Free for academic non-profit institutions. Other users need a Commercial license

Aliases for CDHR2 Gene

Aliases for CDHR2 Gene

  • Cadherin Related Family Member 2 2 3 5
  • Cadherin-Related Family Member 2 2 3
  • Protocadherin LKC 2 4
  • Protocadherin-24 3 4
  • PCDH24 3 4
  • PCLKC 3 4
  • Protocadherin 24 2
  • PC-LKC 4

External Ids for CDHR2 Gene

Previous HGNC Symbols for CDHR2 Gene

  • PCDH24

Previous GeneCards Identifiers for CDHR2 Gene

  • GC05P175976
  • GC05P170893

Summaries for CDHR2 Gene

Entrez Gene Summary for CDHR2 Gene

  • This gene is a member of the protocadherin family, which represents a subset of the larger cadherin superfamily. The members of the protocadherin family encode non-classical cadherins that function as calcium-dependent cell-cell adhesion molecules. This protocadherin represents a new candidate for tumor suppression. Alternatively spliced transcript variants that encode the same protein have been identified. [provided by RefSeq, Jan 2010]

GeneCards Summary for CDHR2 Gene

CDHR2 (Cadherin Related Family Member 2) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDH15.

UniProtKB/Swiss-Prot for CDHR2 Gene

  • Intermicrovillar adhesion molecule that forms, via its extracellular domain, calcium-dependent heterophilic complexes with CDHR5 on adjacent microvilli. Thereby, controls the packing of microvilli at the apical membrane of epithelial cells. Through its cytoplasmic domain, interacts with microvillus cytoplasmic proteins to form the intermicrovillar adhesion complex/IMAC. This complex plays a central role in microvilli and epithelial brush border differentiation (PubMed:24725409). May also play a role in cell-cell adhesion and contact inhibition in epithelial cells (PubMed:12117771).

Gene Wiki entry for CDHR2 Gene

Additional gene information for CDHR2 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDHR2 Gene

Genomics for CDHR2 Gene

Regulatory Elements for CDHR2 Gene

Enhancers for CDHR2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05H176539 1.9 FANTOM5 Ensembl ENCODE dbSUPER 9.2 +3.3 3274 11 HDGF FOXA2 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF766 FAF2 NSD1 ENSG00000250909 ENSG00000251414 ZNF346-IT1 ZNF346 CDHR2 RNF44 UIMC1 CLTB
GH05H176410 1.6 Ensembl ENCODE dbSUPER 10.9 -127.6 -127595 8 PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZNF143 ZNF207 FOS SP5 ENSG00000251414 FAF2 HIGD2A ARL10 NOP16 UIMC1 ENSG00000250909 MIR1271 KIAA1191 CDHR2
GH05H176529 1.8 FANTOM5 ENCODE dbSUPER 7.3 -8.2 -8212 10 HDGF PKNOX1 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 RNF44 UIMC1 CDHR2 THOC3 CLTB HK3 BRCC3P1 HIGD2A GC05P176534 GC05P176517
GH05H176552 1.3 Ensembl ENCODE dbSUPER 8 +11.3 11298 3 BCOR SIN3A ZMYM3 BMI1 BATF ZIC2 ZKSCAN1 GLIS2 POLR2A FOSL2 FAF2 ENSG00000250909 NSD1 ENSG00000251414 ARL10 MIR1271 KIAA1191 UNC5A CDHR2 GC05M176548
GH05H176436 0.9 Ensembl ENCODE 11 -105.6 -105647 1 SOX5 SOX13 GATAD2A PKNOX1 SOX6 CEBPG GATA3 CEBPA FOS CUX1 CDHR2 RN7SL684P ENSG00000280139 CLTB
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CDHR2 on UCSC Golden Path with GeneCards custom track

Promoters for CDHR2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000191236 889 2001 HDGF ATF1 ARNT SIN3A ZNF2 GLIS2 ZNF143 KLF7 RUNX3 SP3

Genomic Location for CDHR2 Gene

Chromosome:
5
Start:
176,542,511 bp from pter
End:
176,595,974 bp from pter
Size:
53,464 bases
Orientation:
Plus strand

Genomic View for CDHR2 Gene

Genes around CDHR2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDHR2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDHR2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDHR2 Gene

Proteins for CDHR2 Gene

  • Protein details for CDHR2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BYE9-CDHR2_HUMAN
    Recommended name:
    Cadherin-related family member 2
    Protein Accession:
    Q9BYE9
    Secondary Accessions:
    • A1L3U4
    • A6NC80
    • Q9NXP8

