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 PCDHGB2 Gene

Aliases for PCDHGB2 Gene

  • Protocadherin Gamma Subfamily B, 2 2 3 5
  • Protocadherin Gamma-B2 3 4
  • PCDH-GAMMA-B2 3
  • PCDH-Gamma-B2 4

External Ids for PCDHGB2 Gene

Previous GeneCards Identifiers for PCDHGB2 Gene

  • GC05P140556
  • GC05P141305
  • GC05P140710
  • GC05P140769
  • GC05P140790
  • GC05P140728
  • GC05P140814
  • GC05P140822
  • GC05P140837
  • GC05P140864
  • GC05P140890
  • GC05P140912
  • GC05P140924
  • GC05P140946
  • GC05P140967
  • GC05P140989
  • GC05P141019
  • GC05P141038
  • GC05P141082
  • GC05P135884
  • GC05P141104
  • GC05P141142
  • GC05P141181
  • GC05P141212
  • GC05P141251
  • GC05P141291
  • GC05P141378
  • GC05P141447
  • GC05P141522
  • GC05P142448
  • GC05P142552
  • GC05P142663
  • GC05P141628
  • GC05P141730
  • GC05P141829
  • GC05P141932
  • GC05P142036
  • GC05P142144
  • GC05P142242
  • GC05P142344

Summaries for PCDHGB2 Gene

Entrez Gene Summary for PCDHGB2 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 PCDHGB2 Gene

PCDHGB2 (Protocadherin Gamma Subfamily B, 2) is a Protein Coding gene. Diseases associated with PCDHGB2 include Prune Belly Syndrome. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGB6.

UniProtKB/Swiss-Prot Summary for PCDHGB2 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 PCDHGB2 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCDHGB2 Gene

Genomics for PCDHGB2 Gene

GeneHancer (GH) Regulatory Elements for PCDHGB2 Gene

Promoters and enhancers for PCDHGB2 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
GH05J141359 Promoter/Enhancer 1.2 EPDnew Ensembl ENCODE 500.7 +0.4 436 1 CTCF FOXA2 SMC3 RAD21 ZNF654 GABPB1 CBX5 KAT8 FOXA1 PCDHGB2 PCDHGA11 PCDHGA5 PCDHGA4 PCDHGB1 PCDHGA3 PCDHGA2 PCDHG@ PCDHGA1
GH05J141362 Promoter 0.3 EPDnew 500.7 +2.0 2028 0.1 PCDHGB2 PCDHGA5 PCDHGA4 PCDHGB1 PCDHGA3 PCDHGA2 PCDHG@ PCDHGA1
GH05J141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 12.6 +609.5 609525 3 EP300 HNRNPK ZBTB40 ZNF217 CTCF ZSCAN5C SIN3A NRF1 TCF12 USF1 RNF14 PCDH12 lnc-GNPDA1-2 PCDHB18P PCDHGA6 PCDHGA7 PCDHGA5 DELE1 PCDHB12 PCDHB19P
GH05J140663 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 12.4 -695.0 -694961 3.4 ZBTB40 ZNF217 EP300 SIN3A NRF1 TCF12 POLR2G SP1 PHF8 ZFX WDR55 TMCO6 ANKHD1 ENSG00000228737 HDAC3 SRA1 IGIP PCDHGC3 PCDHGB2 HARS2
GH05J141318 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 10.9 -40.0 -40041 4.4 ZBTB40 EP300 CTCF NRF1 TCF12 POLR2G SP1 GTF2E2 PHF8 ZFX ENSG00000288095 TAF7 lnc-SLC25A2-1 PCDHB15 PCDHGB4 ENSG00000272108 PCDHB9 PCDHB18P PCDHB6 PCDHGA3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHGB2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDHGB2

Top Transcription factor binding sites by QIAGEN in the PCDHGB2 gene promoter:
  • E47
  • Hand1
  • Ik-1
  • LCR-F1
  • Max1
  • SRF
  • SRF (504 AA)
  • STAT3
  • YY1
  • ZID

Genomic Locations for PCDHGB2 Gene

Genomic Locations for PCDHGB2 Gene
chr5:141,360,042-141,512,979
(GRCh38/hg38)
Size:
152,938 bases
Orientation:
Plus strand
chr5:140,739,703-140,892,546
(GRCh37/hg19)
Size:
152,844 bases
Orientation:
Plus strand

Genomic View for PCDHGB2 Gene

Genes around PCDHGB2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGB2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGB2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGB2 Gene

Proteins for PCDHGB2 Gene

  • Protein details for PCDHGB2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5G2-PCDGE_HUMAN
    Recommended name:
    Protocadherin gamma-B2
    Protein Accession:
    Q9Y5G2
    Secondary Accessions:
    • Q3MIJ3
    • Q9UN65

    Protein attributes for PCDHGB2 Gene

    Size:
    931 amino acids
    Molecular mass:
    100875 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGB2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGB2 Gene

Post-translational modifications for PCDHGB2 Gene

  • Glycosylation at Asn419 and Asn545
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • PCDGE_HUMAN (1687)

Other Protein References for PCDHGB2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGB2 Gene

Domains & Families for PCDHGB2 Gene

Gene Families for PCDHGB2 Gene

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

Protein Domains for PCDHGB2 Gene

Suggested Antigen Peptide Sequences for PCDHGB2 Gene

GenScript: Design optimal peptide antigens:
  • Protocadherin gamma-B2 (PCDGE_HUMAN)
genes like me logo Genes that share domains with PCDHGB2: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PCDHGB2 Gene

Function for PCDHGB2 Gene

Molecular function for PCDHGB2 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 PCDHGB2 Gene

