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    CDH13 cadherin 13 [ Homo sapiens (human) ]

    Gene ID: 1012, updated on 2-Nov-2024

    Summary

    Official Symbol
    CDH13provided by HGNC
    Official Full Name
    cadherin 13provided by HGNC
    Primary source
    HGNC:HGNC:1753
    See related
    Ensembl:ENSG00000140945 MIM:601364; AllianceGenome:HGNC:1753
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CDH13 in Genome Data Viewer
    Location:
    16q23.3
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (82626969..83800640)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (88691276..89866370)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (82660574..83834245)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903788 Neighboring gene uncharacterized LOC101928392 Neighboring gene NANOG hESC enhancer GRCh37_chr16:82632313-82632847 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:82639412-82639926 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr16:82639927-82640441 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:82654558-82655058 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:82662659-82663858 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:82677536-82678144 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:82678145-82678752 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:82687085-82688284 Neighboring gene Sharpr-MPRA regulatory region 6595 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:82732677-82733876 Neighboring gene VISTA enhancer hs1959 Neighboring gene uncharacterized LOC101928446 Neighboring gene microRNA 8058 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:82914857-82915067 Neighboring gene uncharacterized LOC124903733 Neighboring gene RNA, 7SL, cytoplasmic 134, pseudogene Neighboring gene uncharacterized LOC101928417 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:83040047-83040230 Neighboring gene NANOG hESC enhancer GRCh37_chr16:83148253-83148855 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:83377629-83378828 Neighboring gene CDH13 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11230 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83544199-83544719 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr16:83566380-83567579 Neighboring gene NANOG hESC enhancer GRCh37_chr16:83580087-83580647 Neighboring gene microRNA 3182 Neighboring gene uncharacterized LOC124900603 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83714283-83714784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83714785-83715284 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:83716515-83717015 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_46306 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:83761543-83762043 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11231 Neighboring gene uncharacterized LOC124903810 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7767 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:83841377-83841878 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83847557-83848068 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83847045-83847556 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83846533-83847044 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr16:83850559-83851758 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83873977-83874624 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:83874625-83875272 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:83875273-83875919 Neighboring gene CDH13 antisense oligodendrocyte and neuron associated lncRNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83879897-83880398 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83880399-83880898 Neighboring gene MPRA-validated peak2652 silencer Neighboring gene CDH13 antisense RNA 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:83912211-83912369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7770 Neighboring gene NANOG hESC enhancer GRCh37_chr16:83942352-83942873 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:83945234-83946433 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:83947165-83947672 Neighboring gene uncharacterized LOC105371372 Neighboring gene heat shock factor binding protein 1 Neighboring gene malonyl-CoA decarboxylase

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables adiponectin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables beta-catenin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cadherin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cadherin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables lipoprotein particle binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables low-density lipoprotein particle binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Rac protein signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in Rho protein signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in adherens junction organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell-cell adhesion mediated by cadherin IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell-cell junction assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in endothelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in keratinocyte proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in lamellipodium assembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in localization within membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in low-density lipoprotein particle mediated signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of calcium-mediated signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell-matrix adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of endothelial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of positive chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of smooth muscle cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of endocytosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of epidermal growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sprouting angiogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 

    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
    XP_054235331.1
    XP_054235332.1
    XP_054235333.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_052819.2 RefSeqGene

      Range
      5002..1178673
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001220488.2NP_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)
      AC009119, AC092351, AK304733, BG911233, BU627784, CB321814, CF618908, CV024366, DA561809, DA685616, DB003683, DC376661, R41787
      Consensus CDS
      CCDS58485.1
      UniProtKB/TrEMBL
      B7Z9B1
      Related
      ENSP00000268613.10, ENST00000268613.14
      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_001220489.2NP_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)
      AC009119, AK298612, BG911233, BU627784, CB321814, CF618908, DA685616, DC376661, R41787
      Consensus CDS
      CCDS58487.1
      UniProtKB/TrEMBL
      B7Z9B1
      Related
      ENSP00000394557.3, ENST00000428848.7
      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_001220490.2NP_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)
      AC009119, 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
      cl29226
      Location:335426
      Cadherin; Cadherin domain
    4. NM_001220491.2NP_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)
      AC087189, DC376661, EU190358
      Consensus CDS
      CCDS56010.1
      UniProtKB/Swiss-Prot
      P55290
      Related
      ENSP00000408632.3, ENST00000431540.7
      Conserved Domains (1) summary
      pfam08758
      Location:27112
      Cadherin_pro; Cadherin prodomain like
    5. NM_001220492.2NP_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, ENST00000565636.5
      Conserved Domains (1) summary
      pfam08758
      Location:27112
      Cadherin_pro; Cadherin prodomain like
    6. NM_001257.5NP_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)
      AC009119, BC028624, BG911233, BI756586, BU627784, CA445317, CN263227, DC376661, R41787
      Consensus CDS
      CCDS58486.1
      UniProtKB/Swiss-Prot
      A8W476, A8W477, B7Z590, C9JRI6, J3KN62, P55290, Q6GTW4, Q8TBX3
      UniProtKB/TrEMBL
      B7Z9B1
      Related
      ENSP00000479395.1, ENST00000567109.6
      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: 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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      82626969..83800640
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017022848.3XP_016878337.1  cadherin-13 isoform X2

    2. XM_017022849.3XP_016878338.1  cadherin-13 isoform X3

    3. XM_011522804.4XP_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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      88691276..89866370
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054379357.1XP_054235332.1  cadherin-13 isoform X2

    2. XM_054379358.1XP_054235333.1  cadherin-13 isoform X3

    3. XM_054379356.1XP_054235331.1  cadherin-13 isoform X1