This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, sub... See more...

Aliases for PCDHGB5 Gene

Aliases for PCDHGB5 Gene

  • Protocadherin Gamma Subfamily B, 5 2 3 5
  • Protocadherin Gamma-B5 3 4
  • PCDH-GAMMA-B5 3
  • PCDH-Gamma-B5 4

External Ids for PCDHGB5 Gene

Previous GeneCards Identifiers for PCDHGB5 Gene

  • GC05P140594
  • GC05P141311
  • GC05P140713
  • GC05P140771
  • GC05P140792
  • GC05P140731
  • GC05P140808
  • GC05P140828
  • GC05P140845
  • GC05P140870
  • GC05P140877
  • GC05P140897
  • GC05P140930
  • GC05P140952
  • GC05P140973
  • GC05P140995
  • GC05P141025
  • GC05P141043
  • GC05P141070
  • GC05P141090
  • GC05P141109
  • GC05P141151
  • GC05P141168
  • GC05P141204
  • GC05P141244
  • GC05P141327
  • GC05P141386
  • GC05P141454
  • GC05P141531
  • GC05P142454
  • GC05P142558
  • GC05P142669
  • GC05P141634
  • GC05P141736
  • GC05P141835
  • GC05P141938
  • GC05P142042
  • GC05P142150
  • GC05P142248
  • GC05P142350

Summaries for PCDHGB5 Gene

Entrez Gene Summary for PCDHGB5 Gene

  • This gene is a member of the protocadherin gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHGB5 Gene

PCDHGB5 (Protocadherin Gamma Subfamily B, 5) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGB4.

UniProtKB/Swiss-Prot Summary for PCDHGB5 Gene

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

Additional gene information for PCDHGB5 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCDHGB5 Gene

Genomics for PCDHGB5 Gene

GeneHancer (GH) Regulatory Elements for PCDHGB5 Gene

Promoters and enhancers for PCDHGB5 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J141397 Promoter 1.1 EPDnew Ensembl 500.7 +0.3 313 1 ZNF217 CTCF NRF1 ZNF610 ZNF335 ZNF654 ZNF639 RAD21 ZNF2 ZBTB33 PCDHGB5 PCDHGB6 PCDHGA9 PCDHGA8 PCDHGB4 PCDHGA7 PCDHGA6 PCDHGB3 PCDHGA5 PCDHGB2
GH05J141407 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 0.4 +10.4 10414 1.6 CTCF EZH2 SMC3 NRF1 RAD21 TAF1 CBX5 ZNF143 CREM POLR2A PCDHGB6 PCDHGA6 PCDHGA10 PCDHGA9 PCDHGB5 PCDHGA8 PCDHGB4 PCDHGA7 PCDHGB3 PCDHGA5
GH05J141412 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 0.4 +15.3 15314 1.8 CTCF RAD21 TRIM22 POLR2A SMC3 PHF8 SMARCA5 IKZF1 NRF1 ESRRA PCDHGA10 NDUFA2 PCDHGB7 PCDHGB6 PCDHGA9 PCDHGB5 PCDHGA8 PCDHGB4 PCDHGA7 PCDHGA6
GH05J141421 Promoter 1.3 EPDnew Ensembl 0.4 +24.1 24114 3 CTCF ZSCAN5C ZNF10 ZIC2 REST RAD21 TRIM22 ZNF266 KLF9 ZBTB17 PCDHGA11 WDR55 ENSG00000228737 HDAC3 HARS2 TMCO6 FCHSD1 DELE1 IK PCDHGB6
GH05J141417 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 0.4 +20.2 20157 2.2 CTCF NRF1 RAD21 TRIM22 SMC3 SMARCA5 IKZF1 BCL6 TBP ZNF143 PCDHGB7 PCDHGB6 NDUFA2 PCDHA4 PCDHGA11 PCDHGA10 PCDHGA9 PCDHGB5 PCDHGA8 PCDHGB4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHGB5 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDHGB5

Top Transcription factor binding sites by QIAGEN in the PCDHGB5 gene promoter:
  • c-Myc
  • COMP1
  • Egr-2
  • FOXD3
  • FOXL1
  • Max
  • p300
  • Pax-2
  • Pax-2a

Genomic Locations for PCDHGB5 Gene

Genomic Locations for PCDHGB5 Gene
chr5:141,397,987-141,512,979
(GRCh38/hg38)
Size:
114,993 bases
Orientation:
Plus strand
chr5:140,777,695-140,892,546
(GRCh37/hg19)
Size:
114,852 bases
Orientation:
Plus strand

Genomic View for PCDHGB5 Gene

Genes around PCDHGB5 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGB5 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGB5 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGB5 Gene

Proteins for PCDHGB5 Gene

  • Protein details for PCDHGB5 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5G0-PCDGH_HUMAN
    Recommended name:
    Protocadherin gamma-B5
    Protein Accession:
    Q9Y5G0
    Secondary Accessions:
    • Q52LK8
    • Q9Y5C6

