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Aliases for CDH12 Gene

Aliases for CDH12 Gene

  • Cadherin 12 2 3 5
  • Neural Type Cadherin 2 3 4
  • N-Cadherin 2 3 4
  • Cadherin 12, Type 2 (N-Cadherin 2) 2
  • Cadherin, Neural Type, 2 3
  • Neuronal Cadherin 2 3
  • Brain-Cadherin 3
  • Brain Cadherin 4
  • Br-Cadherin 3
  • Cadherin-12 3
  • BR-Cadherin 4
  • CDHB 3

External Ids for CDH12 Gene

Previous GeneCards Identifiers for CDH12 Gene

  • GC05M021436
  • GC05M022187
  • GC05M021750
  • GC05M021796
  • GC05M021604

Summaries for CDH12 Gene

Entrez Gene Summary for CDH12 Gene

  • This gene encodes a type II classical cadherin of the cadherin superfamily. Alternative splicing of this gene results in multiple transcript variants. At least one of these variants encodes a preproprotein that is proteolytically processed to generate the mature cadherin protein. These integral membrane proteins mediate calcium-dependent cell-cell adhesion and are composed of a large N-terminal extracellular domain, a single membrane-spanning domain, and a small, highly conserved C-terminal cytoplasmic domain. Type II (atypical) cadherins are defined based on their lack of a histidine-alanine-valine (HAV) cell adhesion recognition sequence specific to type I cadherins. This particular cadherin appears to be expressed specifically in the brain and its temporal pattern of expression would be consistent with a role during a critical period of neuronal development, perhaps specifically during synaptogenesis. [provided by RefSeq, Nov 2015]

GeneCards Summary for CDH12 Gene

CDH12 (Cadherin 12) is a Protein Coding gene. Diseases associated with CDH12 include Cri-Du-Chat Syndrome. Among its related pathways are ERK Signaling and Presenilin-Mediated Signaling. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is CDH6.

UniProtKB/Swiss-Prot for CDH12 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 CDH12 Gene

Additional gene information for CDH12 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CDH12 Gene

Genomics for CDH12 Gene

GeneHancer (GH) Regulatory Elements for CDH12 Gene

Promoters and enhancers for CDH12 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J022853 Promoter 1.3 EPDnew Ensembl 650.7 +0.2 222 0.4 ZNF335 MXI1 POLR2A L3MBTL2 SIN3A EZH2 CDH12 GC05M022770 GC05M022692
GH05J022852 Promoter 0.7 Ensembl 650.7 +0.7 721 0.2 ZNF335 MXI1 POLR2A CDH12 GC05M022770 GC05M022692
GH05J022212 Promoter 0.5 EPDnew 650 +640.8 640833 0.1 LOC105374682 CDH12 GC05P022355 GC05P022354
GH05J022372 Enhancer 0.3 ENCODE 6.4 +481.2 481162 0.7 FOS CDH12 GC05P022354 GC05P022355 GC05P022480
GH05J022928 Enhancer 0.4 ENCODE 0.2 -75.6 -75563 0.5 ZNF202 EZH2 SETDB1 CDH12 ENSG00000249404 GC05M022692
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CDH12 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CDH12 gene promoter:
  • Sox5
  • MEF-2A
  • aMEF-2
  • SRY
  • Pax-6
  • HNF-1
  • HNF-1A
  • AML1a
  • GR-alpha

Genomic Locations for CDH12 Gene

Genomic Locations for CDH12 Gene
1,102,950 bases
Minus strand
1,102,950 bases
Minus strand

Genomic View for CDH12 Gene

Genes around CDH12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CDH12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CDH12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CDH12 Gene

Proteins for CDH12 Gene

  • Protein details for CDH12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B2RBT1
    • B7Z2U6
    • Q86UD2

