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 ... See more...

Aliases for PCDHB3 Gene

Aliases for PCDHB3 Gene

  • Protocadherin Beta 3 2 3 5
  • Protocadherin Beta-3 3 4
  • PCDH-BETA3 2 3
  • PCDH-Beta-3 4
  • PCDHB3 5

External Ids for PCDHB3 Gene

Previous GeneCards Identifiers for PCDHB3 Gene

  • GC05P140296
  • GC05P141063
  • GC05P140463
  • GC05P140508
  • GC05P140460
  • GC05P135624
  • GC05P140480
  • GC05P141277
  • GC05P141497
  • GC05P142398
  • GC05P142502
  • GC05P142613
  • GC05P142838
  • GC05P141604
  • GC05P141707
  • GC05P141806
  • GC05P141905
  • GC05P142013
  • GC05P142116
  • GC05P142219
  • GC05P142319

Summaries for PCDHB3 Gene

Entrez Gene Summary for PCDHB3 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 PCDHB3 Gene

PCDHB3 (Protocadherin Beta 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB2.

UniProtKB/Swiss-Prot Summary for PCDHB3 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 PCDHB3 Gene

Additional gene information for PCDHB3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCDHB3 Gene

Genomics for PCDHB3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PCDHB3 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHB3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDHB3

Top Transcription factor binding sites by QIAGEN in the PCDHB3 gene promoter:
  • AML1a
  • ATF-2
  • c-Jun
  • C/EBPalpha
  • CUTL1
  • Pax-3
  • Sox9
  • Tal-1beta

Genomic Locations for PCDHB3 Gene

Genomic Locations for PCDHB3 Gene
chr5:141,100,473-141,103,827
(GRCh38/hg38)
Size:
3,355 bases
Orientation:
Plus strand
chr5:140,480,234-140,483,406
(GRCh37/hg19)
Size:
3,173 bases
Orientation:
Plus strand

Genomic View for PCDHB3 Gene

Genes around PCDHB3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB3 Gene

Proteins for PCDHB3 Gene

  • Protein details for PCDHB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5E6-PCDB3_HUMAN
    Recommended name:
    Protocadherin beta-3
    Protein Accession:
    Q9Y5E6
    Secondary Accessions:
    • B2R8P2

    Protein attributes for PCDHB3 Gene

    Size:
    796 amino acids
    Molecular mass:
    86714 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB3 Gene

Post-translational modifications for PCDHB3 Gene

  • Glycosylation at Asn169, Asn418, Asn436, and Asn567
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • PCDB3_HUMAN (1682)

Other Protein References for PCDHB3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB3 Gene

Domains & Families for PCDHB3 Gene

Gene Families for PCDHB3 Gene

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

Protein Domains for PCDHB3 Gene

Suggested Antigen Peptide Sequences for PCDHB3 Gene

GenScript: Design optimal peptide antigens:
  • Protocadherin beta-3 (PCDB3_HUMAN)
  • Protocadherin beta 3 (Q2M3R2_HUMAN)
genes like me logo Genes that share domains with PCDHB3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PCDHB3 Gene

Function for PCDHB3 Gene

Molecular function for PCDHB3 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 PCDHB3 Gene

Gene Ontology (GO) - Molecular Function for PCDHB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB3: view
genes like me logo Genes that share phenotypes with PCDHB3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHB3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHB3 Gene

Localization for PCDHB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB3 Gene

Cell membrane. Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
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 PCDHB3 gene
Compartment Confidence
plasma membrane 4
extracellular 1
nucleus 1
endoplasmic reticulum 1
mitochondrion 0
peroxisome 0
cytosol 0
lysosome 0
golgi apparatus 0

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PCDHB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane TAS,IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS 11322959
GO:0045202 synapse IEA --
genes like me logo Genes that share ontologies with PCDHB3: view

