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SLC39A13 solute carrier family 39 member 13 [ Homo sapiens (human) ]

Gene ID: 91252, updated on 3-Apr-2024

Summary

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Official Symbol
SLC39A13provided by HGNC
Official Full Name
solute carrier family 39 member 13provided by HGNC
Primary source
HGNC:HGNC:20859
See related
Ensembl:ENSG00000165915 MIM:608735; AllianceGenome:HGNC:20859
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
ZIP13; SCDEDS; EDSSPD3; LZT-Hs9
Summary
This gene encodes a member of the LIV-1 subfamily of the ZIP transporter family. The encoded transmembrane protein functions as a zinc transporter. Mutations in this gene have been associated with the spondylocheiro dysplastic form of Ehlers-Danlos syndrome. Alternate transcript variants have been found for this gene. [provided by RefSeq, Jan 2016]
Expression
Ubiquitous expression in placenta (RPKM 19.2), testis (RPKM 13.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11p11.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (47407276..47416500)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (47566179..47575404)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (47428827..47438051)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene Spi-1 proto-oncogene Neighboring gene ReSE screen-validated silencer GRCh37_chr11:47387327-47387502 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47395717-47396218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4696 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4697 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47399745-47400696 Neighboring gene SLC39A13 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47415859-47416416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3327 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:47421989-47422989 Neighboring gene microRNA 4487 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:47429423-47430245 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47430534-47431400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47431401-47432265 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:47435437-47435936 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:47447617-47447828 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4699 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3329 Neighboring gene proteasome 26S subunit, ATPase 3 Neighboring gene uncharacterized LOC124902673 Neighboring gene uncharacterized LOC124902820 Neighboring gene receptor associated protein of the synapse

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
  • 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. Zinc transporter SLC39A13/ZIP13 facilitates the metastasis of human ovarian cancer cells via activating Src/FAK signaling pathway. Cheng X, et al. J Exp Clin Cancer Res, 2021 Jun 21. PMID 34154618, Free PMC Article
  2. The Connective Tissue Disorder Associated with Recessive Variants in the SLC39A13 Zinc Transporter Gene (Spondylo-Dysplastic Ehlers-Danlos Syndrome Type 3): Insights from Four Novel Patients and Follow-Up on Two Original Cases. Kumps C, et al. Genes (Basel), 2020 Apr 14. PMID 32295219, Free PMC Article
  3. Molecular pathogenesis of spondylocheirodysplastic Ehlers-Danlos syndrome caused by mutant ZIP13 proteins. Bin BH, et al. EMBO Mol Med, 2014 Aug. PMID 25007800, Free PMC Article
  4. Promotion of vesicular zinc efflux by ZIP13 and its implications for spondylocheiro dysplastic Ehlers-Danlos syndrome. Jeong J, et al. Proc Natl Acad Sci U S A, 2012 Dec 18. PMID 23213233, Free PMC Article
  5. Mutational analysis of 12 patients with the phenotype of Ehlers-Danlos syndrome type VIB shows no linkage to the zinc transporter gene SLC39A13. Walker LC, et al. Am J Med Genet A, 2011 Aug. PMID 21739577, Free PMC Article

