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Aliases for PCDHB5 Gene

Aliases for PCDHB5 Gene

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

External Ids for PCDHB5 Gene

Previous GeneCards Identifiers for PCDHB5 Gene

  • GC05P140331
  • GC05P141097
  • GC05P140497
  • GC05P140543
  • GC05P140494
  • GC05P135659
  • GC05P140514
  • GC05P141295
  • GC05P141499

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. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGA11.

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

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

Genomics for PCDHB5 Gene

Regulatory Elements for PCDHB5 Gene

Enhancers for PCDHB5 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PCDHB5 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHB5 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PCDHB5 on UCSC Golden Path with GeneCards custom track

Genomic Location for PCDHB5 Gene

141,135,206 bp from pter
141,138,625 bp from pter
3,420 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

Proteomics data for PCDHB5 Gene at MOPED

Post-translational modifications for PCDHB5 Gene

  • Glycosylation at Asn 169, Asn 417, Asn 435, and Asn 566
  • 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

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



  • Contains 6 cadherin domains.
  • Contains 6 cadherin domains.
genes like me logo Genes that share domains with PCDHB5: view

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.
genes like me logo Genes that share phenotypes with PCDHB5: view

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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

Jensen Localization Image for PCDHB5 Gene COMPARTMENTS Subcellular localization image for PCDHB5 gene
Compartment Confidence
plasma membrane 4
extracellular 2
nucleus 2
endoplasmic reticulum 1
lysosome 1
mitochondrion 1
peroxisome 1
vacuole 1

No data available for Gene Ontology (GO) - Cellular Components 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:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
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 Nutra 0
genes like me logo Genes that share compounds with PCDHB5: view

Transcripts for PCDHB5 Gene

mRNA/cDNA for PCDHB5 Gene

Unigene Clusters for PCDHB5 Gene

Protocadherin beta 5:
Representative Sequences:

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 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, PaxDb, and MOPED for PCDHB5 Gene

SOURCE GeneReport for Unigene cluster for PCDHB5 Gene Hs.119693

genes like me logo Genes that share expression patterns with PCDHB5: view

Protein tissue co-expression partners for PCDHB5 Gene

- Elite partner

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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
(Bos Taurus)
Mammalia PCDHB5 35
  • 85.33 (n)
  • 81.97 (a)
(Canis familiaris)
Mammalia PCDHB5 35
  • 87.38 (n)
  • 84.03 (a)
(Mus musculus)
Mammalia Pcdhb10 35
  • 78.75 (n)
  • 77.02 (a)
Pcdhb10 16
Pcdhb10 36
  • 77 (a)
Pcdhb11 36
  • 75 (a)
Pcdhb12 36
  • 75 (a)
Pcdhb4 36
  • 77 (a)
Pcdhb6 36
  • 78 (a)
Pcdhb8 36
  • 79 (a)
(Pan troglodytes)
Mammalia PCDHB5 35
  • 98.57 (n)
  • 98.24 (a)
  • 98 (a)
(Rattus norvegicus)
Mammalia Pcdhb10 35
  • 78.81 (n)
  • 76.14 (a)
(Monodelphis domestica)
Mammalia -- 36
  • 63 (a)
-- 36
  • 64 (a)
-- 36
  • 64 (a)
-- 36
  • 64 (a)
-- 36
  • 63 (a)
-- 36
  • 62 (a)
-- 36
  • 63 (a)
(Ornithorhynchus anatinus)
Mammalia -- 36
  • 61 (a)
-- 36
  • 63 (a)
-- 36
  • 62 (a)
Species with no ortholog for PCDHB5:
  • 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)

Paralogs 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 Sequence Context AA Info Type
rs17096901 - 141,135,901(+) AAAAA(C/T)AGCCC reference, missense
rs400562 - 141,137,592(-) GACCG(A/G)GGCCG reference, missense
rs246725 -- 141,137,849(-) ATGGC(A/G)GAAAA utr-variant-3-prime
rs246726 -- 141,137,213(-) GAGTC(A/G/T)CCGTC reference, synonymous-codon
rs246727 -- 141,136,829(-) AGGGC(A/G)GGGCT reference, synonymous-codon

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

Variant ID Type Subtype PubMed ID
dgv1857e1 CNV Complex 17122850
nsv428127 CNV Loss 18775914
nsv882971 CNV Loss 21882294
dgv6348n71 CNV Loss 21882294
nsv522785 CNV Loss 19592680
nsv471634 CNV Gain+Loss 15918152
dgv6349n71 CNV Loss 21882294
dgv1858e1 CNV Complex 17122850

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)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Relevant External Links for PCDHB5 Gene

Disorders for PCDHB5 Gene

Relevant External Links for PCDHB5

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

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 67
  2. Phospho-tyrosine dependent protein-protein interaction network. (PMID: 25814554) Grossmann A. … Stelzl U. (Mol. Syst. Biol. 2015) 3
  3. Large-scale mapping of human protein-protein interactions by mass spectrometry. (PMID: 17353931) Ewing R.M. … Figeys D. (Mol. Syst. Biol. 2007) 3
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PMID: 16344560) Kimura K. … Sugano S. (Genome Res. 2006) 3
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3

Products for PCDHB5 Gene

Sources for PCDHB5 Gene