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    CDH13 cadherin 13 [ Homo sapiens (human) ]

    Gene ID: 1012, updated on 14-Oct-2018

    Summary

    Official Symbol
    CDH13provided by HGNC
    Official Full Name
    cadherin 13provided by HGNC
    Primary source
    HGNC:HGNC:1753
    See related
    Ensembl:ENSG00000140945 MIM:601364; Vega:OTTHUMG00000176635
    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
    CDHH; P105
    Summary
    This gene encodes a member of the cadherin superfamily. The encoded protein is localized to the surface of the cell membrane and is anchored by a GPI moiety, rather than by a transmembrane domain. The protein lacks the cytoplasmic domain characteristic of other cadherins, and so is not thought to be a cell-cell adhesion glycoprotein. This protein acts as a negative regulator of axon growth during neural differentiation. It also protects vascular endothelial cells from apoptosis due to oxidative stress, and is associated with resistance to atherosclerosis. The gene is hypermethylated in many types of cancer. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2011]
    Expression
    Broad expression in endometrium (RPKM 22.0), heart (RPKM 17.7) and 16 other tissues See more
    Orthologs

    Genomic context

    See CDH13 in Genome Data Viewer
    Location:
    16q23.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 16 NC_000016.10 (82626794..83796610)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (82660399..83830215)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ribosomal protein L21 pseudogene Neighboring gene uncharacterized LOC101928392 Neighboring gene VISTA enhancer hs1959 Neighboring gene uncharacterized LOC101928446 Neighboring gene microRNA 8058 Neighboring gene RNA, 7SL, cytoplasmic 134, pseudogene Neighboring gene uncharacterized LOC101928417 Neighboring gene uncharacterized LOC105371368 Neighboring gene microRNA 3182 Neighboring gene uncharacterized LOC105371366 Neighboring gene uncharacterized LOC102724163 Neighboring gene heat shock factor binding protein 1

    Genomic regions, transcripts, and products

    Expression

    • 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
    NHGRI GWA Catalog
    A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients.
    NHGRI GWA Catalog
    A genome-wide association study of total serum and mite-specific IgEs in asthma patients.
    NHGRI GWA Catalog
    A genome-wide association study reveals a quantitative trait locus of adiponectin on CDH13 that predicts cardiometabolic outcomes.
    NHGRI GWA Catalog
    A meta-analysis of genome-wide association studies for adiponectin levels in East Asians identifies a novel locus near WDR11-FGFR2.
    NHGRI GWA Catalog
    Adiponectin concentrations: a genome-wide association study.
    NHGRI GWA Catalog
    CDH13 gene coding T-cadherin influences variations in plasma adiponectin levels in the Japanese population.
    NHGRI GWA Catalog
    Common genetic variation and performance on standardized cognitive tests.
    NHGRI GWA Catalog
    Framingham Heart Study 100K Project: genome-wide associations for blood pressure and arterial stiffness.
    NHGRI GWA Catalog
    Genetic predictors of fibrin D-dimer levels in healthy adults.
    NHGRI GWA Catalog
    Genome-wide association analyses identifies a susceptibility locus for tuberculosis on chromosome 18q11.2.
    NHGRI GWA Catalog
    Genome-wide association scan of trait depression.
    NHGRI GWA Catalog
    Genome-wide association study for adiponectin levels in Filipino women identifies CDH13 and a novel uncommon haplotype at KNG1-ADIPOQ.
    NHGRI GWA Catalog
    Genome-wide association study identifies three novel genetic markers associated with elite endurance performance.
    NHGRI GWA Catalog
    Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.
    NHGRI GWA Catalog
    Genome-wide association study of chronic periodontitis in a general German population.
    NHGRI GWA Catalog
    Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
    NHGRI GWA Catalog
    Genome-wide association study of smoking behaviours among Bangladeshi adults.
    NHGRI GWA Catalog
    Genome-wide association study on dimethylarginines reveals novel AGXT2 variants associated with heart rate variability but not with overall mortality.
    NHGRI GWA Catalog
    Genome-wide contribution of genotype by environment interaction to variation of diabetes-related traits.
    NHGRI GWA Catalog
    Genome-wide meta-analysis identifies new susceptibility loci for migraine.
    NHGRI GWA Catalog
    Genome-wide scan identifies CDH13 as a novel susceptibility locus contributing to blood pressure determination in two European populations.
    NHGRI GWA Catalog
    Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci.
    NHGRI GWA Catalog
    Genomewide pharmacogenomic study of metabolic side effects to antipsychotic drugs.
    NHGRI GWA Catalog
    Imputation-based meta-analysis of severe malaria in three African populations.
    NHGRI GWA Catalog
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    NHGRI GWA Catalog
    Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies.
    NHGRI GWA Catalog
    Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.
    NHGRI GWA Catalog
    Preliminary evidence of genetic determinants of adiponectin response to fenofibrate in the Genetics of Lipid Lowering Drugs and Diet Network.
    NHGRI GWA Catalog
    The CCND1 c.870G>A polymorphism is a risk factor for t(11;14)(q13;q32) multiple myeloma.
    NHGRI GWA Catalog

