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    CDH12 cadherin 12 [ Homo sapiens (human) ]

    Gene ID: 1010, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CDH12provided by HGNC
    Official Full Name
    cadherin 12provided by HGNC
    Primary source
    HGNC:HGNC:1751
    See related
    Ensembl:ENSG00000154162 MIM:600562; AllianceGenome:HGNC:1751
    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
    CDHB
    Summary
    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]
    Expression
    Biased expression in brain (RPKM 1.2), adrenal (RPKM 1.2) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CDH12 in Genome Data Viewer
    Location:
    5p14.3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (21750673..22853344, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (21857991..22961025, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (21750782..22853453, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900949 Neighboring gene GUSB pseudogene 1 Neighboring gene uncharacterized LOC105374685 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:21614040-21614968 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:21813195-21813389 Neighboring gene uncharacterized LOC105374683 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:21823845-21825044 Neighboring gene small nucleolar RNA, H/ACA box 105A Neighboring gene uncharacterized LOC107986345 Neighboring gene heat shock protein family D (Hsp60) member 1 pseudogene 1 Neighboring gene MPRA-validated peak5184 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:22122549-22123060 Neighboring gene uncharacterized LOC105374682 Neighboring gene pro-melanin concentrating hormone like 1 (pseudogene) Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:22473807-22475006 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:22480518-22480675 Neighboring gene uncharacterized LOC105374681 Neighboring gene glucosaminyl (N-acetyl) transferase 1, core 2 pseudogene 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:22744411-22744586 Neighboring gene uncharacterized LOC101929617 Neighboring gene NANOG hESC enhancer GRCh37_chr5:22835757-22836258 Neighboring gene uncharacterized LOC105374686 Neighboring gene Sharpr-MPRA regulatory region 1276 Neighboring gene uncharacterized LOC105374687 Neighboring gene Sharpr-MPRA regulatory region 8980

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. An N-Cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer. Gouin KH 3rd, et al. Nat Commun, 2021 Aug 12. PMID 34385456, Free PMC Article
    2. A second-generation linkage map of the human genome. Weissenbach J, et al. Nature, 1992 Oct 29. PMID 1436057
    3. Gene expression profiling of post-mortem orbitofrontal cortex in violent suicide victims. Thalmeier A, et al. Int J Neuropsychopharmacol, 2008 Mar. PMID 17608962
    4. CDH12 promotes the invasion of salivary adenoid cystic carcinoma. Wang JF, et al. Oncol Rep, 2011 Jul. PMID 21573496
    5. Cadherin-12 contributes to tumorigenicity in colorectal cancer by promoting migration, invasion, adhersion and angiogenesis. Zhao J, et al. J Transl Med, 2013 Nov 15. PMID 24237488, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The Role of Cadherin 12 (CDH12) in the Peritoneal Fluid among Patients with Endometriosis and Endometriosis-Related Infertility.
      Title: The Role of Cadherin 12 (CDH12) in the Peritoneal Fluid among Patients with Endometriosis and Endometriosis-Related Infertility.
    2. An N-Cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer.
      Title: An N-Cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer.
    3. Identification of a CDH12 potential candidate genetic variant for an autosomal dominant form of transgrediens and progrediens palmoplantar keratoderma in a Tunisian family.
      Title: Identification of a CDH12 potential candidate genetic variant for an autosomal dominant form of transgrediens and progrediens palmoplantar keratoderma in a Tunisian family.
    4. CDH12 may influence CRC cell progression.
      Title: Cadherin-12 enhances proliferation in colorectal cancer cells and increases progression by promoting EMT.
    5. CDH12 may play an important role in the invasion and metastasis of salivary adenoid cystic carcinoma
      Title: CDH12 promotes the invasion of salivary adenoid cystic carcinoma.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: A Large-scale genetic association study of esophageal adenocarcinoma risk.
    8. E2F4, PHACTR3, PRAME family member and CDH12 most probably play important role in non-small-cell lung cancer geneses
      Title: Identification of genes associated with non-small-cell lung cancer promotion and progression.
    9. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genetic utility of broadly defined bipolar schizoaffective disorder as a diagnostic concept.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium.
    EBI GWAS Catalog
    The CCND1 c.870G>A polymorphism is a risk factor for t(11;14)(q13;q32) multiple myeloma.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34857

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    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 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 homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catenin complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    cadherin-12
    Names
    Br-cadherin
    N-cadherin 2
    brain-cadherin
    cadherin, neural type, 2
    neural type cadherin 2
    neuronal cadherin 2

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001317227.2 → NP_001304156.1  cadherin-12 isoform 1 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 4-8 all encode the same isoform (1).
      Source sequence(s)
      AC138854, AC138940, AC139497, AC140132, AC140171
      Consensus CDS
      CCDS3890.1
      UniProtKB/Swiss-Prot
      B2RBT1, B7Z2U6, P55289, Q86UD2
      Conserved Domains (3) summary
      cd11304
      Location:164 → 265
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:80 → 158
      CA; Cadherin repeats
      pfam01049
      Location:638 → 785
      Cadherin_C; Cadherin cytoplasmic region

