This gene encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. The extracellular domain consists of 5 subdoma... See more...

Aliases for CDH9 Gene

Aliases for CDH9 Gene

  • Cadherin 9 2 3 5
  • Cadherin-9 3 4
  • Cadherin 9, Type 2 (T1-Cadherin) 2
  • T1-Cadherin 3
  • CDH9 5

External Ids for CDH9 Gene

Previous GeneCards Identifiers for CDH9 Gene

  • GC05M026567
  • GC05M027314
  • GC05M026880
  • GC05M026926

Summaries for CDH9 Gene

Entrez Gene Summary for CDH9 Gene

  • This gene encodes a type II classical cadherin from the cadherin superfamily, integral membrane proteins that mediate calcium-dependent cell-cell adhesion. Mature cadherin proteins are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. The extracellular domain consists of 5 subdomains, each containing a cadherin motif, and appears to determine the specificity of the protein's homophilic cell adhesion activity. Type II (atypical) cadherins are defined based on their lack of a HAV cell adhesion recognition sequence specific to type I cadherins. [provided by RefSeq, Jul 2008]

GeneCards Summary for CDH9 Gene

CDH9 (Cadherin 9) is a Protein Coding gene. Diseases associated with CDH9 include Microcephaly, Seizures, And Developmental Delay and Craniofacial-Deafness-Hand Syndrome. Among its related pathways are ERK Signaling and Cell junction organization. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is CDH6.

UniProtKB/Swiss-Prot Summary for CDH9 Gene

  • Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.

Gene Wiki entry for CDH9 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CDH9 Gene

Genomics for CDH9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CDH9 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
GH05J027038 Promoter 0.9 EPDnew Ensembl 600.2 +82.9 82949 1.6 RAD21 CTCF SIN3A CDH9 HSALNG0040776 piR-43105-528
GH05J027084 Enhancer 0.6 Ensembl ENCODE 0.3 +37.0 37049 2.2 NR2F2 JUN POU5F1 JUND RF00026-850 RNU6-738P HSALNG0040776 CDH9
GH05J027217 Promoter 0.9 Ensembl 0.2 -96.7 -96651 0.8 CBX3 POLR2A MTA3 TAF9B GTF2F1 ZNF138 AFF1 TBL1XR1 NCOR1 GTF2A2 PURPL piR-46501-077 piR-59056-006 CDH9 L13713-178
GH05J027240 Enhancer 0.9 Ensembl ENCODE 0.1 -120.9 -120908 2.6 CREB1 ARID3A CTCF ATF7 CEBPB SP1 SMARCC1 JUND BRCA1 CTBP1 PURPL L13713-178 CDH9
GH05J027096 Enhancer 0.3 Ensembl 0.4 +24.5 24450 0.6 CTCF RF00026-850 RNU6-738P CDH9 HSALNG0040776
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDH9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CDH9

Top Transcription factor binding sites by QIAGEN in the CDH9 gene promoter:
  • C/EBPalpha
  • CUTL1
  • FOXF2
  • FOXJ2
  • FOXJ2 (long isoform)
  • HFH-3
  • Lhx3a
  • LHX3b
  • POU2F1
  • POU2F1a

Genomic Locations for CDH9 Gene

Genomic Locations for CDH9 Gene
chr5:26,880,597-27,121,150
(GRCh38/hg38)
Size:
240,554 bases
Orientation:
Minus strand
chr5:26,880,709-27,121,257
(GRCh37/hg19)
Size:
240,549 bases
Orientation:
Minus strand

Genomic View for CDH9 Gene

Genes around CDH9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDH9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDH9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDH9 Gene

Proteins for CDH9 Gene

  • Protein details for CDH9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9ULB4-CADH9_HUMAN
    Recommended name:
    Cadherin-9
    Protein Accession:
    Q9ULB4
    Secondary Accessions:
    • Q3B7I5

    Protein attributes for CDH9 Gene

    Size:
    789 amino acids
    Molecular mass:
    88689 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CDH9 Gene

Post-translational modifications for CDH9 Gene

  • Glycosylation at Asn255, Asn437, Asn455, and Asn536
  • Modification sites at PhosphoSitePlus

Other Protein References for CDH9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CDH9 Gene

