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Aliases for PCDHB5 Gene

Aliases for PCDHB5 Gene

  • Protocadherin Beta 5 2 3 5
  • PCDH-Beta-5 3 4
  • Protocadherin Beta-5 3
  • PCDH-BETA5 3

External Ids for PCDHB5 Gene

Previous GeneCards Identifiers for PCDHB5 Gene

  • GC05P140331
  • GC05P141097
  • GC05P140497
  • GC05P140543
  • GC05P140494
  • GC05P135659
  • GC05P140514
  • GC05P141295
  • GC05P141499
  • GC05P141606
  • GC05P141709
  • GC05P141808
  • GC05P141907
  • GC05P142015
  • GC05P142119

Summaries for PCDHB5 Gene

Entrez Gene Summary for PCDHB5 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 PCDHB5 Gene

PCDHB5 (Protocadherin Beta 5) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB4.

UniProtKB/Swiss-Prot for PCDHB5 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 PCDHB5 Gene

Additional gene information for PCDHB5 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB5 Gene

Genomics for PCDHB5 Gene

GeneHancer (GH) Regulatory Elements for PCDHB5 Gene

Promoters and enhancers for PCDHB5 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
GH05J141135 Promoter 0.8 Ensembl 650.7 +0.3 295 0.6 CTCF POLR2A POU5F1 ZNF143 BACH1 RAD21 YY1 PCDHB5 PCDHB6 ENSG00000272154 PCDHB@
GH05J141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 17.1 +834.4 834361 3 CLOCK DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC GLIS1 RNF14 PCDH12 LOC102723915 HDAC3 PCDHB18P PCDHGA6 PCDHGA7 DELE1 PCDHGA5 ENSG00000271871
GH05J141868 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 11.3 +739.2 739204 11 PKNOX1 FOXA2 ARID4B SIN3A YBX1 ZNF2 ZBTB7B IRF4 YY1 ZNF766 PCDH1 GC05P142308 MRPL11P2 PCDHB19P PCDHB5 PCDHB12 PCDHB3 PCDHB11 DELE1 HDAC3
GH05J140174 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.3 -958.2 -958219 5.2 HDGF PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 CYSTM1 PFDN1 UBE2D2 PCDHB5 PCDHB3 IK PCDHB4 ENSG00000250069 GC05M140174
GH05J140717 Promoter/Enhancer 1.6 Ensembl ENCODE 11.1 -416.1 -416070 2.7 MLX IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 PPARGC1A MEF2D GC05P142304 VTRNA1-2 ANKHD1 PURA HARS2 PCDHB18P PCDHB19P HDAC3 WDR55 PCDHGA6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHB5 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHB5 gene promoter:
  • Lmo2
  • GCNF-1
  • GCNF
  • AP-2gamma
  • Sox9
  • GCNF-2
  • E47
  • Tal-1beta
  • MRF-2

Genomic Locations for PCDHB5 Gene

Genomic Locations for PCDHB5 Gene
3,420 bases
Plus strand
2,905 bases
Plus strand

Genomic View for PCDHB5 Gene

Genes around PCDHB5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB5 Gene

Proteins for PCDHB5 Gene

  • Protein details for PCDHB5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin beta-5
    Protein Accession:
    Secondary Accessions:
    • Q549F4
    • Q9UFU9

    Protein attributes for PCDHB5 Gene

    795 amino acids
    Molecular mass:
    86423 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB5 Gene

Post-translational modifications for PCDHB5 Gene

  • Glycosylation at Asn566, Asn435, isoforms=417, and isoforms=169
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB5 Gene

Domains & Families for PCDHB5 Gene

Gene Families for PCDHB5 Gene

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

Protein Domains for PCDHB5 Gene

Suggested Antigen Peptide Sequences for PCDHB5 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHB5: view

No data available for UniProtKB/Swiss-Prot for PCDHB5 Gene

Function for PCDHB5 Gene

Molecular function for PCDHB5 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.

