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Aliases for PCDHGB1 Gene

Aliases for PCDHGB1 Gene

  • Protocadherin Gamma Subfamily B, 1 2 3 5
  • PCDH-GAMMA-B1 3 4
  • Protocadherin Gamma Subfamily B, 1, Isoform 2 2
  • Protocadherin Gamma-B1 3

External Ids for PCDHGB1 Gene

Previous GeneCards Identifiers for PCDHGB1 Gene

  • GC05P140546
  • GC05P141303
  • GC05P140709
  • GC05P140768
  • GC05P140788
  • GC05P140727
  • GC05P140813
  • GC05P140824
  • GC05P140853
  • GC05P140859
  • GC05P140885
  • GC05P140907
  • GC05P140922
  • GC05P140944
  • GC05P140965
  • GC05P140987
  • GC05P141014
  • GC05P141037
  • GC05P141081
  • GC05P135874
  • GC05P141102
  • GC05P141141
  • GC05P141180
  • GC05P141211
  • GC05P141250
  • GC05P141279
  • GC05P141377
  • GC05P141446
  • GC05P141521
  • GC05P141627
  • GC05P141729
  • GC05P141828
  • GC05P141931
  • GC05P142035

Summaries for PCDHGB1 Gene

Entrez Gene Summary for PCDHGB1 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 PCDHGB1 Gene

PCDHGB1 (Protocadherin Gamma Subfamily B, 1) is a Protein Coding gene. Diseases associated with PCDHGB1 include Protocadherin-Gamma Gene Cluster. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGB2.

UniProtKB/Swiss-Prot for PCDHGB1 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 PCDHGB1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGB1 Gene

Genomics for PCDHGB1 Gene

GeneHancer (GH) Regulatory Elements for PCDHGB1 Gene

Promoters and enhancers for PCDHGB1 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
GH05I141349 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE 550.8 +0.1 96 0.4 ELF3 ARID4B SIN3A ZNF2 RAD21 ZNF335 ZNF143 SMARCA5 ZNF654 ZBTB11 ENSG00000280026 PCDHGB1 PCDHGA3 PCDHGA2 PCDHG@ PCDHGA1
GH05I140717 Promoter/Enhancer 1.6 Ensembl ENCODE 22.7 -631.0 -630966 2.7 MLX IRF4 ZNF213 E2F8 ZNF416 ZNF143 SP3 PPARGC1A MEF2D GLIS1 GC05P142207 VTRNA1-2 PURA PCDHB18P PCDHB19P PCDHB15 PCDHB12 PCDHB3 PCDHB9 PCDHB13
GH05I142221 Enhancer 1.4 Ensembl ENCODE dbSUPER 24.5 +872.6 872552 3.3 FOXA2 SMAD1 FEZF1 ZNF2 ZNF213 ZNF143 FOS SP3 JUNB REST PCDHB18P PCDHB15 PCDHGA7 PCDHGA6 PCDHGB4 PCDHGB3 PCDHB19P PCDHGA8 PCDHGA5 PCDHGA2
GH05I141319 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 14.8 -29.5 -29452 1.9 PKNOX1 SMAD1 ARNT ARID4B SIN3A ZNF2 YY1 SLC30A9 POLR2B ZNF213 TAF7 PCDHB15 ANKHD1 ENSG00000272108 WDR55 PCDHB9 LOC102723915 FCHSD1 PCDHB18P PCDHB6
GH05I141968 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 10.8 +619.5 619465 3 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B RNF14 PCDH12 PCDHB18P PCDHGA6 PCDHGA7 LOC102723915 HDAC3 KIAA0141 PCDHGA5 PCDHB12
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PCDHGB1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PCDHGB1 gene promoter:

Genomic Locations for PCDHGB1 Gene

Genomic Locations for PCDHGB1 Gene
chr5:141,350,102-141,512,979
(GRCh38/hg38)
Size:
162,878 bases
Orientation:
Plus strand
chr5:140,729,828-140,892,546
(GRCh37/hg19)

Genomic View for PCDHGB1 Gene

Genes around PCDHGB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGB1 Gene

Proteins for PCDHGB1 Gene

  • Protein details for PCDHGB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5G3-PCDGD_HUMAN
    Recommended name:
    Protocadherin gamma-B1
    Protein Accession:
    Q9Y5G3
    Secondary Accessions:
    • Q3SY75
    • Q9Y5C8

    Protein attributes for PCDHGB1 Gene

    Size:
    927 amino acids
    Molecular mass:
    100360 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGB1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGB1 Gene

Post-translational modifications for PCDHGB1 Gene

  • Glycosylation at Asn41, isoforms=273, isoforms=2300, isoforms=2415, and Asn541

Other Protein References for PCDHGB1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGB1 Gene

Domains & Families for PCDHGB1 Gene

Gene Families for PCDHGB1 Gene

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

Protein Domains for PCDHGB1 Gene

Suggested Antigen Peptide Sequences for PCDHGB1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHGB1: view

No data available for UniProtKB/Swiss-Prot for PCDHGB1 Gene

Function for PCDHGB1 Gene

Molecular function for PCDHGB1 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 PCDHGB1 Gene

Gene Ontology (GO) - Molecular Function for PCDHGB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGB1: view
genes like me logo Genes that share phenotypes with PCDHGB1: view

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHGB1 Gene

Localization for PCDHGB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGB1 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 PCDHGB1 gene
Compartment Confidence
plasma membrane 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Focal adhesion sites (2)
  • Midbody (2)
  • Nucleus (2)
  • Plasma membrane (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PCDHGB1 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 --
GO:0030426 growth cone IEA --
genes like me logo Genes that share ontologies with PCDHGB1: view