Domains & Families for CDH9 Gene

Gene Families for CDH9 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CDH9 Gene

InterPro:
Blocks:
  • Cadherin cytoplasmic region
  • Cadherin
ProtoNet:

Suggested Antigen Peptide Sequences for CDH9 Gene

GenScript: Design optimal peptide antigens:
  • Cadherin-9 (CADH9_HUMAN)
  • CDH9 protein (Q32LY1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9ULB4

UniProtKB/Swiss-Prot:

CADH9_HUMAN :
  • Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain.
Domain:
  • Three calcium ions are usually bound at the interface of each cadherin domain and rigidify the connections, imparting a strong curvature to the full-length ectodomain.
genes like me logo Genes that share domains with CDH9: view

Function for CDH9 Gene

Molecular function for CDH9 Gene

UniProtKB/Swiss-Prot Function:
Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types.

Phenotypes From GWAS Catalog for CDH9 Gene

Gene Ontology (GO) - Molecular Function for CDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005509 calcium ion binding IEA,IBA 21873635
GO:0008092 cytoskeletal protein binding IBA --
GO:0045296 cadherin binding IBA 21873635
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CDH9: view
genes like me logo Genes that share phenotypes with CDH9: view

Animal Models for CDH9 Gene

MGI Knock Outs for CDH9:
  • Cdh9 Cdh9<tm1b(KOMP)Wtsi>

Animal Model Products

CRISPR Products

miRNA for CDH9 Gene

miRTarBase miRNAs that target CDH9

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDH9

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CDH9 Gene

Localization for CDH9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDH9 Gene

Cell membrane. Single-pass type I 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 CDH9 gene
Compartment Confidence
plasma membrane 4
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for CDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005912 adherens junction IBA 21873635
GO:0009986 cell surface IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with CDH9: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CDH9 Gene

Pathways & Interactions for CDH9 Gene

PathCards logo

SuperPathways for CDH9 Gene

SuperPathway Contained pathways
1 Cell junction organization
2 ERK Signaling
.61
.49
3 G12-G13 in Cellular Signaling
-
4 Nanog in Mammalian ESC Pluripotency
.62
5 Presenilin-Mediated Signaling
-
genes like me logo Genes that share pathways with CDH9: view

Pathways by source for CDH9 Gene

7 Qiagen pathways for CDH9 Gene
  • G12-G13 in Cellular Signaling
  • GSK3 Signaling
  • ILK Signaling
  • Presenilin-Mediated Signaling
  • Rho Family GTPases

Gene Ontology (GO) - Biological Process for CDH9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 cell morphogenesis IBA 21873635
GO:0007043 cell-cell junction assembly IBA 21873635
GO:0007155 cell adhesion IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007275 multicellular organism development IBA --
genes like me logo Genes that share ontologies with CDH9: view

No data available for SIGNOR curated interactions for CDH9 Gene

Drugs & Compounds for CDH9 Gene

(1) Drugs for CDH9 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6556
genes like me logo Genes that share compounds with CDH9: view

Transcripts for CDH9 Gene

mRNA/cDNA for CDH9 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDH9

Alternative Splicing Database (ASD) splice patterns (SP) for CDH9 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
SP1: -
SP2:

Relevant External Links for CDH9 Gene

GeneLoc Exon Structure for
CDH9

Expression for CDH9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CDH9 Gene

mRNA differential expression in normal tissues according to GTEx for CDH9 Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (x8.3), Brain - Nucleus accumbens (basal ganglia) (x7.6), Brain - Cortex (x7.5), Brain - Frontal Cortex (BA9) (x7.2), Brain - Amygdala (x5.2), and Brain - Putamen (basal ganglia) (x4.2).

