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Aliases for SLC39A13 Gene

Aliases for SLC39A13 Gene

  • Solute Carrier Family 39 Member 13 2 3 4 5
  • Solute Carrier Family 39 (Metal Ion Transporter), Member 13 2 3
  • Solute Carrier Family 39 (Zinc Transporter), Member 13 2 3
  • LIV-1 Subfamily Of ZIP Zinc Transporter 9 3 4
  • Zrt- And Irt-Like Protein 13 3 4
  • LZT-Hs9 3 4
  • ZIP13 3 4
  • Zinc Transporter ZIP13 3
  • SCDEDS 3
  • ZIP-13 4

External Ids for SLC39A13 Gene

Previous GeneCards Identifiers for SLC39A13 Gene

  • GC00U912991
  • GC11P047393
  • GC11P047394
  • GC11P047350
  • GC11P047130

Summaries for SLC39A13 Gene

Entrez Gene Summary for SLC39A13 Gene

  • 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]

GeneCards Summary for SLC39A13 Gene

SLC39A13 (Solute Carrier Family 39 Member 13) is a Protein Coding gene. Diseases associated with SLC39A13 include Ehlers-Danlos Syndrome, Spondylodysplastic Type, 3 and Ehlers-Danlos Syndrome. Among its related pathways are Metal ion SLC transporters and NRF2 pathway. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and zinc ion transmembrane transporter activity. An important paralog of this gene is SLC39A7.

UniProtKB/Swiss-Prot for SLC39A13 Gene

  • Acts as a zinc-influx transporter.

Additional gene information for SLC39A13 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC39A13 Gene

Genomics for SLC39A13 Gene

GeneHancer (GH) Regulatory Elements for SLC39A13 Gene

Promoters and enhancers for SLC39A13 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11I047406 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 +1.9 1872 4.3 HDGF PKNOX1 CLOCK ARNT ZFP64 ARID4B SIN3A DMAP1 YBX1 IRF4 ENSG00000255197 SLC39A13 C1QTNF4 FNBP4 PSMC3
GH11I047373 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 23.2 -30.5 -30490 6.2 HDGF PKNOX1 SMAD1 ARID4B SIN3A YBX1 POLR2B ZNF766 CBX5 ZNF207 SPI1 GC11M054465 FNBP4 NUP160 ENSG00000200090 ENSG00000270060 C1QTNF4 SLC39A13 PSMC3 DDB2
GH11I047506 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 30.2 +106.4 106449 14.4 HDGF PKNOX1 ZFP64 ZNF213 FOS JUNB ZC3H11A REST SREBF1 SMARCA4 ENSG00000270072 NUP160 FNBP4 ENSG00000200090 ENSG00000270060 C1QTNF4 ZNF408 DDB2 AMBRA1 CELF1
GH11I047267 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.6 -136.8 -136788 5.4 HDGF PKNOX1 CLOCK FOXA2 ARNT ZFP64 ARID4B SIN3A FEZF1 YY1 MADD LOC101928943 FNBP4 NUP160 ENSG00000270060 ENSG00000200090 DDB2 ACP2 RPS10P19 PACSIN3
GH11I047354 Enhancer 1.4 Ensembl ENCODE dbSUPER 13.1 -51.7 -51700 1.7 HDGF PKNOX1 CLOCK ARID4B NEUROD1 SIN3A DMAP1 ZNF2 ZBTB7B POLR2B NUP160 FNBP4 ENSG00000200090 C1QTNF4 ENSG00000270060 AMBRA1 RPS10P19 DDB2 ZNF408 SLC39A13
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SLC39A13 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SLC39A13 gene promoter:

Genomic Locations for SLC39A13 Gene

Genomic Locations for SLC39A13 Gene
chr11:47,407,132-47,416,501
(GRCh38/hg38)
Size:
9,370 bases
Orientation:
Plus strand
chr11:47,428,683-47,438,051
(GRCh37/hg19)

Genomic View for SLC39A13 Gene

Genes around SLC39A13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC39A13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC39A13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC39A13 Gene

Proteins for SLC39A13 Gene

  • Protein details for SLC39A13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96H72-S39AD_HUMAN
    Recommended name:
    Zinc transporter ZIP13
    Protein Accession:
    Q96H72
    Secondary Accessions:
    • D3DQR6
    • D3DQR7
    • E9PLY1
    • E9PQV3
    • Q659D9
    • Q8N7C9
    • Q8WV10

    Protein attributes for SLC39A13 Gene

    Size:
    371 amino acids
    Molecular mass:
    39011 Da
    Quaternary structure:
    • Homodimer.
    SequenceCaution:
    • Sequence=BAC05365.1; Type=Frameshift; Positions=314; Evidence={ECO:0000305};

    Alternative splice isoforms for SLC39A13 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC39A13 Gene