Pathways & Interactions for PCDHGB1 Gene

SuperPathways for PCDHGB1 Gene

No Data Available

Interacting Proteins for PCDHGB1 Gene

Gene Ontology (GO) - Biological Process for PCDHGB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IBA --
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development IBA --
genes like me logo Genes that share ontologies with PCDHGB1: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGB1 Gene

Drugs & Compounds for PCDHGB1 Gene

(1) Drugs for PCDHGB1 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 PCDHGB1: view

Transcripts for PCDHGB1 Gene

mRNA/cDNA for PCDHGB1 Gene

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGB1 Gene

No ASD Table

Relevant External Links for PCDHGB1 Gene

GeneLoc Exon Structure for
PCDHGB1
ECgene alternative splicing isoforms for
PCDHGB1

Expression for PCDHGB1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHGB1 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PCDHGB1 Gene



Protein tissue co-expression partners for PCDHGB1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHGB1 Gene:

PCDHGB1

Evidence on tissue expression from TISSUES for PCDHGB1 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHGB1: 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 PCDHGB1 Gene

Orthologs for PCDHGB1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PCDHGB1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHGB1 33
  • 99.53 (n)
mouse
(Mus musculus)
Mammalia Pcdhgb1 33 16
  • 83.17 (n)
dog
(Canis familiaris)
Mammalia PCDHGB1 34
  • 83 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 64 (a)
ManyToMany
-- 34
  • 61 (a)
ManyToMany
-- 34
  • 56 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 59 (a)
ManyToMany
-- 34
  • 58 (a)
ManyToMany
-- 34
  • 58 (a)
ManyToMany
-- 34
  • 58 (a)
ManyToMany
-- 34
  • 56 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 53 (a)
ManyToMany
-- 34
  • 52 (a)
ManyToMany
-- 34
  • 52 (a)
ManyToMany
-- 34
  • 51 (a)
ManyToMany
-- 34
  • 51 (a)
ManyToMany
-- 34
  • 51 (a)
ManyToMany
-- 34
  • 51 (a)
ManyToMany
-- 34
  • 51 (a)
ManyToMany
-- 34
  • 51 (a)
ManyToMany
-- 34
  • 50 (a)
ManyToMany
-- 34
  • 50 (a)
ManyToMany
-- 34
  • 50 (a)
ManyToMany
-- 34
  • 50 (a)
ManyToMany
-- 34
  • 50 (a)
ManyToMany
-- 34
  • 50 (a)
ManyToMany
-- 34
  • 50 (a)
ManyToMany
-- 34
  • 50 (a)
ManyToMany
-- 34
  • 49 (a)
ManyToMany
-- 34
  • 49 (a)
ManyToMany
-- 34
  • 49 (a)
ManyToMany
-- 34
  • 49 (a)
ManyToMany
fruit fly
(Drosophila melanogaster)
Insecta Cad89D 35
  • 28 (a)
Species where no ortholog for PCDHGB1 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)
  • cow (Bos Taurus)
  • 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)
  • 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 PCDHGB1 Gene

ENSEMBL:
Gene Tree for PCDHGB1 (if available)
TreeFam:
Gene Tree for PCDHGB1 (if available)

Paralogs for PCDHGB1 Gene

genes like me logo Genes that share paralogs with PCDHGB1: view

Variants for PCDHGB1 Gene

Sequence variations from dbSNP and Humsavar for PCDHGB1 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs386352347 uncertain-significance, not provided 141,485,635(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000014772 -- 141,409,727(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000022316 -- 141,472,751(+) G/A genic_downstream_transcript_variant, intron_variant
rs1000098905 -- 141,353,769(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000136303 -- 141,452,887(+) C/T genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHGB1 Gene

Variant ID Type Subtype PubMed ID
esv25744 CNV gain 19812545
esv2730847 CNV deletion 23290073
esv2759382 CNV gain 17122850
nsv980740 CNV duplication 23825009
nsv980739 CNV duplication 23825009
nsv968259 CNV duplication 23825009
nsv823280 CNV loss 20364138
nsv823279 CNV gain 20364138
nsv599923 CNV loss 21841781
nsv599922 CNV loss 21841781
nsv519627 CNV loss 19592680
nsv518799 CNV loss 19592680
nsv462470 CNV loss 19166990
nsv327707 CNV deletion 16902084
nsv1125852 CNV tandem duplication 24896259
nsv1123990 CNV deletion 24896259
esv3606987 CNV gain 21293372
esv3606985 CNV gain 21293372
esv3606984 CNV loss 21293372
esv3606983 CNV gain 21293372
esv3606982 CNV loss 21293372
esv3422812 CNV insertion 20981092

Variation tolerance for PCDHGB1 Gene

Residual Variation Intolerance Score: 33.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.09; 60.96% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHGB1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGB1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGB1 Gene

Disorders for PCDHGB1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PCDHGB1 Gene - From: GeneCards

Disorder Aliases PubMed IDs
protocadherin-gamma gene cluster
  • pcdhg@
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDHGB1

genes like me logo Genes that share disorders with PCDHGB1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDHGB1 Gene

Publications for PCDHGB1 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. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  3. Cell Surface Proteomic Map of HIV Infection Reveals Antagonism of Amino Acid Metabolism by Vpu and Nef. (PMID: 26439863) Matheson NJ … Lehner PJ (Cell host & microbe 2015) 3 58
  4. 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 58
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg RL … Mammalian Gene Collection Program Team (Proceedings of the National Academy of Sciences of the United States of America 2002) 3 58

Products for PCDHGB1 Gene

Sources for PCDHGB1 Gene

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