    Protein attributes for CDH12 Gene

    794 amino acids
    Molecular mass:
    88332 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CDH12 Gene


neXtProt entry for CDH12 Gene

Post-translational modifications for CDH12 Gene

  • Glycosylation at posLast=545545, posLast=537537, posLast=456456, and posLast=256256
  • Modification sites at PhosphoSitePlus

Other Protein References for CDH12 Gene

Antibody Products

  • Abcam antibodies for CDH12
  • Boster Bio Antibodies for CDH12

No data available for DME Specific Peptides for CDH12 Gene

Domains & Families for CDH12 Gene

Gene Families for CDH12 Gene

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

Suggested Antigen Peptide Sequences for CDH12 Gene

Graphical View of Domain Structure for InterPro Entry



  • 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.
  • 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 CDH12: view

Function for CDH12 Gene

Molecular function for CDH12 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.
GENATLAS Biochemistry:
cadherin 12,Br-(N) cadherin,neuronal,transmembrane glycoprotein component of adherens junction,expressed in the brain,putatively involved in synaptic adhesion,axon outgrowth and guidance

Phenotypes From GWAS Catalog for CDH12 Gene

Gene Ontology (GO) - Molecular Function for CDH12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
GO:0008092 cytoskeletal protein binding IBA --
GO:0042803 protein homodimerization activity IBA --
GO:0045296 cadherin binding IBA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with CDH12: view
genes like me logo Genes that share phenotypes with CDH12: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDH12

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CDH12 Gene

Localization for CDH12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CDH12 Gene

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

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 CDH12 gene
Compartment Confidence
plasma membrane 5
extracellular 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CDH12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005913 cell-cell adherens junction IBA --
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 CDH12: view

Pathways & Interactions for CDH12 Gene

genes like me logo Genes that share pathways with CDH12: view

Gene Ontology (GO) - Biological Process for CDH12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 cell morphogenesis IBA --
GO:0007043 cell-cell junction assembly IBA --
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 CDH12: view

No data available for SIGNOR curated interactions for CDH12 Gene

Drugs & Compounds for CDH12 Gene

(2) Drugs for CDH12 Gene - From: ApexBio and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
Cadherin Peptide, avian Pharma Role in cell adhesion 0
genes like me logo Genes that share compounds with CDH12: view

Transcripts for CDH12 Gene

mRNA/cDNA for CDH12 Gene

(6) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(1) Selected AceView cDNA sequences:
(8) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CDH12 Gene

Cadherin 12, type 2 (N-cadherin 2):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CDH12

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CDH12 Gene

No ASD Table

Relevant External Links for CDH12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CDH12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CDH12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CDH12 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x5.6), Brain - Frontal Cortex (BA9) (x4.8), Adrenal Gland (x4.4), and Brain - Cortex (x4.4).

Protein differential expression in normal tissues from HIPED for CDH12 Gene

This gene is overexpressed in Liver (38.0) and Spleen (30.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CDH12 Gene

Protein tissue co-expression partners for CDH12 Gene

NURSA nuclear receptor signaling pathways regulating expression of CDH12 Gene:


SOURCE GeneReport for Unigene cluster for CDH12 Gene:


mRNA Expression by UniProt/SwissProt for CDH12 Gene:

Tissue specificity: Brain.

Evidence on tissue expression from TISSUES for CDH12 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with CDH12: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CDH12 Gene

Orthologs for CDH12 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CDH12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CDH12 34 33
  • 99.62 (n)
(Monodelphis domestica)
Mammalia CDH12 34
  • 95 (a)
(Bos Taurus)
Mammalia CDH12 34 33
  • 93.12 (n)
(Canis familiaris)
Mammalia CDH12 34 33
  • 92.61 (n)
(Ornithorhynchus anatinus)
Mammalia CDH12 34
  • 91 (a)
(Mus musculus)
Mammalia Cdh12 16 34 33
  • 89.67 (n)
(Rattus norvegicus)
Mammalia Cdh12 33
  • 89.42 (n)
(Gallus gallus)
Aves CDH12 34 33
  • 84.51 (n)
(Anolis carolinensis)
Reptilia CDH12 34
  • 91 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cdh12 33
  • 75.91 (n)
(Danio rerio)
Actinopterygii CDH12 (1 of 2) 34
  • 70 (a)
si:dkeyp-68h1.1 33
  • 66.11 (n)
CDH12 (2 of 2) 34
  • 65 (a)
Species where no ortholog for CDH12 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)
  • 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 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 CDH12 Gene

