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

    Gene ID: 91252, updated on 10-Dec-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
    mouse all
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    Genomic context

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    See SLC39A13 in Genome Data Viewer
    Location:
    11p11.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (47407276..47416500)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (47566179..47575404)
    RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. 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
    2. 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
    3. 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
    4. 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
    5. 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

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Possible involvement of zinc transporter ZIP13 in myogenic differentiation.
      Title: Possible involvement of zinc transporter ZIP13 in myogenic differentiation.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. human ZIP13 releases zinc from vesicular stores
      Title: Promotion of vesicular zinc efflux by ZIP13 and its implications for spondylocheiro dysplastic Ehlers-Danlos syndrome.
    7. 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.
    8. 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.
    9. 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
    		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)

    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_2024_08

    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

      UniProtKB/TrEMBL
      K4DIA9

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

      UniProtKB/TrEMBL
      K4DIA9
      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

      UniProtKB/TrEMBL
      K4DIA9

    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

      UniProtKB/TrEMBL
      K4DIA9

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

      UniProtKB/TrEMBL
      K4DIA9

    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

      UniProtKB/TrEMBL
      K4DIA9

    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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