Post-translational modifications for SLC39A13 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SLC39A13 Gene

Domains & Families for SLC39A13 Gene

Gene Families for SLC39A13 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Disease related genes
  • Potential drug targets
  • Predicted membrane proteins
  • Transporters

Protein Domains for SLC39A13 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for SLC39A13 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96H72

UniProtKB/Swiss-Prot:

S39AD_HUMAN :
  • Belongs to the ZIP transporter (TC 2.A.5) family.
Family:
  • Belongs to the ZIP transporter (TC 2.A.5) family.
genes like me logo Genes that share domains with SLC39A13: view

Function for SLC39A13 Gene

Molecular function for SLC39A13 Gene

UniProtKB/Swiss-Prot Function:
Acts as a zinc-influx transporter.

Phenotypes From GWAS Catalog for SLC39A13 Gene

Gene Ontology (GO) - Molecular Function for SLC39A13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005385 zinc ion transmembrane transporter activity IDA 21917916
GO:0005515 protein binding IPI 25416956
GO:0042803 protein homodimerization activity IPI 21917916
GO:0046873 metal ion transmembrane transporter activity IEA --
genes like me logo Genes that share ontologies with SLC39A13: view
genes like me logo Genes that share phenotypes with SLC39A13: view

Human Phenotype Ontology for SLC39A13 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SLC39A13 Gene

MGI Knock Outs for SLC39A13:

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SLC39A13 Gene

Localization for SLC39A13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC39A13 Gene

Golgi apparatus membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SLC39A13 gene
Compartment Confidence
golgi apparatus 4
plasma membrane 3
endoplasmic reticulum 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SLC39A13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005794 Golgi apparatus ISS 18985159
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,IDA 21917916
GO:0030173 integral component of Golgi membrane IC 21917916
genes like me logo Genes that share ontologies with SLC39A13: view

Pathways & Interactions for SLC39A13 Gene

SuperPathways for SLC39A13 Gene

SuperPathway Contained pathways
1 NRF2 pathway
2 Metal ion SLC transporters
genes like me logo Genes that share pathways with SLC39A13: view

Pathways by source for SLC39A13 Gene

2 BioSystems pathways for SLC39A13 Gene

Interacting Proteins for SLC39A13 Gene

Gene Ontology (GO) - Biological Process for SLC39A13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006810 transport IEA --
GO:0006811 ion transport IEA --
GO:0006829 zinc II ion transport IEA --
GO:0006882 cellular zinc ion homeostasis ISS 18985159
GO:0010043 response to zinc ion IEA --
genes like me logo Genes that share ontologies with SLC39A13: view

No data available for SIGNOR curated interactions for SLC39A13 Gene

Drugs & Compounds for SLC39A13 Gene

No Compound Related Data Available

Transcripts for SLC39A13 Gene

Unigene Clusters for SLC39A13 Gene

Solute carrier family 39 (zinc transporter), member 13:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC39A13 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14a · 14b · 14c ^ 15a · 15b ·
SP1: - - - - - - - - - -
SP2: - - - - - - -
SP3: - - - - - - -
SP4: - - - - - -
SP5: - - - - -
SP6: - - - - -
SP7: - - -
SP8: -
SP9: -
SP10: - - -
SP11: -
SP12:
SP13:
SP14:

ExUns: 15c ^ 16
SP1: -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for SLC39A13 Gene

GeneLoc Exon Structure for
SLC39A13
ECgene alternative splicing isoforms for
SLC39A13

Expression for SLC39A13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SLC39A13 Gene

Protein differential expression in normal tissues from HIPED for SLC39A13 Gene

This gene is overexpressed in Lung (36.4), Heart (21.6), and Bone marrow stromal cell (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SLC39A13 Gene



Protein tissue co-expression partners for SLC39A13 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SLC39A13 Gene:

SLC39A13

SOURCE GeneReport for Unigene cluster for SLC39A13 Gene:

Hs.523664

Evidence on tissue expression from TISSUES for SLC39A13 Gene

  • Nervous system(4.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SLC39A13 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • eye
  • eyelid
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • pharynx
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with SLC39A13: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SLC39A13 Gene

Orthologs for SLC39A13 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SLC39A13 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLC39A13 33 34
  • 97.89 (n)
dog
(Canis familiaris)
Mammalia SLC39A13 33 34
  • 91.83 (n)
cow
(Bos Taurus)
Mammalia SLC39A13 33 34
  • 89.9 (n)
rat
(Rattus norvegicus)
Mammalia Slc39a13 33
  • 88.1 (n)
mouse
(Mus musculus)
Mammalia Slc39a13 33 16 34
  • 87.53 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SLC39A13 34
  • 78 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SLC39A13 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves SLC39A13 33 34
  • 69.25 (n)
lizard
(Anolis carolinensis)
Reptilia SLC39A13 34
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia slc39a13 33
  • 64.42 (n)
zebrafish
(Danio rerio)
Actinopterygii slc39a13 33 34
  • 62.24 (n)
wufa55a07 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8902 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003300 33
  • 55.98 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG7816 33 34
  • 55.16 (n)
worm
(Caenorhabditis elegans)
Secernentea C14H10.1 33 34
  • 49.5 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes YKE4 34
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 49 (a)
OneToOne
Species where no ortholog for SLC39A13 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC39A13 Gene