    Pathways from BioSystems

    • Adherens junctions interactions, organism-specific biosystem (from REACTOME)
      Adherens junctions interactions, organism-specific biosystemThe adherens junctions (AJ) are multiprotein complexes that promote homotypic cell adhesion in nearly all types of tissue by linking membrane and cytoskeletal components at discrete contact regions (...
    • Cell junction organization, organism-specific biosystem (from REACTOME)
      Cell junction organization, organism-specific biosystem
      Cell junction organization
    • Cell-Cell communication, organism-specific biosystem (from REACTOME)
      Cell-Cell communication, organism-specific biosystemCell-to-Cell communication is crucial for multicellular organisms because it allows organisms to coordinate the activity of their cells. Some cell-to-cell communication requires direct cell-cell cont...
    • Cell-cell junction organization, organism-specific biosystem (from REACTOME)
      Cell-cell junction organization, organism-specific biosystemEpithelial cell-cell contacts consist of three major adhesion systems: adherens junctions (AJs), tight junctions (TJs), and desmosomes. These adhesion systems differ in their function and compositio...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    adiponectin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    cadherin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cadherin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    calcium ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytoskeletal protein binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    lipoprotein particle binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    low-density lipoprotein particle binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein homodimerization activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    Rac protein signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Rho protein signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    adherens junction organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    adherens junction organization TAS
    Traceable Author Statement
    more info
     
    calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell-cell adhesion mediated by cadherin IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell-cell junction assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    endothelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    homophilic cell adhesion via plasma membrane adhesion molecules IDA
    Inferred from Direct Assay
    more info
    PubMed 
    keratinocyte proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    lamellipodium assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    localization within membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    low-density lipoprotein particle mediated signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    mitotic cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of cell adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of calcium-mediated signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of cell-matrix adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of endothelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of positive chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of smooth muscle cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of epidermal growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    sprouting angiogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    sprouting angiogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    GABA-ergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    anchored component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    catenin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    caveola IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell-cell adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    collagen-containing extracellular matrix HDA PubMed 
    cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular exosome HDA PubMed 
    extracellular region HDA PubMed 
    extracellular space IDA
    Inferred from Direct Assay
    more info
    PubMed 
    focal adhesion HDA PubMed 
    neuron projection IDA
    Inferred from Direct Assay
    more info
    PubMed 
    perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    cadherin-13
    Names
    H-cadherin (heart)
    T-cad
    T-cadherin
    cadherin 13, H-cadherin (heart)
    heart cadherin
    NP_001207417.1
    NP_001207418.1
    NP_001207419.1
    NP_001207420.1
    NP_001207421.1
    NP_001248.1
    XP_011521106.1
    XP_016878337.1
    XP_016878338.1

    NCBI Reference Sequences (RefSeq)

    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_052819.1 RefSeqGene

      Range
      5001..1174817
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001220488.1NP_001207417.1  cadherin-13 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes an alternate exon in the 5' coding region, compared to variant 1. It encodes isoform 2, which is longer and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AC092351, AK304733, BG911233, BU627784, CB321814, CF618908, CV024366, DA561809, DA685616, DB003683, DC376661, R41787
      Consensus CDS
      CCDS58485.1
      UniProtKB/TrEMBL
      B7Z9B1
      Related
      ENSP00000268613.10, OTTHUMP00000254669, ENST00000268613.14, OTTHUMT00000432918
      Conserved Domains (5) summary
      cd11304
      Location:535628
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:208290
      CA; Cadherin repeats
      pfam00028
      Location:415516
      Cadherin; Cadherin domain
      pfam08758
      Location:74159
      Cadherin_pro; Cadherin prodomain like
      cl09101
      Location:636727
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    2. NM_001220489.1NP_001207418.1  cadherin-13 isoform 3 precursor