Gene Ontology (GO) - Molecular Function for PCDHGB2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGB2: view
genes like me logo Genes that share phenotypes with PCDHGB2: view

miRNA for PCDHGB2 Gene

miRTarBase miRNAs that target PCDHGB2

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHGB2 Gene

Localization for PCDHGB2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGB2 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 PCDHGB2 gene
Compartment Confidence
plasma membrane 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Plasma membrane (3)
  • Vesicles (3)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDHGB2 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 --
genes like me logo Genes that share ontologies with PCDHGB2: view

Pathways & Interactions for PCDHGB2 Gene

PathCards logo

SuperPathways for PCDHGB2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHGB2 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 --
genes like me logo Genes that share ontologies with PCDHGB2: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGB2 Gene

Drugs & Compounds for PCDHGB2 Gene

(1) Drugs for PCDHGB2 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 PCDHGB2: view

Transcripts for PCDHGB2 Gene

mRNA/cDNA for PCDHGB2 Gene

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

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGB2 Gene

No ASD Table

Relevant External Links for PCDHGB2 Gene

GeneLoc Exon Structure for
PCDHGB2

Expression for PCDHGB2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDHGB2 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PCDHGB2 Gene



Protein tissue co-expression partners for PCDHGB2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDHGB2

Evidence on tissue expression from TISSUES for PCDHGB2 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHGB2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHGB2 Gene

Orthologs for PCDHGB2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGB2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHGB2 30
  • 99.18 (n)
dog
(Canis familiaris)
Mammalia PCDHGB2 30
  • 85.2 (n)
cow
(Bos Taurus)
Mammalia PCDHGB2 31
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pcdhgb2 17 30
  • 82.73 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 63 (a)
ManyToMany
-- 31
  • 61 (a)
ManyToMany
-- 31
  • 57 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 59 (a)
ManyToMany
-- 31
  • 59 (a)
ManyToMany
-- 31
  • 58 (a)
ManyToMany
-- 31
  • 57 (a)
ManyToMany
-- 31
  • 56 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 31
  • 52 (a)
ManyToMany
-- 31
  • 51 (a)
ManyToMany
-- 31
  • 51 (a)
ManyToMany
-- 31
  • 51 (a)
ManyToMany
-- 31
  • 50 (a)
ManyToMany
-- 31
  • 50 (a)
ManyToMany
-- 31
  • 50 (a)
ManyToMany
-- 31
  • 50 (a)
ManyToMany
-- 31
  • 50 (a)
ManyToMany
-- 31
  • 50 (a)
ManyToMany
-- 31
  • 50 (a)
ManyToMany
-- 31
  • 50 (a)
ManyToMany
-- 31
  • 49 (a)
ManyToMany
-- 31
  • 49 (a)
ManyToMany
-- 31
  • 49 (a)
ManyToMany
-- 31
  • 49 (a)
ManyToMany
-- 31
  • 49 (a)
ManyToMany
-- 31
  • 49 (a)
ManyToMany
-- 31
  • 49 (a)
ManyToMany
-- 31
  • 48 (a)
ManyToMany
-- 31
  • 48 (a)
ManyToMany
Species where no ortholog for PCDHGB2 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)
  • 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)
  • rat (Rattus norvegicus)
  • 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 PCDHGB2 Gene

ENSEMBL:
Gene Tree for PCDHGB2 (if available)
TreeFam:
Gene Tree for PCDHGB2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDHGB2: view image

Paralogs for PCDHGB2 Gene

Pseudogenes.org Pseudogenes for PCDHGB2 Gene

genes like me logo Genes that share paralogs with PCDHGB2: view

Variants for PCDHGB2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDHGB2 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
716118 Benign: not provided 141,408,401(+) C/A SYNONYMOUS_VARIANT,INTRON_VARIANT
720930 Likely Benign: not provided 141,413,426(+) G/T MISSENSE_VARIANT,INTRON_VARIANT
736375 Likely Benign: not provided 141,413,207(+) C/G NONSENSE,INTRON_VARIANT
776069 Likely Benign: not provided 141,415,107(+) A/G SYNONYMOUS_VARIANT,INTRON_VARIANT
780961 Benign: not provided 141,413,826(+) C/T SYNONYMOUS_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for PCDHGB2 Gene

Structural Variations from Database of Genomic Variants (DGV) for PCDHGB2 Gene

Variant ID Type Subtype PubMed ID
esv25744 CNV gain 19812545
esv2730847 CNV deletion 23290073
esv2759382 CNV gain 17122850
esv3422812 CNV insertion 20981092
esv3606982 CNV loss 21293372
esv3606983 CNV gain 21293372
esv3606984 CNV loss 21293372
esv3606985 CNV gain 21293372
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
nsv823279 CNV gain 20364138
nsv823280 CNV loss 20364138
nsv968259 CNV duplication 23825009
nsv980740 CNV duplication 23825009

Variation tolerance for PCDHGB2 Gene

Residual Variation Intolerance Score: 38.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.97; 84.06% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHGB2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGB2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGB2 Gene

Disorders for PCDHGB2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCDHGB2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
prune belly syndrome
  • pbs
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDHGB2

genes like me logo Genes that share disorders with PCDHGB2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDHGB2 Gene

Publications for PCDHGB2 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. VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. (PMID: 29507755) Yue Y … Liu J (Cell discovery 2018) 3 54
  3. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54
  4. Bcl2-associated athanogene 3 interactome analysis reveals a new role in modulating proteasome activity. (PMID: 23824909) Chen Y … Ge F (Molecular & cellular proteomics : MCP 2013) 3 54
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3 54

Products for PCDHGB2 Gene

Sources for PCDHGB2 Gene