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Aliases for PCDHB1 Gene

Aliases for PCDHB1 Gene

  • Protocadherin Beta 1 2 3 5
  • PCDH-Beta-1 3 4
  • Protocadherin Beta-1 3
  • PCDH-BETA1 3

External Ids for PCDHB1 Gene

Previous GeneCards Identifiers for PCDHB1 Gene

  • GC05P140247
  • GC05P141013
  • GC05P140414
  • GC05P140459
  • GC05P140411
  • GC05P135575
  • GC05P140432
  • GC05P140433
  • GC05P140452
  • GC05P141275
  • GC05P141495
  • GC05P141602
  • GC05P141702

Summaries for PCDHB1 Gene

Entrez Gene Summary for PCDHB1 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 PCDHB1 Gene

PCDHB1 (Protocadherin Beta 1) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB3.

UniProtKB/Swiss-Prot for PCDHB1 Gene

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

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHB1 Gene

Genomics for PCDHB1 Gene

Regulatory Elements for PCDHB1 Gene

Enhancers for PCDHB1 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
GH05F141084 1.3 FANTOM5 Ensembl ENCODE 17.4 +33.7 33684 1.6 CTCF PKNOX1 SAP130 RAD21 YY1 E2F1 ZNF23 GATA3 POLR2A ZNF143 PCDHB1 PCDHB3 PCDHB10 PCDHB9 PCDHB2 ENSG00000272154 PCDHB14 PCDHB18P PCDHGB6 PCDHB7
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCDHB1 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHB1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001874423 266 1199 SCRT1 E2F1 RFX1 SCRT2

Genomic Location for PCDHB1 Gene

141,051,135 bp from pter
141,059,344 bp from pter
8,210 bases
Plus strand

Genomic View for PCDHB1 Gene

Genes around PCDHB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB1 Gene

Proteins for PCDHB1 Gene

  • Protein details for PCDHB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protocadherin beta-1
    Protein Accession:
    Secondary Accessions:
    • Q2M257

    Protein attributes for PCDHB1 Gene

    818 amino acids
    Molecular mass:
    90491 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB1 Gene

Post-translational modifications for PCDHB1 Gene

  • Glycosylation at Asn 169, Asn 209, Asn 257, Asn 419, and Asn 568
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB1 Gene

Domains & Families for PCDHB1 Gene

Gene Families for PCDHB1 Gene

Protein Domains for PCDHB1 Gene

Suggested Antigen Peptide Sequences for PCDHB1 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 PCDHB1: view

Function for PCDHB1 Gene

Molecular function for PCDHB1 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 PCDHB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB1: view

Phenotypes for PCDHB1 Gene

genes like me logo Genes that share phenotypes with PCDHB1: 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 PCDHB1 Gene

Localization for PCDHB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB1 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 PCDHB1 gene
Compartment Confidence
plasma membrane 5
extracellular 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for PCDHB1 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 IEA --
genes like me logo Genes that share ontologies with PCDHB1: view

Pathways & Interactions for PCDHB1 Gene

SuperPathways for PCDHB1 Gene

No Data Available

Interacting Proteins for PCDHB1 Gene

STRING Interaction Network Preview (showing 5 interactants - click image to see details)
Selected Interacting proteins: ENSP00000307234 Q9Y5F3-PCDB1_HUMAN for PCDHB1 Gene via STRING IID

Gene Ontology (GO) - Biological Process for PCDHB1 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 IBA --
GO:0007416 synapse assembly IBA --
genes like me logo Genes that share ontologies with PCDHB1: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB1 Gene

Drugs & Compounds for PCDHB1 Gene

(1) Drugs for PCDHB1 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 PCDHB1: view

Transcripts for PCDHB1 Gene

mRNA/cDNA for PCDHB1 Gene

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

Unigene Clusters for PCDHB1 Gene

Protocadherin beta 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB1 Gene

No ASD Table

Relevant External Links for PCDHB1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PCDHB1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDHB1 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHB1 Gene

This gene is overexpressed in Testis (x12.5) and Pituitary (x8.5).

Protein differential expression in normal tissues from HIPED for PCDHB1 Gene

This gene is overexpressed in Bone (58.1) and Heart (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHB1 Gene

Protein tissue co-expression partners for PCDHB1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHB1 Gene:


SOURCE GeneReport for Unigene cluster for PCDHB1 Gene:

genes like me logo Genes that share expression patterns with PCDHB1: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for PCDHB1 Gene

Orthologs for PCDHB1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PCDHB1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PCDHB1 34 35
  • 99.39 (n)
(Bos Taurus)
Mammalia PCDHB1 34 35
  • 88.26 (n)
(Canis familiaris)
Mammalia PCDHB1 35
  • 87 (a)
(Mus musculus)
Mammalia Pcdhb1 34 16 35
  • 85.04 (n)
(Rattus norvegicus)
Mammalia Pcdhb1 34
  • 84.39 (n)
(Monodelphis domestica)
Mammalia PCDHB1 35
  • 76 (a)
(Ornithorhynchus anatinus)
Mammalia PCDHB1 35
  • 71 (a)
fruit fly
(Drosophila melanogaster)
Insecta Cad89D 36
  • 26 (a)
Species where no ortholog for PCDHB1 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)
  • 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 PCDHB1 Gene

Gene Tree for PCDHB1 (if available)
Gene Tree for PCDHB1 (if available)

Paralogs for PCDHB1 Gene

genes like me logo Genes that share paralogs with PCDHB1: view

Variants for PCDHB1 Gene

Sequence variations from dbSNP and Humsavar for PCDHB1 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs193920928 Uncertain significance 141,053,125(+) GGTTG(C/T)CCTAG intron-variant, reference, missense
rs10476822 -- 141,053,302(+) GGCCA(C/T)TGACC intron-variant, reference, missense
rs111433907 -- 141,049,496(+) TTAAC(G/T)CCACT intron-variant, upstream-variant-2KB
rs113752853 -- 141,054,359(+) TATGC(A/T)TGCAT intron-variant, downstream-variant-500B
rs115315895 -- 141,050,772(+) TGCAC(A/G)TGTAT intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for PCDHB1 Gene

Variant ID Type Subtype PubMed ID
esv2759382 CNV gain 17122850
nsv428127 CNV loss 18775914
nsv818387 CNV gain 17921354

Variation tolerance for PCDHB1 Gene

Residual Variation Intolerance Score: 70.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.91; 67.70% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHB1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB1 Gene

Disorders for PCDHB1 Gene

Relevant External Links for PCDHB1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for PCDHB1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHB1 Gene

Publications for PCDHB1 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) 4 64
  3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3 64
  4. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q. … Maniatis T. (Genome Res. 2001) 3 64
  5. 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 64

Products for PCDHB1 Gene

Sources for PCDHB1 Gene

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