See all (22) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Zinc transporter SLC39A13/ZIP13 facilitates the metastasis of human ovarian cancer cells via activating Src/FAK signaling pathway.
    Title: Zinc transporter SLC39A13/ZIP13 facilitates the metastasis of human ovarian cancer cells via activating Src/FAK signaling pathway.
  2. The Connective Tissue Disorder Associated with Recessive Variants in the SLC39A13 Zinc Transporter Gene (Spondylo-Dysplastic Ehlers-Danlos Syndrome Type 3): Insights from Four Novel Patients and Follow-Up on Two Original Cases.
    Title: The Connective Tissue Disorder Associated with Recessive Variants in the SLC39A13 Zinc Transporter Gene (Spondylo-Dysplastic Ehlers-Danlos Syndrome Type 3): Insights from Four Novel Patients and Follow-Up on Two Original Cases.
  3. The spondylocheiro dysplastic form of Ehlers-Danlos syndrome, in which ZIP13 is defective, is likely due to a failure of iron delivery to the secretory compartments.
    Title: The metal transporter ZIP13 supplies iron into the secretory pathway in Drosophila melanogaster.
  4. Authors demonstrated that both the ZIP13(G64D) and ZIP13(DeltaFLA) protein levels are decreased by degradation via the valosin-containing protein (VCP)-linked ubiquitin proteasome pathway.
    Title: Molecular pathogenesis of spondylocheirodysplastic Ehlers-Danlos syndrome caused by mutant ZIP13 proteins.
  5. human ZIP13 releases zinc from vesicular stores
    Title: Promotion of vesicular zinc efflux by ZIP13 and its implications for spondylocheiro dysplastic Ehlers-Danlos syndrome.
  6. Biochemical characterization of human ZIP13 protein: a homo-dimerized zinc transporter involved in the spondylocheiro dysplastic Ehlers-Danlos syndrome.
    Title: Biochemical characterization of human ZIP13 protein: a homo-dimerized zinc transporter involved in the spondylocheiro dysplastic Ehlers-Danlos syndrome.
  7. mutations in the SLC39A13 gene do not account for the Ehlers-Danlos syndrome type VIB phenotype
    Title: Mutational analysis of 12 patients with the phenotype of Ehlers-Danlos syndrome type VIB shows no linkage to the zinc transporter gene SLC39A13.
  8. clinical features of 6 patients from 2 consanguineous families with Ehlers-Danlos syndrome-like features caused by a mutation in the zinc transporter gene SLC39A13
    Title: Spondylocheiro dysplastic form of the Ehlers-Danlos syndrome--an autosomal-recessive entity caused by mutations in the zinc transporter gene SLC39A13.
Submit: New GeneRIF Correction

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
Ehlers-Danlos syndrome, spondylocheirodysplastic type
MedGen: C2676510 OMIM: 612350 GeneReviews: Not available
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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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Homology

Clone Names

  • FLJ25785

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity 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 IC
Inferred by Curator
more info
 PubMed 
enables zinc ion transmembrane transporter activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables zinc ion transmembrane transporter activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in brown fat cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in connective tissue development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intracellular zinc ion homeostasis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular zinc ion homeostasis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in intracellular zinc ion homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
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 ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in zinc ion transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in Golgi membrane IC
Inferred by Curator
more info
 PubMed 
located_in Golgi membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic vesicle membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 

General protein information

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Preferred Names
zinc transporter ZIP13
Names
LIV-1 subfamily of ZIP zinc transporter 9
LIV-1 subfamily of ZIP zinc transporters human member 9
ZRT/IRT-like protein 13
solute carrier family 39 (metal ion transporter), member 13
solute carrier family 39 (zinc transporter), member 13
zinc transporter 13
zrt- and Irt-like protein 13

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

  1. NG_017073.2 RefSeqGene

    Range
    6316..14222
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001128225.3 → NP_001121697.2  zinc transporter ZIP13 isoform a precursor

    Status: REVIEWED

    Source sequence(s)
    AC090559
    Consensus CDS
    CCDS44592.1
    UniProtKB/Swiss-Prot
    D3DQR6, D3DQR7, E9PLY1, E9PQV3, Q659D9, Q8N7C9, Q8WV10, Q96H72
    Related
    ENSP00000354689.4, ENST00000362021.9
    Conserved Domains (1) summary
    pfam02535
    Location:65 → 365
    Zip; ZIP Zinc transporter

  2. NM_001330245.2 → NP_001317174.2  zinc transporter ZIP13 isoform c precursor

    Status: REVIEWED

    Source sequence(s)
    AC090559
    Consensus CDS
    CCDS81564.1
    UniProtKB/TrEMBL
    G3V1B2
    Related
    ENSP00000434290.1, ENST00000533076.5
    Conserved Domains (1) summary
    pfam02535
    Location:65 → 298
    Zip; ZIP Zinc transporter

  3. NM_152264.5 → NP_689477.3  zinc transporter ZIP13 isoform b precursor

    Status: REVIEWED

    Source sequence(s)
    AC090559
    Consensus CDS
    CCDS7934.1
    Related
    ENSP00000346956.4, ENST00000354884.8
    Conserved Domains (1) summary
    pfam02535
    Location:65 → 358
    Zip; ZIP Zinc transporter

RNA

  1. NR_134854.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AK098651, AL133581

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    47407276..47416500
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520467.2 → XP_011518769.1  zinc transporter ZIP13 isoform X13