Gene Tree for CDH12 (if available)
Gene Tree for CDH12 (if available)
Evolutionary constrained regions (ECRs) for CDH12: view image

Paralogs for CDH12 Gene

Paralogs for CDH12 Gene

(17) SIMAP similar genes for CDH12 Gene using alignment to 2 proteins:

  • B7Z2U6_HUMAN
genes like me logo Genes that share paralogs with CDH12: view

Variants for CDH12 Gene

Sequence variations from dbSNP and Humsavar for CDH12 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000001454 -- 22,834,207(-) G/C genic_upstream_transcript_variant, intron_variant
rs1000005121 -- 22,744,349(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000005366 -- 22,316,733(-) A/G genic_upstream_transcript_variant, intron_variant
rs1000009781 -- 21,750,554(-) G/C/T 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant
rs1000010667 -- 22,717,500(-) A/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CDH12 Gene

Variant ID Type Subtype PubMed ID
dgv1082e214 CNV gain 21293372
dgv3057n106 CNV tandem duplication 24896259
dgv338n21 CNV gain 19592680
dgv9670n54 CNV loss 21841781
esv1005606 CNV insertion 20482838
esv1373915 CNV insertion 17803354
esv1672813 CNV insertion 17803354
esv2033765 CNV deletion 18987734
esv21518 CNV gain+loss 19812545
esv2527456 CNV loss 19546169
esv2534629 CNV loss 19546169
esv2657445 CNV deletion 23128226
esv2668800 CNV deletion 23128226
esv2672622 CNV deletion 23128226
esv2673390 CNV deletion 23128226
esv2675606 CNV deletion 23128226
esv2676592 CNV deletion 23128226
esv2678078 CNV deletion 23128226
esv2678390 CNV deletion 23128226
esv26842 CNV gain 19812545
esv2729914 CNV deletion 23290073
esv2729915 CNV deletion 23290073
esv2729916 CNV deletion 23290073
esv2729919 CNV deletion 23290073
esv2729920 CNV deletion 23290073
esv2729921 CNV deletion 23290073
esv2729922 CNV deletion 23290073
esv2729923 CNV deletion 23290073
esv2729924 CNV deletion 23290073
esv2729925 CNV deletion 23290073
esv2729926 CNV deletion 23290073
esv2729927 CNV deletion 23290073
esv2729928 CNV deletion 23290073
esv2729930 CNV deletion 23290073
esv2752064 CNV loss 17911159
esv2759332 CNV gain+loss 17122850
esv2762506 CNV gain 21179565
esv3305026 CNV mobile element insertion 20981092
esv3310161 CNV mobile element insertion 20981092
esv3324518 CNV insertion 20981092
esv33296 CNV gain 17666407
esv3351534 CNV insertion 20981092
esv3363085 CNV insertion 20981092
esv3364900 CNV insertion 20981092
esv3380329 OTHER inversion 20981092
esv3413488 CNV duplication 20981092
esv3565656 CNV deletion 23714750
esv3565662 CNV deletion 23714750
esv3565663 CNV deletion 23714750
esv3570045 CNV loss 25503493
esv3604328 CNV loss 21293372
esv3604332 CNV loss 21293372
esv3604334 CNV loss 21293372
esv3604335 CNV gain 21293372
esv3604338 CNV loss 21293372
esv3604339 CNV loss 21293372
esv3604340 CNV loss 21293372
esv3604341 CNV gain 21293372
esv3604342 CNV loss 21293372
esv3604343 CNV gain 21293372
esv3604344 CNV gain 21293372
esv3604346 CNV gain 21293372
esv3604347 CNV gain 21293372
esv3604348 CNV gain 21293372
esv3604351 CNV gain 21293372
esv3604352 CNV loss 21293372
esv3604354 CNV loss 21293372
esv3604355 CNV loss 21293372
esv3604356 CNV loss 21293372
esv3741 CNV loss 18987735
nsv1016735 CNV loss 25217958
nsv1020363 CNV loss 25217958