Protein differential expression in normal tissues from HIPED for CDH9 Gene

This gene is overexpressed in Pancreatic juice (66.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CDH9 Gene



Protein tissue co-expression partners for CDH9 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CDH9

SOURCE GeneReport for Unigene cluster for CDH9 Gene:

Hs.272212

Evidence on tissue expression from TISSUES for CDH9 Gene

  • Nervous system(2.8)
  • Skin(2.3)
genes like me logo Genes that share expression patterns with CDH9: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for CDH9 Gene

Orthologs for CDH9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CDH9 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CDH9 30 31
  • 99.7 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CDH9 30 31
  • 91.85 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CDH9 30 31
  • 91.14 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia CDH9 31
  • 90 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Cdh9 30
  • 86.97 (n)
Mouse
(Mus musculus)
Mammalia Cdh9 30 17 31
  • 86.47 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CDH9 31
  • 84 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CDH9 30 31
  • 79.26 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CDH9 31
  • 83 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia cdh9 30
  • 71.79 (n)
Zebrafish
(Danio rerio)
Actinopterygii CABZ01067945.1 31
  • 65 (a)
ManyToMany
cdh10 31
  • 62 (a)
ManyToMany
cdh6 31
  • 61 (a)
ManyToMany
Species where no ortholog for CDH9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)
  • Worm (Caenorhabditis elegans)

Evolution for CDH9 Gene

ENSEMBL:
Gene Tree for CDH9 (if available)
TreeFam:
Gene Tree for CDH9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CDH9: view image

Paralogs for CDH9 Gene

(18) SIMAP similar genes for CDH9 Gene using alignment to 4 proteins:

  • CADH9_HUMAN
  • D6RBT9_HUMAN
  • E7EPN0_HUMAN
  • Q32LY1_HUMAN
genes like me logo Genes that share paralogs with CDH9: view

Variants for CDH9 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CDH9 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
731220 Benign: not provided 26,902,723(-) C/T MISSENSE_VARIANT
770716 Benign: not provided 26,885,688(-) T/C MISSENSE_VARIANT
791256 Benign: not provided 26,889,890(-) C/T SYNONYMOUS_VARIANT
rs145815030 Uncertain Significance: not provided 26,881,304(-) C/T SYNONYMOUS_VARIANT
rs2288466 - p.Ala38Val

Additional dbSNP identifiers (rs#s) for CDH9 Gene

Structural Variations from Database of Genomic Variants (DGV) for CDH9 Gene

Variant ID Type Subtype PubMed ID
dgv9699n54 CNV loss 21841781
esv1001329 CNV insertion 20482838
esv2759335 CNV loss 17122850
esv3380329 OTHER inversion 20981092
esv3604457 CNV gain 21293372
esv3604458 CNV gain 21293372
nsv1022430 CNV gain 25217958
nsv1110788 CNV insertion 24896259
nsv1120505 CNV tandem duplication 24896259
nsv1131880 CNV deletion 24896259
nsv462021 CNV gain 19166990
nsv462023 CNV loss 19166990
nsv462024 CNV loss 19166990
nsv597645 CNV gain 21841781
nsv597679 CNV loss 21841781

Variation tolerance for CDH9 Gene

Residual Variation Intolerance Score: 8.61% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.10; 92.24% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDH9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDH9

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDH9 Gene

Disorders for CDH9 Gene

MalaCards: The human disease database

(7) MalaCards diseases for CDH9 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
microcephaly, seizures, and developmental delay
  • mcsz
craniofacial-deafness-hand syndrome
  • cdhs
childhood disintegrative disease
  • disintegrative psychosis
autism
  • autistic disorder
asperger syndrome
  • asperger disorder
- elite association - COSMIC cancer census association via MalaCards
Search CDH9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CDH9

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with CDH9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDH9 Gene

Publications for CDH9 Gene

  1. Identification of three human type-II classic cadherins and frequent heterophilic interactions between different subclasses of type-II classic cadherins. (PMID: 10861224) Shimoyama Y … Natori M (The Biochemical journal 2000) 3 4 23
  2. Common genetic variants on 5p14.1 associate with autism spectrum disorders. (PMID: 19404256) Wang K … Hakonarson H (Nature 2009) 3 41
  3. Cadherin-9 is a novel cell surface marker for the heterogeneous pool of renal fibroblasts. (PMID: 17668045) Thedieck C … Klein G (PloS one 2007) 3 23
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Diversity of the cadherin family: evidence for eight new cadherins in nervous tissue. (PMID: 2059658) Suzuki S … Tanihara H (Cell regulation 1991) 2 3

Products for CDH9 Gene

  • Signalway Proteins for CDH9

Sources for CDH9 Gene