SLC39A5 solute carrier family 39 member 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SLC39A5provided by HGNC
Official Full Name: solute carrier family 39 member 5provided by HGNC
Primary source: HGNC:HGNC:20502
See related: Ensembl:ENSG00000139540 MIM:608730; AllianceGenome:HGNC:20502
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: ZIP5; MYP24; LZT-Hs7
Summary: The protein encoded by this gene belongs to the ZIP family of zinc transporters that transport zinc into cells from outside, and play a crucial role in controlling intracellular zinc levels. Zinc is an essential cofactor for many enzymes and proteins involved in gene transcription, growth, development and differentiation. Mutations in this gene have been associated with autosomal dominant high myopia (MYP24). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]
Expression: Biased expression in duodenum (RPKM 78.5), small intestine (RPKM 76.3) and 4 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q13.3

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (56230051..56237846)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (56197676..56205471)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (56623835..56631630)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Genome-wide association study in the Taiwan Biobank identifies four novel genes for human height: NABP2, RASA2, RNF41 and SLC39A5.
Title: Genome-wide association study in the Taiwan Biobank identifies four novel genes for human height: NABP2, RASA2, RNF41 and SLC39A5.
SLC39A5 dysfunction impairs extracellular matrix synthesis in high myopia pathogenesis.
Title: SLC39A5 dysfunction impairs extracellular matrix synthesis in high myopia pathogenesis.
SLC39A5 promotes lung adenocarcinoma cell proliferation by activating PI3K/AKT signaling.
Title: SLC39A5 promotes lung adenocarcinoma cell proliferation by activating PI3K/AKT signaling.
we found that downregulation of ZIP5 by RNA interference inhibited esophageal cancer growth in vivo, reduced the expression of COX2, and promoted the expression of E-cadherin.
Title: Knockdown of Zinc Transporter ZIP5 by RNA Interference Inhibits Esophageal Cancer Growth In Vivo.
ZIP5 knockdown inhibited the proliferation, migration and invasion of ESCC and suppressed COX2, cyclin D1 and E-cadherin expression, which led to the inhibition of cell progression in esophageal squamous cell carcinoma .
Title: Knockdown of zinc transporter ZIP5 (SLC39A5) expression significantly inhibits human esophageal cancer progression.
mutation in LRPAP1 is associated with high myopia. Further studies are expected to evaluate the pathogenicity of the variants in CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2.
Title: Detection of mutations in LRPAP1, CTSH, LEPREL1, ZNF644, SLC39A5, and SCO2 in 298 families with early-onset high myopia by exome sequencing.
Zip5 protein is a zinc transporter that localizes to the basolateral surface of polarized cells
Title: The mammalian Zip5 protein is a zinc transporter that localizes to the basolateral surface of polarized cells.

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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
Myopia 24, autosomal dominant MedGen: C4014762 OMIM: 615946 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

RH98394 (e-PCR)
- UniSTS:89952

SGC34394 (e-PCR)
- UniSTS:644

RH70180 (e-PCR)
- UniSTS:78315

Homology

Homologs of the SLC39A5 gene: The SLC39A5 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, and rat.
Orthologs from Annotation Pipeline: 279 organisms have orthologs with human gene SLC39A5
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables molecular_function	ND No biological Data available more info
enables zinc ion transmembrane transporter activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Process	Evidence Code	Pubs
involved_in BMP signaling pathway	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in BMP signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in G1 to G0 transition involved in cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to zinc ion starvation	IEA Inferred from Electronic Annotation more info
involved_in eye development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular zinc ion homeostasis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in neural precursor cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of mRNA splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in zinc ion import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Component	Evidence Code	Pubs
located_in basolateral plasma membrane	IEA Inferred from Electronic Annotation more info
located_in extracellular exosome	HDA more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed

General protein information

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Preferred Names: zinc transporter ZIP5

Names: ZRT/IRT-like protein 5; solute carrier family 39 (metal ion transporter), member 5; solute carrier family 39 (zinc transporter), member 5; zinc transporter 5; zrt- and Irt-like protein 5

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_034265.2 RefSeqGene

Range

5002..12797

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001135195.1 → NP_001128667.1 zinc transporter ZIP5 precursor

See identical proteins and their annotated locations for NP_001128667.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AK172768, DA640935

Consensus CDS

CCDS8912.2

UniProtKB/Swiss-Prot

Q6ZMH5, Q8N6Y3

UniProtKB/TrEMBL

A0A024RB24

Related

ENSP00000266980.4, ENST00000266980.8

Conserved Domains (1) summary

pfam02535
Location:248 → 504

Zip; ZIP Zinc transporter
NM_173596.3 → NP_775867.2 zinc transporter ZIP5 precursor

See identical proteins and their annotated locations for NP_775867.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AC073896

Consensus CDS

CCDS8912.2

UniProtKB/Swiss-Prot

Q6ZMH5, Q8N6Y3

UniProtKB/TrEMBL

A0A024RB24

Related

ENSP00000405360.2, ENST00000454355.7

Conserved Domains (1) summary

pfam02535
Location:248 → 504

Zip; ZIP Zinc transporter