      See identical proteins and their annotated locations for NP_001207418.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, compared to variant 1. It encodes isoform 3, which is shorter than isoform 1.
      Source sequence(s)
      AK298612, BG911233, BU627784, CB321814, CF618908, DA685616, DC376661, R41787
      Consensus CDS
      CCDS58487.1
      UniProtKB/Swiss-Prot
      P55290
      Related
      ENSP00000394557.3, OTTHUMP00000254675, ENST00000428848.7, OTTHUMT00000432925
      Conserved Domains (5) summary
      cd11304
      Location:449542
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:122204
      CA; Cadherin repeats
      pfam00028
      Location:329430
      Cadherin; Cadherin domain
      pfam08758
      Location:27112
      Cadherin_pro; Cadherin prodomain like
      cl09101
      Location:550641
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    3. NM_001220490.1NP_001207419.1  cadherin-13 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an exon in the coding region resulting in use of a downstream start codon, compared to variant 1. It encodes isoform 4, which is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK295886, BU162665, BU627784, CB321814, CF618908, DA685616, DC376661, R41787
      UniProtKB/TrEMBL
      B7Z3H7
      Conserved Domains (3) summary
      cd11304
      Location:234327
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam00028
      Location:114215
      Cadherin; Cadherin domain
      cl09101
      Location:335426
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
    4. NM_001220491.1NP_001207420.1  cadherin-13 isoform 5 precursor

      See identical proteins and their annotated locations for NP_001207420.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks several coding exons and uses an alternate 3' terminal exon, compared to variant 1. It encodes isoform 5, which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      DC376661, EU190358
      Consensus CDS
      CCDS56010.1
      UniProtKB/Swiss-Prot
      P55290
      Related
      ENSP00000408632.3, OTTHUMP00000254674, ENST00000431540.7, OTTHUMT00000432924
      Conserved Domains (1) summary
      pfam08758
      Location:27112
      Cadherin_pro; Cadherin prodomain like
    5. NM_001220492.1NP_001207421.1  cadherin-13 isoform 6 precursor

      See identical proteins and their annotated locations for NP_001207421.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) lacks several coding exons and includes two alternate exons at the 3' end, compared to variant 1. It encodes isoform 6, which is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      DC376661, EU190357
      Consensus CDS
      CCDS56009.1
      UniProtKB/Swiss-Prot
      P55290
      Related
      ENSP00000456491.1, OTTHUMP00000254673, ENST00000565636.5, OTTHUMT00000432923
      Conserved Domains (1) summary
      pfam08758
      Location:27112
      Cadherin_pro; Cadherin prodomain like
    6. NM_001257.4NP_001248.1  cadherin-13 isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_001248.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform 1.
      Source sequence(s)
      BC028624, BG911233, BI756586, BU627784, CA445317, CN263227, DC376661, R41787
      Consensus CDS
      CCDS58486.1
      UniProtKB/Swiss-Prot
      P55290
      Related
      ENSP00000479395.1, OTTHUMP00000254668, ENST00000567109.5, OTTHUMT00000432917
      Conserved Domains (5) summary
      cd11304
      Location:488581
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:161243
      CA; Cadherin repeats
      pfam00028
      Location:368469
      Cadherin; Cadherin domain
      pfam08758
      Location:27112
      Cadherin_pro; Cadherin prodomain like
      cl09101
      Location:589680
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p12 Primary Assembly

      Range
      82626794..83796610
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017022849.2XP_016878338.1  cadherin-13 isoform X3

    2. XM_017022848.2XP_016878337.1  cadherin-13 isoform X2

    3. XM_011522804.3XP_011521106.1  cadherin-13 isoform X1

      Conserved Domains (4) summary
      cd11304
      Location:387480
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:60142
      CA; Cadherin repeats
      pfam00028
      Location:267368
      Cadherin; Cadherin domain
      cl09101
      Location:488579
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus
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