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CDH12 cadherin 12 [ Homo sapiens (human) ]

Gene ID: 1010, updated on 6-Sep-2021

Summary

Official Symbol
CDH12provided by HGNC
Official Full Name
cadherin 12provided by HGNC
Primary source
HGNC:HGNC:1751
See related
Ensembl:ENSG00000154162 MIM:600562
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

See CDH12 in Genome Data Viewer
Location:
5p14.3
Exon count:
18
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (21750673..22853344, complement)
105.20201022 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 GUSB pseudogene 1 Neighboring gene uncharacterized LOC105374685 Neighboring gene uncharacterized LOC105374683 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 uncharacterized LOC105374682 Neighboring gene pro-melanin concentrating hormone like 1 (pseudogene) Neighboring gene uncharacterized LOC105374681 Neighboring gene glucosaminyl (N-acetyl) transferase 1, core 2 pseudogene 2 Neighboring gene uncharacterized LOC101929617 Neighboring gene uncharacterized LOC105374686 Neighboring gene uncharacterized LOC105374687

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
NRXN3 is a novel locus for waist circumference: a genome-wide association study from the CHARGE Consortium.
GeneReviews: Not available
The CCND1 c.870G>A polymorphism is a risk factor for t(11;14)(q13;q32) multiple myeloma.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ34857

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cadherin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables calcium ion binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in adherens junction organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell-cell adhesion via plasma-membrane adhesion molecules IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell-cell junction assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
Inferred from Electronic Annotation
more info
 
involved_in multicellular organism development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
is_active_in adherens junction IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of catenin complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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_001317227.2NP_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
    P55289
    Conserved Domains (3) summary
    cd11304
    Location:164265
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80158
    CA; Cadherin repeats
    pfam01049
    Location:638785
    Cadherin_C; Cadherin cytoplasmic region
  2. NM_001317228.1NP_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:233340
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80158
    CA; Cadherin repeats
    pfam01049
    Location:606743
    Cadherin_C; Cadherin cytoplasmic region
  3. NM_001364104.2NP_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
    Related
    ENSP00000423577.1, ENST00000504376.6
    Conserved Domains (3) summary
    cd11304
    Location:164265
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80158
    CA; Cadherin repeats
    pfam01049
    Location:638785
    Cadherin_C; Cadherin cytoplasmic region
  4. NM_001364105.2NP_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
    Conserved Domains (3) summary
    cd11304
    Location:164265
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80158
    CA; Cadherin repeats
    pfam01049
    Location:638785
    Cadherin_C; Cadherin cytoplasmic region
  5. NM_001364106.2NP_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
    Conserved Domains (3) summary
    cd11304
    Location:164265
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80158
    CA; Cadherin repeats
    pfam01049
    Location:638785
    Cadherin_C; Cadherin cytoplasmic region
  6. NM_001364107.2NP_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
    Conserved Domains (3) summary
    cd11304
    Location:164265
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80158
    CA; Cadherin repeats
    pfam01049
    Location:638785
    Cadherin_C; Cadherin cytoplasmic region
  7. NM_001364108.2NP_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
    Conserved Domains (3) summary
    cd11304
    Location:164265
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80158
    CA; Cadherin repeats
    pfam01049
    Location:638785
    Cadherin_C; Cadherin cytoplasmic region
  8. NM_001364109.2NP_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:49156
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:243
    CA; Cadherin repeats
    pfam01049
    Location:414561
    Cadherin_C; Cadherin cytoplasmic region
  9. NM_004061.5NP_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
    P55289
    Related
    ENSP00000371689.1, ENST00000382254.6
    Conserved Domains (3) summary
    cd11304
    Location:164265
    Cadherin_repeat; Cadherin tandem repeat domain
    smart00112
    Location:80158
    CA; Cadherin repeats
    pfam01049
    Location:638785
    Cadherin_C; Cadherin cytoplasmic region

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

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

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NW_003315917.2 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    1444129..1445481 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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