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

Summary

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

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_000011.10 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?

Possible involvement of zinc transporter ZIP13 in myogenic differentiation.
Title: Possible involvement of zinc transporter ZIP13 in myogenic differentiation.
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.
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.
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.
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.
human ZIP13 releases zinc from vesicular stores
Title: Promotion of vesicular zinc efflux by ZIP13 and its implications for spondylocheiro dysplastic Ehlers-Danlos syndrome.
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.
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.
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.

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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
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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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

NG_017073.2 RefSeqGene

Range

6316..14222

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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

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

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

47407276..47416500

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

pfam02535
Location:65 → 329

Zip; ZIP Zinc transporter
XM_017018541.3 → XP_016874030.1 zinc transporter ZIP13 isoform X8
XM_047427859.1 → XP_047283815.1 zinc transporter ZIP13 isoform X11
XM_047427860.1 → XP_047283816.1 zinc transporter ZIP13 isoform X12

Related

ENSP00000432499.1, ENST00000526614.5
XM_011520466.2 → XP_011518768.1 zinc transporter ZIP13 isoform X1

Conserved Domains (1) summary

pfam02535
Location:80 → 380

Zip; ZIP Zinc transporter
XM_006718381.4 → XP_006718444.1 zinc transporter ZIP13 isoform X2

Conserved Domains (1) summary

pfam02535
Location:80 → 373

Zip; ZIP Zinc transporter
XM_006718384.3 → XP_006718447.1 zinc transporter ZIP13 isoform X6

Conserved Domains (1) summary

pfam02535
Location:80 → 313

Zip; ZIP Zinc transporter
XM_011520469.1 → XP_011518771.1 zinc transporter ZIP13 isoform X4

Conserved Domains (1) summary

pfam02535
Location:80 → 344

Zip; ZIP Zinc transporter
XM_006718383.4 → XP_006718446.1 zinc transporter ZIP13 isoform X5

Conserved Domains (1) summary

pfam02535
Location:80 → 337

Zip; ZIP Zinc transporter
XM_047427857.1 → XP_047283813.1 zinc transporter ZIP13 isoform X9
XM_047427858.1 → XP_047283814.1 zinc transporter ZIP13 isoform X10