    Protein attributes for CDHR2 Gene

    Size:
    1310 amino acids
    Molecular mass:
    141543 Da
    Quaternary structure:
    • Part of the IMAC/intermicrovillar adhesion complex/intermicrovillar tip-link complex composed of ANKS4B, MYO7B, USH1C, CDHR2 and CDHR5 (PubMed:26812018). Interacts with MAST2 (PubMed:12117771). Interacts (via cytoplasmic domain) with USH1C and MYO7B; required for proper localization of CDHR2 to microvilli tips and its function in brush border differentiation (PubMed:24725409, PubMed:26812017).
    SequenceCaution:
    • Sequence=BAA90962.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CDHR2 Gene

neXtProt entry for CDHR2 Gene

Post-translational modifications for CDHR2 Gene

  • Glycosylation at posLast=2929, posLast=134134, Asn182, posLast=188188, posLast=195195, posLast=300300, Asn355, Asn371, Asn401, posLast=460460, Asn565, Asn600, Asn616, Asn632, posLast=680680, posLast=696696, posLast=701701, posLast=775775, posLast=821821, Asn871, posLast=877877, Asn911, posLast=932932, and Asn1107
  • Modification sites at PhosphoSitePlus

Other Protein References for CDHR2 Gene

No data available for DME Specific Peptides for CDHR2 Gene

Domains & Families for CDHR2 Gene

Gene Families for CDHR2 Gene

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

Protein Domains for CDHR2 Gene

Suggested Antigen Peptide Sequences for CDHR2 Gene

Graphical View of Domain Structure for InterPro Entry

Q9BYE9

UniProtKB/Swiss-Prot:

CDHR2_HUMAN :
  • The cadherin 1 domain is required for binding to CDHR5.
Domain:
  • The cadherin 1 domain is required for binding to CDHR5.
genes like me logo Genes that share domains with CDHR2: view

Function for CDHR2 Gene

Molecular function for CDHR2 Gene

UniProtKB/Swiss-Prot Function:
Intermicrovillar adhesion molecule that forms, via its extracellular domain, calcium-dependent heterophilic complexes with CDHR5 on adjacent microvilli. Thereby, controls the packing of microvilli at the apical membrane of epithelial cells. Through its cytoplasmic domain, interacts with microvillus cytoplasmic proteins to form the intermicrovillar adhesion complex/IMAC. This complex plays a central role in microvilli and epithelial brush border differentiation (PubMed:24725409). May also play a role in cell-cell adhesion and contact inhibition in epithelial cells (PubMed:12117771).

Phenotypes From GWAS Catalog for CDHR2 Gene

Gene Ontology (GO) - Molecular Function for CDHR2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0005515 protein binding IPI 12117771
GO:0050839 cell adhesion molecule binding IDA 24725409
genes like me logo Genes that share ontologies with CDHR2: view

Phenotypes for CDHR2 Gene

GenomeRNAi human phenotypes for CDHR2:
genes like me logo Genes that share phenotypes with CDHR2: view

Animal Model Products

CRISPR Products

miRNA for CDHR2 Gene

miRTarBase miRNAs that target CDHR2

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CDHR2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CDHR2 Gene

Localization for CDHR2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDHR2 Gene

Apical cell membrane; Single-pass type I membrane protein. Cell projection, microvillus membrane; Single-pass type I membrane protein. Cell junction.

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 CDHR2 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for CDHR2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005903 brush border IDA 21330445
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0016324 apical plasma membrane IEA,IDA 12117771
genes like me logo Genes that share ontologies with CDHR2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CDHR2 Gene

Pathways & Interactions for CDHR2 Gene

SuperPathways for CDHR2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CDHR2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0030154 cell differentiation IEA --
GO:0030855 epithelial cell differentiation IDA 12117771
GO:0032532 regulation of microvillus length IMP 24725409
genes like me logo Genes that share ontologies with CDHR2: view

No data available for Pathways by source and SIGNOR curated interactions for CDHR2 Gene

Drugs & Compounds for CDHR2 Gene

No Compound Related Data Available

Transcripts for CDHR2 Gene

Unigene Clusters for CDHR2 Gene

Cadherin-related family member 2:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for CDHR2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for CDHR2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b · 20c ^ 21 ^ 22 ^ 23a · 23b ^
SP1: - -
SP2:
SP3:

ExUns: 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31
SP1:
SP2:
SP3:

Relevant External Links for CDHR2 Gene

GeneLoc Exon Structure for
CDHR2
ECgene alternative splicing isoforms for
CDHR2

Expression for CDHR2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDHR2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CDHR2 Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (x24.1), Liver (x10.4), and Colon - Transverse (x8.4).

