title: Molecular Basis of Transient Neonatal Zinc Deficiency: NOVEL ZnT2 MUTATIONS DISRUPTING ZINC BINDING AND PERMEATION.

Submit: New GeneRIF Correction See all GeneRIFs (22)

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

Associated conditions

Description	Tests
Zinc deficiency, transient neonatal MedGen: C1842486 OMIM: 608118 GeneReviews: Not available	Compare labs

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

SLC30A2_7908 (e-PCR)
- UniSTS:466445

WI-17216 (e-PCR)
- UniSTS:36397

D1S1361 (e-PCR)
- UniSTS:149557

D15S1477 (e-PCR)
- UniSTS:474482

D1S1423 (e-PCR)
- UniSTS:149619

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
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
enables zinc:proton antiporter activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in intracellular zinc ion homeostasis	IC Inferred by Curator more info	PubMed
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 lysosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in zinc ion import into mitochondrion	ISS Inferred from Sequence or Structural Similarity more info
involved_in zinc ion import into organelle	IDA Inferred from Direct Assay more info	PubMed
involved_in zinc ion import into organelle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in zinc ion import into zymogen granule	ISS Inferred from Sequence or Structural Similarity more info
involved_in zinc ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	HDA more info	PubMed
located_in lysosomal membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial inner membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in transport vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in zymogen granule membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: proton-coupled zinc antiporter SLC30A2

Names: solute carrier family 30 (zinc transporter), member 2; zinc transporter 2

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

NG_042808.1 RefSeqGene

Range

5021..13887

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001004434.3 → NP_001004434.1 proton-coupled zinc antiporter SLC30A2 isoform 1

See identical proteins and their annotated locations for NP_001004434.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AF370409, AI161067, AL391650, DR004258

Consensus CDS

CCDS30644.1

UniProtKB/Swiss-Prot

Q71RC8, Q9BRI3

Related

ENSP00000363394.3, ENST00000374276.4

Conserved Domains (2) summary

TIGR01297
Location:83 → 357

CDF; cation diffusion facilitator family transporter

pfam01545
Location:83 → 278

Cation_efflux; Cation efflux family
NM_032513.5 → NP_115902.1 proton-coupled zinc antiporter SLC30A2 isoform 2

See identical proteins and their annotated locations for NP_115902.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame segment, compared to variant 1, resulting in a shorter protein (isoform 2) that has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AF370409, AI161067, AL391650, BC006251, DR004258

Consensus CDS

CCDS272.1

UniProtKB/Swiss-Prot

Q9BRI3

Related

ENSP00000363396.3, ENST00000374278.7

Conserved Domains (1) summary

TIGR01297
Location:91 → 308

CDF; cation diffusion facilitator family transporter