    2. NM_001317228.1 → NP_001304157.1  cadherin-12 isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate in-frame exon in the 5' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1. This isoform (2) may undergo proteolytic processing similar to isoform 1.
      Source sequence(s)
      AK295123, BC047608, L33477
      Consensus CDS
      CCDS82991.1
      UniProtKB/Swiss-Prot
      P55289
      Related
      ENSP00000428786.1, ENST00000522262.1
      Conserved Domains (3) summary
      cd11304
      Location:233 → 340
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:80 → 158
      CA; Cadherin repeats
      pfam01049
      Location:606 → 743
      Cadherin_C; Cadherin cytoplasmic region

    3. NM_001364104.2 → NP_001351033.1  cadherin-12 isoform 1 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 4-8 all encode the same isoform (1).
      Source sequence(s)
      AC026716, AC109455, AC138854, AC138940, AC139497, AC140132, AC140171
      Consensus CDS
      CCDS3890.1
      UniProtKB/Swiss-Prot
      B2RBT1, B7Z2U6, P55289, Q86UD2
      Related
      ENSP00000423577.1, ENST00000504376.6
      Conserved Domains (3) summary
      cd11304
      Location:164 → 265
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:80 → 158
      CA; Cadherin repeats
      pfam01049
      Location:638 → 785
      Cadherin_C; Cadherin cytoplasmic region

    4. NM_001364105.2 → NP_001351034.1  cadherin-12 isoform 1 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 4-8 all encode the same isoform (1).
      Source sequence(s)
      AC026716, AC093263, AC109455, AC138854, AC138940, AC139497, AC140132, AC140171
      Consensus CDS
      CCDS3890.1
      UniProtKB/Swiss-Prot
      B2RBT1, B7Z2U6, P55289, Q86UD2
      Conserved Domains (3) summary
      cd11304
      Location:164 → 265
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:80 → 158
      CA; Cadherin repeats
      pfam01049
      Location:638 → 785
      Cadherin_C; Cadherin cytoplasmic region

    5. NM_001364106.2 → NP_001351035.1  cadherin-12 isoform 1 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 4-8 all encode the same isoform (1).
      Source sequence(s)
      AC026716, AC109455, AC138854, AC138940, AC139497, AC140132, AC140171
      Consensus CDS
      CCDS3890.1
      UniProtKB/Swiss-Prot
      B2RBT1, B7Z2U6, P55289, Q86UD2
      Conserved Domains (3) summary
      cd11304
      Location:164 → 265
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:80 → 158
      CA; Cadherin repeats
      pfam01049
      Location:638 → 785
      Cadherin_C; Cadherin cytoplasmic region

    6. NM_001364107.2 → NP_001351036.1  cadherin-12 isoform 1 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 4-8 all encode the same isoform (1).
      Source sequence(s)
      AC138854, AC138940, AC139497, AC140132, AC140171
      Consensus CDS
      CCDS3890.1
      UniProtKB/Swiss-Prot
      B2RBT1, B7Z2U6, P55289, Q86UD2
      Conserved Domains (3) summary
      cd11304
      Location:164 → 265
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:80 → 158
      CA; Cadherin repeats
      pfam01049
      Location:638 → 785
      Cadherin_C; Cadherin cytoplasmic region

    7. NM_001364108.2 → NP_001351037.1  cadherin-12 isoform 1 preproprotein

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 4-8 all encode the same isoform (1).
      Source sequence(s)
      AC138854, AC138940, AC139497, AC140132, AC140171
      Consensus CDS
      CCDS3890.1
      UniProtKB/Swiss-Prot
      B2RBT1, B7Z2U6, P55289, Q86UD2
      Conserved Domains (3) summary
      cd11304
      Location:164 → 265
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:80 → 158
      CA; Cadherin repeats
      pfam01049
      Location:638 → 785
      Cadherin_C; Cadherin cytoplasmic region

    8. NM_001364109.2 → NP_001351038.1  cadherin-12 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (9) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC138940, AC140132, AC140171, AK092176
      Conserved Domains (3) summary
      cd11304
      Location:49 → 156
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:2 → 43
      CA; Cadherin repeats
      pfam01049
      Location:414 → 561
      Cadherin_C; Cadherin cytoplasmic region

    9. NM_004061.5 → NP_004052.2  cadherin-12 isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_004052.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1, 2, and 4-8 all encode the same isoform (1).
      Source sequence(s)
      AC026716, AC093263, AC109455, AC138854, AC138940, AC139497, AC140132, AC140171
      Consensus CDS
      CCDS3890.1
      UniProtKB/Swiss-Prot
      B2RBT1, B7Z2U6, P55289, Q86UD2
      Related
      ENSP00000371689.1, ENST00000382254.6
      Conserved Domains (3) summary
      cd11304
      Location:164 → 265
      Cadherin_repeat; Cadherin tandem repeat domain
      smart00112
      Location:80 → 158
      CA; Cadherin repeats
      pfam01049
      Location:638 → 785
      Cadherin_C; Cadherin cytoplasmic region

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      21750673..22853344 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416602.1 → XP_047272558.1  cadherin-12 isoform X1

      UniProtKB/Swiss-Prot
      B2RBT1, B7Z2U6, P55289, Q86UD2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      21857991..22961025 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351385.1 → XP_054207360.1  cadherin-12 isoform X1

      UniProtKB/Swiss-Prot
      B2RBT1, B7Z2U6, P55289, Q86UD2
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P55289.2 GenPept UniProtKB/Swiss-Prot:P55289

    Gene LinkOut

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