Protein differential expression in normal tissues from HIPED for CDHR2 Gene

This gene is overexpressed in Pancreatic juice (58.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CDHR2 Gene



Protein tissue co-expression partners for CDHR2 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CDHR2 Gene:

CDHR2

SOURCE GeneReport for Unigene cluster for CDHR2 Gene:

Hs.4205

mRNA Expression by UniProt/SwissProt for CDHR2 Gene:

Q9BYE9-CDHR2_HUMAN
Tissue specificity: Highly expressed in liver, kidney and colon. Moderately expressed in small intestine. Down-regulated in a number of liver and colon cancers (PubMed:12117771, PubMed:15534908). Expressed in duodenum with higher expression in enterocytes along the villus axis and lower expression in crypts (at protein level) (PubMed:24725409).

Evidence on tissue expression from TISSUES for CDHR2 Gene

  • Liver(4.3)
genes like me logo Genes that share expression patterns with CDHR2: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CDHR2 Gene

Orthologs for CDHR2 Gene

This gene was present in the common ancestor of animals.

Orthologs for CDHR2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CDHR2 33 34
  • 99 (n)
dog
(Canis familiaris)
Mammalia CDHR2 33 34
  • 83.18 (n)
cow
(Bos Taurus)
Mammalia CDHR2 33 34
  • 81.43 (n)
rat
(Rattus norvegicus)
Mammalia Cdhr2 33
  • 77.68 (n)
mouse
(Mus musculus)
Mammalia Cdhr2 33 16 34
  • 77.45 (n)
oppossum
(Monodelphis domestica)
Mammalia CDHR2 34
  • 56 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CDHR2 34
  • 37 (a)
OneToOne
chicken
(Gallus gallus)
Aves CDHR2 33 34
  • 59 (n)
lizard
(Anolis carolinensis)
Reptilia CDHR2 34
  • 45 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia cdhr2 33
  • 52.14 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100536704 33
  • 47.89 (n)
CDHR2 (1 of 2) 34
  • 37 (a)
OneToMany
CDHR2 (2 of 2) 34
  • 36 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Cad86C 34
  • 11 (a)
OneToMany
Species where no ortholog for CDHR2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • 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 squirt (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 CDHR2 Gene

ENSEMBL:
Gene Tree for CDHR2 (if available)
TreeFam:
Gene Tree for CDHR2 (if available)

Paralogs for CDHR2 Gene

(6) SIMAP similar genes for CDHR2 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with CDHR2: view

Variants for CDHR2 Gene

Sequence variations from dbSNP and Humsavar for CDHR2 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs1000015036 -- 176,588,750(+) CAGTG(G/T)AGGGG intron-variant
rs1000078586 -- 176,552,825(+) TGCCG(C/T)TGACA intron-variant
rs1000216487 -- 176,575,084(+) CCCAG(A/G)TCATC reference, missense
rs1000218139 -- 176,574,451(+) AACCC(A/C)TTTCT intron-variant
rs1000231844 -- 176,548,112(+) GGCAA(C/T)TGTAA intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for CDHR2 Gene

Variant ID Type Subtype PubMed ID
dgv1057e199 CNV deletion 23128226
esv1281149 CNV insertion 17803354
esv2341441 CNV deletion 18987734
esv3385289 CNV duplication 20981092
esv3607673 CNV loss 21293372
nsv1114762 CNV deletion 24896259
nsv1117426 CNV tandem duplication 24896259
nsv1149931 CNV deletion 26484159
nsv471056 CNV loss 18288195
nsv527791 CNV loss 19592680
nsv600344 CNV loss 21841781
nsv600345 CNV loss 21841781
nsv955854 CNV deletion 24416366

Variation tolerance for CDHR2 Gene

Residual Variation Intolerance Score: 7.79% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.68; 89.24% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CDHR2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CDHR2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDHR2 Gene

Disorders for CDHR2 Gene

Relevant External Links for CDHR2

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CDHR2

No disorders were found for CDHR2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CDHR2 Gene

Publications for CDHR2 Gene

  1. Differentially expressed genes between solitary large hepatocellular carcinoma and nodular hepatocellular carcinoma. (PMID: 15534908) Yang LY … Huang GW (World journal of gastroenterology 2004) 3 4 22 60
  2. Protocadherin LKC, a new candidate for a tumor suppressor of colon and liver cancers, its association with contact inhibition of cell proliferation. (PMID: 12117771) Okazaki N … Koga H (Carcinogenesis 2002) 2 3 4 60
  3. Intestinal brush border assembly driven by protocadherin-based intermicrovillar adhesion. (PMID: 24725409) Crawley SW … Tyska MJ (Cell 2014) 3 4 60
  4. PCDH24-induced contact inhibition involves downregulation of beta-catenin signaling. (PMID: 19383367) Ose R … Koga H (Molecular oncology 2009) 3 22 60
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60

Products for CDHR2 Gene

Sources for CDHR2 Gene

Content
Loading form....