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Aliases for PCDHB12 Gene

Aliases for PCDHB12 Gene

  • Protocadherin Beta 12 2 3 5
  • PCDH-Beta-12 3 4
  • Protocadherin Beta-12 3
  • PCDH-BETA12 3

External Ids for PCDHB12 Gene

Previous GeneCards Identifiers for PCDHB12 Gene

  • GC05P140404
  • GC05P141172
  • GC05P140571
  • GC05P140616
  • GC05P140568
  • GC05P140656
  • GC05P140661
  • GC05P135733
  • GC05P140667
  • GC05P140672
  • GC05P140677
  • GC05P140683
  • GC05P140692
  • GC05P141284
  • GC05P141365
  • GC05P141425
  • GC05P141510
  • GC05P141616
  • GC05P141719
  • GC05P141818
  • GC05P141917
  • GC05P142025
  • GC05P142132

Summaries for PCDHB12 Gene

Entrez Gene Summary for PCDHB12 Gene

  • This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHB12 Gene

PCDHB12 (Protocadherin Beta 12) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB11.

UniProtKB/Swiss-Prot for PCDHB12 Gene

  • Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Gene Wiki entry for PCDHB12 Gene

Additional gene information for PCDHB12 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB12 Gene

Genomics for PCDHB12 Gene

GeneHancer (GH) Regulatory Elements for PCDHB12 Gene

Promoters and enhancers for PCDHB12 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
GH05J141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 20.5 +760.9 760870 3 CLOCK DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC GLIS1 RNF14 PCDH12 LOC102723915 HDAC3 PCDHB18P PCDHGA6 PCDHGA7 DELE1 PCDHGA5 ENSG00000271871
GH05J140717 Promoter/Enhancer 1.6 Ensembl ENCODE 22.4 -489.6 -489561 2.7 MLX IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 PPARGC1A MEF2D GC05P142304 VTRNA1-2 ANKHD1 PURA HARS2 PCDHB18P PCDHB19P HDAC3 WDR55 PCDHGA6
GH05J141868 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.5 +665.7 665713 11 PKNOX1 FOXA2 ARID4B SIN3A YBX1 ZNF2 ZBTB7B IRF4 YY1 ZNF766 PCDH1 GC05P142308 MRPL11P2 PCDHB19P PCDHB5 PCDHB12 PCDHB3 PCDHB11 DELE1 HDAC3
GH05J140725 Promoter/Enhancer 1.6 Ensembl ENCODE 12.1 -482.7 -482715 1.1 PKNOX1 ARNT ARID4B SIN3A ZNF2 IRF4 YY1 POLR2B ZNF766 ZNF213 GC05P142300 VTRNA1-3 ANKHD1 LOC102723915 WDR55 HDAC3 HARS2 TMCO6 FCHSD1 PCDHA4
GH05J140710 Promoter/Enhancer 1.6 Ensembl ENCODE 12.1 -497.7 -497713 1.9 CLOCK FEZF1 IRF4 YY1 ZNF213 ZNF143 SP3 SSRP1 ZNF610 GLIS1 GC05P142295 LOC105378198 VTRNA1-1 HARS2 ANKHD1 WDR55 LOC102723915 HDAC3 PCDHB18P PURA
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHB12 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHB12 gene promoter:
  • HEN1
  • FOXD1
  • PPAR-alpha
  • Arnt
  • AhR
  • E47
  • CUTL1
  • NRSF form 1
  • NRSF form 2

Genomic Locations for PCDHB12 Gene

Genomic Locations for PCDHB12 Gene
3,875 bases
Plus strand
3,430 bases
Plus strand

Genomic View for PCDHB12 Gene

Genes around PCDHB12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB12 Gene

Proteins for PCDHB12 Gene

  • Protein details for PCDHB12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin beta-12
    Protein Accession:
    Secondary Accessions:
    • B4DDU1

    Protein attributes for PCDHB12 Gene

    795 amino acids
    Molecular mass:
    86770 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHB12 Gene


neXtProt entry for PCDHB12 Gene

Post-translational modifications for PCDHB12 Gene

  • Glycosylation at isoforms=2567, Asn487, isoforms=2436, and Asn418
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB12 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB12 Gene

Domains & Families for PCDHB12 Gene

Gene Families for PCDHB12 Gene

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

Protein Domains for PCDHB12 Gene

Suggested Antigen Peptide Sequences for PCDHB12 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHB12: view

No data available for UniProtKB/Swiss-Prot for PCDHB12 Gene

Function for PCDHB12 Gene

Molecular function for PCDHB12 Gene

UniProtKB/Swiss-Prot Function:
Potential calcium-dependent cell-adhesion protein. May be involved in the establishment and maintenance of specific neuronal connections in the brain.