    See identical proteins and their annotated locations for XP_011518769.1

    UniProtKB/Swiss-Prot
    D3DQR6, D3DQR7, E9PLY1, E9PQV3, Q659D9, Q8N7C9, Q8WV10, Q96H72
    Conserved Domains (1) summary
    pfam02535
    Location:65 → 365
    Zip; ZIP Zinc transporter

  2. XM_017018540.2 → XP_016874029.1  zinc transporter ZIP13 isoform X3

    UniProtKB/Swiss-Prot
    Q96H72
    Conserved Domains (1) summary
    pfam02535
    Location:65 → 358
    Zip; ZIP Zinc transporter

  3. XM_011520470.2 → XP_011518772.1  zinc transporter ZIP13 isoform X7

    Conserved Domains (1) summary
    pfam02535
    Location:65 → 329
    Zip; ZIP Zinc transporter

  4. XM_017018541.3 → XP_016874030.1  zinc transporter ZIP13 isoform X8

  5. XM_047427859.1 → XP_047283815.1  zinc transporter ZIP13 isoform X11

  6. XM_047427860.1 → XP_047283816.1  zinc transporter ZIP13 isoform X12

    Related
    ENSP00000432499.1, ENST00000526614.5

  7. XM_011520466.2 → XP_011518768.1  zinc transporter ZIP13 isoform X1

    Conserved Domains (1) summary
    pfam02535
    Location:80 → 380
    Zip; ZIP Zinc transporter

  8. XM_006718381.4 → XP_006718444.1  zinc transporter ZIP13 isoform X2

    Conserved Domains (1) summary
    pfam02535
    Location:80 → 373
    Zip; ZIP Zinc transporter

  9. XM_006718384.3 → XP_006718447.1  zinc transporter ZIP13 isoform X6

    Conserved Domains (1) summary
    pfam02535
    Location:80 → 313
    Zip; ZIP Zinc transporter

  10. XM_011520469.1 → XP_011518771.1  zinc transporter ZIP13 isoform X4

    Conserved Domains (1) summary
    pfam02535
    Location:80 → 344
    Zip; ZIP Zinc transporter

  11. XM_006718383.4 → XP_006718446.1  zinc transporter ZIP13 isoform X5

    Conserved Domains (1) summary
    pfam02535
    Location:80 → 337
    Zip; ZIP Zinc transporter

  12. XM_047427857.1 → XP_047283813.1  zinc transporter ZIP13 isoform X9

  13. XM_047427858.1 → XP_047283814.1  zinc transporter ZIP13 isoform X10

RNA

  1. XR_007062524.1 RNA Sequence

  2. XR_007062525.1 RNA Sequence

  3. XR_007062527.1 RNA Sequence

  4. XR_930928.3 RNA Sequence

  5. XR_428862.4 RNA Sequence

  6. XR_007062526.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    47566179..47575404
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370479.1 → XP_054226454.1  zinc transporter ZIP13 isoform X13

  2. XM_054370469.1 → XP_054226444.1  zinc transporter ZIP13 isoform X3

  3. XM_054370473.1 → XP_054226448.1  zinc transporter ZIP13 isoform X7

  4. XM_054370474.1 → XP_054226449.1  zinc transporter ZIP13 isoform X8

  5. XM_054370477.1 → XP_054226452.1  zinc transporter ZIP13 isoform X11

  6. XM_054370478.1 → XP_054226453.1  zinc transporter ZIP13 isoform X12

  7. XM_054370467.1 → XP_054226442.1  zinc transporter ZIP13 isoform X1

  8. XM_054370468.1 → XP_054226443.1  zinc transporter ZIP13 isoform X2

  9. XM_054370472.1 → XP_054226447.1  zinc transporter ZIP13 isoform X6

  10. XM_054370470.1 → XP_054226445.1  zinc transporter ZIP13 isoform X4

  11. XM_054370471.1 → XP_054226446.1  zinc transporter ZIP13 isoform X5

  12. XM_054370475.1 → XP_054226450.1  zinc transporter ZIP13 isoform X9

  13. XM_054370476.1 → XP_054226451.1  zinc transporter ZIP13 isoform X10

RNA

  1. XR_008488487.1 RNA Sequence

  2. XR_008488488.1 RNA Sequence

  3. XR_008488490.1 RNA Sequence

  4. XR_008488485.1 RNA Sequence

  5. XR_008488486.1 RNA Sequence

  6. XR_008488489.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96H72.3 GenPept UniProtKB/Swiss-Prot:Q96H72

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