Phenotypes From GWAS Catalog for PCDHB5 Gene

Gene Ontology (GO) - Molecular Function for PCDHB5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB5: view
genes like me logo Genes that share phenotypes with PCDHB5: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHB5 Gene

Localization for PCDHB5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB5 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 PCDHB5 gene
Compartment Confidence
plasma membrane 4
extracellular 2
nucleus 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for PCDHB5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IBA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS 11322959
genes like me logo Genes that share ontologies with PCDHB5: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDHB5 Gene

Pathways & Interactions for PCDHB5 Gene

SuperPathways for PCDHB5 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHB5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA,IBA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007268 chemical synaptic transmission TAS 12231349
GO:0007416 synapse assembly TAS 12231349
genes like me logo Genes that share ontologies with PCDHB5: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB5 Gene

Drugs & Compounds for PCDHB5 Gene

(1) Drugs for PCDHB5 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 PCDHB5: view

Transcripts for PCDHB5 Gene

mRNA/cDNA for PCDHB5 Gene

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

Unigene Clusters for PCDHB5 Gene

Protocadherin beta 5:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB5 Gene

No ASD Table

Relevant External Links for PCDHB5 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHB5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHB5 Gene

Protein differential expression in normal tissues from HIPED for PCDHB5 Gene

This gene is overexpressed in Ovary (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDHB5 Gene

Protein tissue co-expression partners for PCDHB5 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHB5 Gene:


SOURCE GeneReport for Unigene cluster for PCDHB5 Gene:


Evidence on tissue expression from TISSUES for PCDHB5 Gene

  • Muscle(4.1)
genes like me logo Genes that share expression patterns with PCDHB5: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHB5 Gene

Orthologs for PCDHB5 Gene

This gene was present in the common ancestor of mammals.

Orthologs for PCDHB5 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHB5 34 33
  • 98.57 (n)
(Canis familiaris)
Mammalia PCDHB5 33
  • 87.38 (n)
(Bos Taurus)
Mammalia PCDHB5 33
  • 85.33 (n)
(Mus musculus)
Mammalia Pcdhb8 34
  • 79 (a)
Pcdhb10 16 34 33
  • 78.75 (n)
Pcdhb6 34
  • 78 (a)
Pcdhb4 34
  • 77 (a)
Pcdhb12 34
  • 75 (a)
Pcdhb11 34
  • 75 (a)
(Rattus norvegicus)
Mammalia Pcdhb10 33
  • 78.81 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 64 (a)
-- 34
  • 64 (a)
-- 34
  • 64 (a)
-- 34
  • 63 (a)
-- 34
  • 63 (a)
-- 34
  • 63 (a)
-- 34
  • 62 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 63 (a)
-- 34
  • 62 (a)
-- 34
  • 61 (a)
Species where no ortholog for PCDHB5 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)
  • 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 PCDHB5 Gene

Gene Tree for PCDHB5 (if available)
Gene Tree for PCDHB5 (if available)
Evolutionary constrained regions (ECRs) for PCDHB5: view image

Paralogs for PCDHB5 Gene Pseudogenes for PCDHB5 Gene

genes like me logo Genes that share paralogs with PCDHB5: view

Variants for PCDHB5 Gene

Sequence variations from dbSNP and Humsavar for PCDHB5 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1002723486 -- 141,136,295(+) T/C coding_sequence_variant, synonymous_variant
rs1003876715 -- 141,135,676(+) C/A coding_sequence_variant, missense_variant
rs1003951884 -- 141,135,318(+) T/C 5_prime_UTR_variant
rs1005558179 -- 141,134,309(+) C/T upstream_transcript_variant
rs1006780946 -- 141,133,905(+) T/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHB5 Gene

Variant ID Type Subtype PubMed ID
esv2759382 CNV gain 17122850
esv3606962 CNV loss 21293372
nsv428127 CNV loss 18775914
nsv471634 CNV gain+loss 15918152
nsv522785 CNV loss 19592680
nsv599907 CNV loss 21841781
nsv968993 CNV duplication 23825009

Variation tolerance for PCDHB5 Gene

Residual Variation Intolerance Score: 70.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.54; 64.84% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHB5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB5 Gene

Disorders for PCDHB5 Gene

Additional Disease Information for PCDHB5

No disorders were found for PCDHB5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHB5 Gene

Publications for PCDHB5 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. Phospho-tyrosine dependent protein-protein interaction network. (PMID: 25814554) Grossmann A … Stelzl U (Molecular systems biology 2015) 3 58

Products for PCDHB5 Gene

Sources for PCDHB5 Gene

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