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CDH13 cadherin 13 [ Homo sapiens (human) ]

Gene ID: 1012, updated on 12-Aug-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 
calcium ion binding IEA
Inferred from Electronic Annotation
more info
 
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 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
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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