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CDH13 cadherin 13 [ Homo sapiens (human) ]

Gene ID: 1012, updated on 11-Apr-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (82626969..83800640)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (88691276..89866370)
105.20220307 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
  • 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 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 multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
 
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_2023_10

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