Gene Ontology (GO) - Molecular Function for PCDHB12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB12: view
genes like me logo Genes that share phenotypes with PCDHB12: view

Animal Model Products

CRISPR Products

miRNA for PCDHB12 Gene

miRTarBase miRNAs that target PCDHB12

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHB12

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHB12 Gene

Localization for PCDHB12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB12 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 PCDHB12 gene
Compartment Confidence
plasma membrane 5
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDHB12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane TAS 10380929
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDHB12: view

Pathways & Interactions for PCDHB12 Gene

SuperPathways for PCDHB12 Gene

No Data Available

Interacting Proteins for PCDHB12 Gene

Gene Ontology (GO) - Biological Process for PCDHB12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS 10380929
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007268 chemical synaptic transmission IBA --
GO:0007399 nervous system development TAS 10380929
genes like me logo Genes that share ontologies with PCDHB12: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB12 Gene

Drugs & Compounds for PCDHB12 Gene

(1) Drugs for PCDHB12 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
genes like me logo Genes that share compounds with PCDHB12: view

Transcripts for PCDHB12 Gene

mRNA/cDNA for PCDHB12 Gene

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

Unigene Clusters for PCDHB12 Gene

Protocadherin beta 12:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHB12

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB12 Gene

No ASD Table

Relevant External Links for PCDHB12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHB12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHB12 Gene

Protein differential expression in normal tissues from HIPED for PCDHB12 Gene

This gene is overexpressed in Bone marrow mesenchymal stem cell (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDHB12 Gene

Protein tissue co-expression partners for PCDHB12 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHB12 Gene:


SOURCE GeneReport for Unigene cluster for PCDHB12 Gene:


Evidence on tissue expression from TISSUES for PCDHB12 Gene

  • Nervous system(4.3)
genes like me logo Genes that share expression patterns with PCDHB12: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHB12 Gene

Orthologs for PCDHB12 Gene

This gene was present in the common ancestor of mammals.

Orthologs for PCDHB12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHB12 34 33
  • 98.31 (n)
(Bos Taurus)
Mammalia -- 34
  • 83 (a)
(Rattus norvegicus)
Mammalia Pcdhb19 33
  • 79.75 (n)
(Mus musculus)
Mammalia Pcdhb19 16 34 33
  • 79.41 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 65 (a)
-- 34
  • 65 (a)
-- 34
  • 65 (a)
-- 34
  • 64 (a)
-- 34
  • 64 (a)
-- 34
  • 63 (a)
-- 34
  • 63 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 63 (a)
-- 34
  • 62 (a)
-- 34
  • 60 (a)
Species where no ortholog for PCDHB12 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)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • 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)
  • lizard (Anolis carolinensis)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for PCDHB12 Gene

Gene Tree for PCDHB12 (if available)
Gene Tree for PCDHB12 (if available)
Evolutionary constrained regions (ECRs) for PCDHB12: view image

Paralogs for PCDHB12 Gene

genes like me logo Genes that share paralogs with PCDHB12: view

Variants for PCDHB12 Gene

Sequence variations from dbSNP and Humsavar for PCDHB12 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1001864731 -- 141,208,923(+) G/A coding_sequence_variant, missense_variant
rs1003438177 -- 141,207,813(+) G/T upstream_transcript_variant
rs1004274883 -- 141,208,825(+) A/G 5_prime_UTR_variant
rs1004369728 -- 141,208,568(+) G/A/T upstream_transcript_variant
rs1004660542 -- 141,207,399(+) T/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHB12 Gene

Variant ID Type Subtype PubMed ID
dgv958e201 CNV deletion 23290073
esv2664767 CNV deletion 23128226
esv2730846 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv3606973 CNV loss 21293372
esv3606974 CNV gain 21293372
nsv1024594 CNV loss 25217958
nsv428127 CNV loss 18775914
nsv471634 CNV gain+loss 15918152
nsv599908 CNV loss 21841781
nsv599919 CNV loss 21841781
nsv823266 CNV gain 20364138
nsv823277 CNV gain 20364138
nsv969261 CNV duplication 23825009
nsv980737 CNV duplication 23825009

Variation tolerance for PCDHB12 Gene

Residual Variation Intolerance Score: 89% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.06; 90.13% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHB12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB12 Gene

Disorders for PCDHB12 Gene

Additional Disease Information for PCDHB12

No disorders were found for PCDHB12 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHB12 Gene

Publications for PCDHB12 Gene

  1. A striking organization of a large family of human neural cadherin-like cell adhesion genes. (PMID: 10380929) Wu Q … Maniatis T (Cell 1999) 2 3 4 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number. (PMID: 11322959) Vanhalst K … van Roy F (FEBS letters 2001) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 4 58

Products for PCDHB12 Gene

Sources for PCDHB12 Gene

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