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Aliases for PCDHB3 Gene

Aliases for PCDHB3 Gene

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

External Ids for PCDHB3 Gene

Previous GeneCards Identifiers for PCDHB3 Gene

  • GC05P140296
  • GC05P141063
  • GC05P140463
  • GC05P140508
  • GC05P140460
  • GC05P135624
  • GC05P140480
  • GC05P141277
  • GC05P141497
  • GC05P141604
  • GC05P141707
  • GC05P141806
  • GC05P141905
  • GC05P142013
  • GC05P142116

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 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 , fRNAdb sequence ontologies and piRNA Summary for PCDHB3 Gene

Genomics for PCDHB3 Gene

GeneHancer (GH) Regulatory Elements for PCDHB3 Gene

Promoters and enhancers for PCDHB3 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
GH05J141100 Enhancer 0.6 ENCODE 650.7 +0.2 200 0.2 CTCF ZNF654 MAX RAD21 GATA3 POLR2A CREB1 ZNF143 CUX1 ZNF444 PCDHB3 PCDHB2 PIR39382 PCDHB@ ENSG00000272154
GH05J140717 Promoter/Enhancer 1.6 Ensembl ENCODE 22 -381.1 -381106 2.7 MLX IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 SP3 PPARGC1A MEF2D GC05P142304 VTRNA1-2 ANKHD1 PURA HARS2 PCDHB18P PCDHB19P HDAC3 WDR55 PCDHGA6
GH05J141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 15.7 +869.3 869325 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 10.5 +774.2 774168 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 10.5 -923.3 -923255 5.2 HDGF PKNOX1 SMAD1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 CYSTM1 PFDN1 UBE2D2 PCDHB5 PCDHB3 IK PCDHB4 ENSG00000250069 GC05M140174
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for PCDHB3 Gene

Genomic Locations for PCDHB3 Gene
3,586 bases
Plus strand
3,173 bases
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:
    Recommended name:
    Protocadherin beta-3
    Protein Accession:
    Secondary Accessions:
    • B2R8P2

    Protein attributes for PCDHB3 Gene

    796 amino acids
    Molecular mass:
    86773 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB3 Gene

Post-translational modifications for PCDHB3 Gene

  • Glycosylation at Asn567, isoforms=436, isoforms=418, and isoforms=169
  • Modification sites at PhosphoSitePlus

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

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:

Graphical View of Domain Structure for InterPro Entry

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

No data available for 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

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 5
extracellular 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

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 10380929
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS 11322959
genes like me logo Genes that share ontologies with PCDHB3: view

Pathways & Interactions for PCDHB3 Gene

SuperPathways for PCDHB3 Gene

No Data Available

Interacting Proteins for PCDHB3 Gene

Gene Ontology (GO) - Biological Process for PCDHB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS 10380929
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:0007399 nervous system development TAS 10380929
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 Approved Nutra 0
genes like me logo Genes that share compounds with PCDHB3: view

Transcripts for PCDHB3 Gene

mRNA/cDNA for PCDHB3 Gene

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

Unigene Clusters for PCDHB3 Gene

Protocadherin beta 3:
Representative Sequences:

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
ECgene alternative splicing isoforms for

Expression for PCDHB3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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

NURSA nuclear receptor signaling pathways regulating expression of PCDHB3 Gene:


SOURCE GeneReport for Unigene cluster for PCDHB3 Gene:


Evidence on tissue expression from TISSUES for PCDHB3 Gene

  • Nervous system(4.3)
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
(Pan troglodytes)
Mammalia PCDHB3 34 33
  • 98.79 (n)
(Canis familiaris)
Mammalia LOC487168 33
  • 86.15 (n)
(Rattus norvegicus)
Mammalia Pcdhb3 33
  • 80.54 (n)
(Mus musculus)
Mammalia Pcdhb3 16 34 33
  • 80.28 (n)
(Bos Taurus)
Mammalia LOC786512 33
  • 75.04 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 66 (a)
-- 34
  • 66 (a)
-- 34
  • 66 (a)
-- 34
  • 66 (a)
-- 34
  • 65 (a)
-- 34
  • 65 (a)
-- 34
  • 64 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 64 (a)
-- 34
  • 63 (a)
-- 34
  • 63 (a)
(Gallus gallus)
Aves LOC100857544 33
  • 58.8 (n)
(Danio rerio)
Actinopterygii pcdh2g17 33
  • 52.45 (n)
Species where no ortholog for PCDHB3 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)
  • 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)

Evolution for PCDHB3 Gene

Gene Tree for PCDHB3 (if available)
Gene Tree for PCDHB3 (if available)
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 from dbSNP and Humsavar for PCDHB3 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs1000186656 -- 141,100,012(+) C/T upstream_transcript_variant
rs1000522248 -- 141,098,256(+) C/T upstream_transcript_variant
rs1001310963 -- 141,099,442(+) G/A upstream_transcript_variant
rs1001356476 -- 141,099,050(+) C/T upstream_transcript_variant
rs1004662548 -- 141,104,015(+) A/T downstream_transcript_variant

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

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 58
  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 58
  3. 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 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 4 58
  5. Protocadherins. (PMID: 12231349) Frank M … Kemler R (Current opinion in cell biology 2002) 3 58

Products for PCDHB3 Gene

Sources for PCDHB3 Gene

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