nsv1020448 CNV gain 25217958
nsv1026739 CNV loss 25217958
nsv1031398 CNV gain 25217958
nsv1034137 CNV loss 25217958
nsv10684 CNV loss 18304495
nsv10685 CNV loss 18304495
nsv10686 CNV gain+loss 18304495
nsv10687 CNV gain 18304495
nsv1073869 CNV deletion 25765185
nsv1123926 CNV deletion 24896259
nsv1123927 CNV deletion 24896259
nsv1133598 CNV deletion 24896259
nsv1136978 CNV deletion 24896259
nsv1140522 CNV deletion 24896259
nsv1140523 CNV deletion 24896259
nsv1142431 CNV tandem duplication 24896259
nsv1143128 CNV tandem duplication 24896259
nsv1143311 CNV deletion 24896259
nsv327318 CNV deletion 16902084
nsv327326 CNV deletion 16902084
nsv327391 CNV deletion 16902084
nsv327838 CNV deletion 16902084
nsv328954 CNV insertion 16902084
nsv329065 CNV deletion 16902084
nsv428115 CNV gain+loss 18775914
nsv462009 CNV loss 19166990
nsv471371 CNV gain 19718026
nsv474870 CNV novel sequence insertion 20440878
nsv4761 CNV insertion 18451855
nsv478277 CNV novel sequence insertion 20440878
nsv507236 OTHER sequence alteration 20534489
nsv507237 OTHER sequence alteration 20534489
nsv509963 OTHER sequence alteration 20534489
nsv597532 CNV gain 21841781
nsv597535 CNV gain 21841781
nsv597536 CNV loss 21841781
nsv7369 OTHER inversion 18451855
nsv823035 CNV loss 20364138
nsv830230 CNV gain 17160897
nsv830231 CNV gain 17160897
nsv830232 CNV gain 17160897
nsv830233 CNV loss 17160897
nsv955848 CNV deletion 24416366
nsv968152 CNV duplication 23825009
nsv968894 CNV duplication 23825009
nsv968895 CNV duplication 23825009
nsv968896 CNV duplication 23825009

Variation tolerance for CDH12 Gene

Residual Variation Intolerance Score: 14.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 12.67; 94.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CDH12 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CDH12 Gene

Disorders for CDH12 Gene

MalaCards: The human disease database

(1) MalaCards diseases for CDH12 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
cri-du-chat syndrome
  • cat cry syndrome
- elite association - COSMIC cancer census association via MalaCards
Search CDH12 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CDH12

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CDH12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CDH12 Gene

Publications for CDH12 Gene

  1. Expressed cadherin pseudogenes are localized to the critical region of the spinal muscular atrophy gene. (PMID: 7731968) Selig S … Kunkel LM (Proceedings of the National Academy of Sciences of the United States of America 1995) 2 3 4 22 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  3. A Large-scale genetic association study of esophageal adenocarcinoma risk. (PMID: 20453000) Liu CY … Christiani DC (Carcinogenesis 2010) 3 44 58
  4. Genetic utility of broadly defined bipolar schizoaffective disorder as a diagnostic concept. (PMID: 19567891) Hamshere ML … Craddock N (The British journal of psychiatry : the journal of mental science 2009) 3 44 58
  5. NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium. (PMID: 19557197) Heard-Costa NL … North KE (PLoS genetics 2009) 3 44 58

Products for CDH12 Gene

Sources for CDH12 Gene

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