Pathways & Interactions for PCDHB3 Gene

PathCards logo

SuperPathways for PCDHB3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS,IBA 21873635
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007268 chemical synaptic transmission TAS 12231349
GO:0007399 nervous system development TAS 10380929
GO:0007416 synapse assembly TAS 12231349
genes like me logo Genes that share ontologies with PCDHB3: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB3 Gene

Drugs & Compounds for PCDHB3 Gene

(1) Drugs for PCDHB3 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Nutra 6556
genes like me logo Genes that share compounds with PCDHB3: view

Transcripts for PCDHB3 Gene

mRNA/cDNA for PCDHB3 Gene

1 REFSEQ mRNAs :
8 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PCDHB3

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB3 Gene

No ASD Table

Relevant External Links for PCDHB3 Gene

GeneLoc Exon Structure for
PCDHB3

Expression for PCDHB3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDHB3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PCDHB3 Gene

This gene is overexpressed in Blymphocyte (26.9), Frontal cortex (14.0), Fetal gut (11.1), and Retina (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDHB3 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDHB3

SOURCE GeneReport for Unigene cluster for PCDHB3 Gene:

Hs.674730

Evidence on tissue expression from TISSUES for PCDHB3 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with PCDHB3: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHB3 Gene

Orthologs for PCDHB3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHB3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PCDHB3 30 31
  • 98.79 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia LOC487168 30
  • 86.15 (n)
Rat
(Rattus norvegicus)
Mammalia Pcdhb3 30
  • 80.54 (n)
Mouse
(Mus musculus)
Mammalia Pcdhb3 30 17 31
  • 80.28 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LOC786512 30
  • 75.04 (n)
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 66 (a)
ManyToMany
-- 31
  • 66 (a)
ManyToMany
-- 31
  • 66 (a)
ManyToMany
-- 31
  • 66 (a)
ManyToMany
-- 31
  • 65 (a)
ManyToMany
-- 31
  • 65 (a)
ManyToMany
-- 31
  • 64 (a)
ManyToMany
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 64 (a)
ManyToMany
-- 31
  • 63 (a)
ManyToMany
-- 31
  • 63 (a)
ManyToMany
Chicken
(Gallus gallus)
Aves LOC100857544 30
  • 58.8 (n)
Zebrafish
(Danio rerio)
Actinopterygii pcdh2g17 30
  • 52.45 (n)
Species where no ortholog for PCDHB3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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 Vase (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)

Evolution for PCDHB3 Gene

ENSEMBL:
Gene Tree for PCDHB3 (if available)
TreeFam:
Gene Tree for PCDHB3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDHB3: view image

Paralogs for PCDHB3 Gene

genes like me logo Genes that share paralogs with PCDHB3: view

Variants for PCDHB3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDHB3 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs12515688 - p.Glu207Lys
rs31849 - p.Lys41Arg
rs3733699 - p.Arg414Ser

Additional dbSNP identifiers (rs#s) for PCDHB3 Gene

Structural Variations from Database of Genomic Variants (DGV) for PCDHB3 Gene

Variant ID Type Subtype PubMed ID
esv2759382 CNV gain 17122850
esv3606961 CNV loss 21293372
nsv428127 CNV loss 18775914
nsv516514 CNV gain 19592680
nsv522785 CNV loss 19592680
nsv599905 CNV gain 21841781
nsv599906 CNV loss 21841781
nsv599907 CNV loss 21841781
nsv968254 CNV duplication 23825009

Variation tolerance for PCDHB3 Gene

Residual Variation Intolerance Score: 79.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.47; 82.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHB3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHB3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB3 Gene

Disorders for PCDHB3 Gene

Additional Disease Information for PCDHB3

No disorders were found for PCDHB3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHB3 Gene

Publications for PCDHB3 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
  2. 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
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. Exome sequencing reveals the genetic landscape and frequent inactivation of PCDHB3 in Chinese rectal cancers. (PMID: 29537081) Ye W … Huang W (The Journal of pathology 2018) 3
  5. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal KB … Olsen JV (Science signaling 2015) 3

Products for PCDHB3 Gene

Sources for PCDHB3 Gene