    Protein attributes for PCDHGB5 Gene

    Size:
    923 amino acids
    Molecular mass:
    99875 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGB5 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGB5 Gene

Post-translational modifications for PCDHGB5 Gene

  • Glycosylation at Asn415 and Asn541
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • PCDGH_HUMAN (1689)

Other Protein References for PCDHGB5 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGB5 Gene

Domains & Families for PCDHGB5 Gene

Gene Families for PCDHGB5 Gene

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

Protein Domains for PCDHGB5 Gene

Suggested Antigen Peptide Sequences for PCDHGB5 Gene

GenScript: Design optimal peptide antigens:
  • Protocadherin gamma-B5 (PCDGH_HUMAN)
genes like me logo Genes that share domains with PCDHGB5: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PCDHGB5 Gene

Function for PCDHGB5 Gene

Molecular function for PCDHGB5 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 PCDHGB5 Gene

Gene Ontology (GO) - Molecular Function for PCDHGB5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGB5: view
genes like me logo Genes that share phenotypes with PCDHGB5: view

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHGB5 Gene

Localization for PCDHGB5 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGB5 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 PCDHGB5 gene
Compartment Confidence
plasma membrane 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (1)
  • Nucleoplasm (1)
  • Plasma membrane (1)
  • Vesicles (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDHGB5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0005887 integral component of plasma membrane IBA 21873635
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0070062 extracellular exosome HDA 19199708
genes like me logo Genes that share ontologies with PCDHGB5: view

Pathways & Interactions for PCDHGB5 Gene

PathCards logo

SuperPathways for PCDHGB5 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHGB5 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IBA 21873635
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0008150 biological_process ND --
genes like me logo Genes that share ontologies with PCDHGB5: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGB5 Gene

Drugs & Compounds for PCDHGB5 Gene

(1) Drugs for PCDHGB5 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7884
genes like me logo Genes that share compounds with PCDHGB5: view

Transcripts for PCDHGB5 Gene

mRNA/cDNA for PCDHGB5 Gene

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

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGB5 Gene

No ASD Table

Relevant External Links for PCDHGB5 Gene

GeneLoc Exon Structure for
PCDHGB5

Expression for PCDHGB5 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDHGB5 Gene

Protein differential expression in normal tissues from HIPED for PCDHGB5 Gene

This gene is overexpressed in Breast (68.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PCDHGB5 Gene



Protein tissue co-expression partners for PCDHGB5 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDHGB5

genes like me logo Genes that share expression patterns with PCDHGB5: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHGB5 Gene

Orthologs for PCDHGB5 Gene

This gene was present in the common ancestor of mammals.

Orthologs for PCDHGB5 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHGB5 30
  • 99.24 (n)
cow
(Bos Taurus)
Mammalia PCDHGB5 30
  • 87.51 (n)
dog
(Canis familiaris)
Mammalia PCDHGB5 30
  • 86.38 (n)
mouse
(Mus musculus)
Mammalia Pcdhgb5 17 30
  • 83.19 (n)
rat
(Rattus norvegicus)
Mammalia Pcdhgb5 30
  • 81.94 (n)
Species where no ortholog for PCDHGB5 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • 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 PCDHGB5 Gene

ENSEMBL:
Gene Tree for PCDHGB5 (if available)
TreeFam:
Gene Tree for PCDHGB5 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDHGB5: view image

Paralogs for PCDHGB5 Gene

Pseudogenes.org Pseudogenes for PCDHGB5 Gene

genes like me logo Genes that share paralogs with PCDHGB5: view

Variants for PCDHGB5 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDHGB5 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs386352347 Uncertain Significance: not provided 141,485,635(+) G/A SYNONYMOUS_VARIANT,INTRON_VARIANT
rs6867460 - p.Gly188Ser

Additional dbSNP identifiers (rs#s) for PCDHGB5 Gene

Structural Variations from Database of Genomic Variants (DGV) for PCDHGB5 Gene

Variant ID Type Subtype PubMed ID
esv25744 CNV gain 19812545
esv2730847 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv3422812 CNV insertion 20981092
esv3606987 CNV gain 21293372
nsv1123990 CNV deletion 24896259
nsv1125852 CNV tandem duplication 24896259
nsv327707 CNV deletion 16902084
nsv462470 CNV loss 19166990
nsv518799 CNV loss 19592680
nsv519627 CNV loss 19592680
nsv599922 CNV loss 21841781
nsv599923 CNV loss 21841781
nsv968259 CNV duplication 23825009
nsv980740 CNV duplication 23825009

Additional Variant Information for PCDHGB5 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGB5

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for PCDHGB5 Gene

Disorders for PCDHGB5 Gene

Additional Disease Information for PCDHGB5

No disorders were found for PCDHGB5 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGB5 Gene

Publications for PCDHGB5 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 54
  2. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3 54
  4. Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). (PMID: 19199708) Gonzalez-Begne M … Yates JR (Journal of proteome research 2009) 3 54
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 4 54

Products for PCDHGB5 Gene

Sources for PCDHGB5 Gene