ENSEMBL:
Gene Tree for SLC39A13 (if available)
TreeFam:
Gene Tree for SLC39A13 (if available)

Paralogs for SLC39A13 Gene

genes like me logo Genes that share paralogs with SLC39A13: view

Variants for SLC39A13 Gene

Sequence variations from dbSNP and Humsavar for SLC39A13 Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs121434363 pathogenic, Spondylocheirodysplasia, Ehlers-Danlos syndrome-like 47,410,315(+) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs140574574 conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign, not specified, Abnormality of connective tissue, Abnormality of the skeletal system, Cutis laxa, Mitral valve prolapse, Myopia, Scleroderma, not provided, Spondylocheirodysplasia, Ehlers-Danlos syndrome-like 47,412,022(+) C/A/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs140844921 likely-benign, Spondylocheirodysplasia, Ehlers-Danlos syndrome-like 47,410,172(+) C/A coding_sequence_variant, non_coding_transcript_variant, synonymous_variant
rs147495812 likely-benign, Spondylocheirodysplasia, Ehlers-Danlos syndrome-like 47,413,477(+) C/G/T coding_sequence_variant, intron_variant, non_coding_transcript_variant, synonymous_variant
rs148291843 benign, conflicting-interpretations-of-pathogenicity, likely-benign, not specified, not provided, Spondylocheirodysplasia, Ehlers-Danlos syndrome-like 47,412,369(+) C/G coding_sequence_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for SLC39A13 Gene

Variant ID Type Subtype PubMed ID
nsv554210 CNV loss 21841781
nsv825871 CNV gain 20364138
nsv832141 CNV loss 17160897

Variation tolerance for SLC39A13 Gene

Residual Variation Intolerance Score: 42.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.42; 63.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SLC39A13 Gene

Human Gene Mutation Database (HGMD)
SLC39A13
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SLC39A13

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SLC39A13 Gene

Disorders for SLC39A13 Gene

MalaCards: The human disease database

(3) MalaCards diseases for SLC39A13 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

S39AD_HUMAN
  • Ehlers-Danlos syndrome-like spondylocheirodysplasia (SCD-EDS) [MIM:612350]: Spondylocheiro dysplastic form of Ehlers-Danlos syndrome. The syndrome consists of a generalized skeletal dysplasia involving mainly the spine (spondylo) and striking clinical abnormalities of the hands (cheiro) in addition to the EDS-like features. Clinical features included postnatal growth retardation, moderate short stature, protuberant eyes with bluish sclerae, hands with finely wrinkled palms, atrophy of the thenar muscles, and tapering fingers. Patients have thin, hyperelastic skin and hypermobile small joints consistent with an Ehlers-Danlos-like phenotype. Radiologic features included mild to moderate platyspondyly, mild to moderate osteopenia of the spine, small ileum, flat proximal femoral epiphyses, short, wide femoral necks, and broad metaphyses (elbows, knees, wrists, and interphalangeal joints). {ECO:0000269 PubMed:18513683}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SLC39A13

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SLC39A13: view

No data available for Genatlas for SLC39A13 Gene

Publications for SLC39A13 Gene

  1. Biochemical characterization of human ZIP13 protein: a homo-dimerized zinc transporter involved in the spondylocheiro dysplastic Ehlers-Danlos syndrome. (PMID: 21917916) Bin BH … Hirano T (The Journal of biological chemistry 2011) 3 4 58
  2. Polymorphisms in mitochondrial genes and prostate cancer risk. (PMID: 19064571) Wang L … Thibodeau SN (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2008) 3 44 58
  3. Spondylocheiro dysplastic form of the Ehlers-Danlos syndrome--an autosomal-recessive entity caused by mutations in the zinc transporter gene SLC39A13. (PMID: 18513683) Giunta C … Steinmann B (American journal of human genetics 2008) 3 4 58
  4. The LZT proteins; the LIV-1 subfamily of zinc transporters. (PMID: 12659941) Taylor KM … Nicholson RI (Biochimica et biophysica acta 2003) 2 3 58
  5. Phospho-tyrosine dependent protein-protein interaction network. (PMID: 25814554) Grossmann A … Stelzl U (Molecular systems biology 2015) 3 58

Products for SLC39A13 Gene

Sources for SLC39A13 Gene

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