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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

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 PCDHGB3.

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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05F141868 1.7 FANTOM5 Ensembl ENCODE 10.2 +739.2 739205 11.0 PKNOX1 WRNIP1 ARID4B SIN3A YBX1 ZNF2 YY1 ZNF143 ZNF263 SP3 MRPL11P2 PCDHB5 KIAA0141 HDAC3 LOC102723915 PCDHGC5 PCDH1 PCDHGA9 NDFIP1 PCDHGC4
GH05F141493 1.2 FANTOM5 Ensembl ENCODE 10.2 +359.9 359949 3.2 CTCF SIX4 HLF SIN3A ZIC2 RAD21 SMARCA4 POLR2A GLIS1 FOXP2 PCDHB5 ENSG00000272070 CD14 PCDHB2 DIAPH1 RELL2 PCDHB16 TAF7 PCDHGC5 LOC100505658
GH05F140399 1.2 ENCODE 9.9 -733.2 -733178 4.7 CREB3L1 ZFP64 DMAP1 YY1 ZNF143 ZNF263 SP3 NFYC TBX21 ZNF610 PURA PCDHA3 PCDHA2 PCDHA7 SRA1 VTRNA1-1 CD14 PCDHA1 PCDHB18P PCDHGA6
GH05F140357 1.2 Ensembl ENCODE 9.9 -777.6 -777587 1.2 ELF3 KLF17 ARID4B FEZF1 ZNF48 ZNF2 RAD21 RFX5 SLC30A9 ELK1 PCDHB19P PCDHB17P PCDHB5 PCDHA3 LINC01024 ENSG00000253965 HBEGF
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

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
ENSR00001874427 394 800 CTCF ZNF654 POLR2A RAD21 YY1

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

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.

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

Inhibitory RNA Products

Clone Products

Flow Cytometry 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

Pathways & Interactions for PCDHB5 Gene

SuperPathways for PCDHB5 Gene

No Data Available

Interacting Proteins for PCDHB5 Gene

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:0007268 chemical synaptic transmission TAS 12231349
GO:0007416 synapse assembly TAS 12231349
GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules NAS 11322959
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:

Inhibitory RNA Products

Clone Products

Flow Cytometry 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 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, PaxDb, 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:

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

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
(Pan troglodytes)
Mammalia PCDHB5 34 35
  • 98.57 (n)
(Canis familiaris)
Mammalia PCDHB5 34
  • 87.38 (n)
(Bos Taurus)
Mammalia PCDHB5 34
  • 85.33 (n)
(Mus musculus)
Mammalia Pcdhb8 35
  • 79 (a)
Pcdhb10 34 16 35
  • 78.75 (n)
Pcdhb6 35
  • 78 (a)
Pcdhb4 35
  • 77 (a)
Pcdhb11 35
  • 75 (a)
Pcdhb12 35
  • 75 (a)
(Rattus norvegicus)
Mammalia Pcdhb10 34
  • 78.81 (n)
(Monodelphis domestica)
Mammalia -- 35
  • 64 (a)
-- 35
  • 64 (a)
-- 35
  • 64 (a)
-- 35
  • 63 (a)
-- 35
  • 63 (a)
-- 35
  • 63 (a)
-- 35
  • 62 (a)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 63 (a)
-- 35
  • 62 (a)
-- 35
  • 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)

Paralogs for PCDHB5 Gene

Variants for PCDHB5 Gene

Sequence variations from dbSNP and Humsavar for PCDHB5 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs111324703 -- 141,134,776(+) TTCTA(C/T)TTACA upstream-variant-2KB
rs111516128 -- 141,138,478(+) TCACT(A/G)GCACC downstream-variant-500B
rs112955864 -- 141,136,892(+) GTCAC(A/C/T)TACTC reference, synonymous-codon
rs113637338 -- 141,136,876(+) AGGCA(A/C/T)CAACG reference, missense
rs113715414 -- 141,133,321(+) TGTAG(-/A)TTCAT upstream-variant-2KB

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)

Relevant External Links 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

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 64
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  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 Lett. 2001) 3 4 64
  4. Phospho-tyrosine dependent protein-protein interaction network. (PMID: 25814554) Grossmann A. … Stelzl U. (Mol. Syst. Biol. 2015) 3 64
  5. Large-scale mapping of human protein-protein interactions by mass spectrometry. (PMID: 17353931) Ewing R.M. … Figeys D. (Mol. Syst. Biol. 2007) 3 64

Products for PCDHB5 Gene

Sources for PCDHB5 Gene

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