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CDH12 cadherin 12 [ Homo sapiens (human) ]

Gene ID: 1010, updated on 2-Nov-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
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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 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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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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