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Aliases for PCDHGB4 Gene

Aliases for PCDHGB4 Gene

  • Protocadherin Gamma Subfamily B, 4 2 3 5
  • Fibroblast Cadherin FIB2 2 3
  • Fibroblast Cadherin-2 3 4
  • PCDH-GAMMA-B4 3 4
  • Cadherin 20 2 3
  • CDH20 3 4
  • Fib2 3 4
  • Protocadherin Gamma-B4 3
  • Cadherin-20 4

External Ids for PCDHGB4 Gene

Previous GeneCards Identifiers for PCDHGB4 Gene

  • GC05P140583
  • GC05P141309
  • GC05P140712
  • GC05P140770
  • GC05P140791
  • GC05P140729
  • GC05P140807
  • GC05P140827
  • GC05P140843
  • GC05P140869
  • GC05P140894
  • GC05P140916
  • GC05P140929
  • GC05P140951
  • GC05P140972
  • GC05P140994
  • GC05P141024
  • GC05P141042
  • GC05P141069
  • GC05P141089
  • GC05P141107
  • GC05P141148
  • GC05P141166
  • GC05P141201
  • GC05P141242
  • GC05P141324
  • GC05P141384
  • GC05P141452
  • GC05P141529
  • GC05P141632
  • GC05P141734
  • GC05P141833

Summaries for PCDHGB4 Gene

Entrez Gene Summary for PCDHGB4 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. This particular family member is expressed in fibroblasts and is thought to play a role in wound healing in response to injury. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHGB4 Gene

PCDHGB4 (Protocadherin Gamma Subfamily B, 4) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGB6.

UniProtKB/Swiss-Prot for PCDHGB4 Gene

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

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGB4 Gene

Genomics for PCDHGB4 Gene

Regulatory Elements for PCDHGB4 Gene

Enhancers for PCDHGB4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH05G141506 2 FANTOM5 Ensembl ENCODE dbSUPER 9.9 +128.8 128781 20.0 HDGF PKNOX1 FOXA2 MLX WRNIP1 ARID4B SIN3A FEZF1 ZNF2 YY1 PCDHGC4 DIAPH1 PCDHGB6 PCDHGA2 PCDHGC5 PCDHGA11 RN7SL68P PCDHGC3 PCDHGB7 PCDHGA10
GH05G141968 1.2 ENCODE 15.6 +581.9 581869 3.0 DMAP1 YY1 SLC30A9 ZNF143 ZNF548 ZNF263 SP3 NFYC TBX21 ZNF610 KIAA0141 PCDHGA5 PCDHB12 RNF14 PCDHB11 PCDHB4 PCDHB18P PCDHB15 PCDHB9 PCDHGA6
GH05G141527 1.2 Ensembl ENCODE dbSUPER 10.3 +141.5 141545 2.9 BHLHE40 NR2F1 HLF CEBPB JUNB RELA JUND ZNF302 EED IKZF1 PCDHGB6 PCDHGA11 PCDHGB7 PCDHGA10 PCDHGC4 LOC100505658 DIAPH1 PCDHGC5 PCDHGB4 PCDHGA7
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCDHGB4 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHGB4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000187856 15 601 CTCF FOXA2 NRF1 ZBTB33 RAD21 ZNF558
ENSR00000187856 202 601 CTCF FOXA2 NRF1 ZBTB33 RAD21 ZNF558

Genomic Location for PCDHGB4 Gene

Chromosome:
5
Start:
141,387,698 bp from pter
End:
141,512,979 bp from pter
Size:
125,282 bases
Orientation:
Plus strand

Genomic View for PCDHGB4 Gene

Genes around PCDHGB4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGB4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGB4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGB4 Gene

Proteins for PCDHGB4 Gene

  • Protein details for PCDHGB4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UN71-PCDGG_HUMAN
    Recommended name:
    Protocadherin gamma-B4
    Protein Accession:
    Q9UN71
    Secondary Accessions:
    • O15099
    • Q2M267
    • Q9UN64

    Protein attributes for PCDHGB4 Gene

    Size:
    923 amino acids
    Molecular mass:
    99927 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGB4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGB4 Gene

Post-translational modifications for PCDHGB4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PCDHGB4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGB4 Gene

Domains & Families for PCDHGB4 Gene

Gene Families for PCDHGB4 Gene

Suggested Antigen Peptide Sequences for PCDHGB4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHGB4: view

No data available for UniProtKB/Swiss-Prot for PCDHGB4 Gene

Function for PCDHGB4 Gene

Molecular function for PCDHGB4 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.

Gene Ontology (GO) - Molecular Function for PCDHGB4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGB4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PCDHGB4 Gene

Localization for PCDHGB4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGB4 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 PCDHGB4 gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for PCDHGB4 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 NAS 9199196
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PCDHGB4: view

Pathways & Interactions for PCDHGB4 Gene

SuperPathways for PCDHGB4 Gene

No Data Available

Interacting Proteins for PCDHGB4 Gene

Gene Ontology (GO) - Biological Process for PCDHGB4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion TAS 9199196
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules IEA --
GO:0007267 cell-cell signaling IBA --
GO:0007399 nervous system development IBA --
GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules NAS 9199196
genes like me logo Genes that share ontologies with PCDHGB4: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGB4 Gene

Drugs & Compounds for PCDHGB4 Gene

(1) Drugs for PCDHGB4 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Nutra 0
genes like me logo Genes that share compounds with PCDHGB4: view

Transcripts for PCDHGB4 Gene

mRNA/cDNA for PCDHGB4 Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGB4 Gene

No ASD Table

Relevant External Links for PCDHGB4 Gene

GeneLoc Exon Structure for
PCDHGB4
ECgene alternative splicing isoforms for
PCDHGB4

Expression for PCDHGB4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHGB4 Gene

Protein differential expression in normal tissues from HIPED for PCDHGB4 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PCDHGB4 Gene



Protein tissue co-expression partners for PCDHGB4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PCDHGB4 Gene:

PCDHGB4

Evidence on tissue expression from TISSUES for PCDHGB4 Gene

  • Nervous system(4.1)
  • Lung(4)
genes like me logo Genes that share expression patterns with PCDHGB4: view

Primer Products

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 and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHGB4 Gene

Orthologs for PCDHGB4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGB4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHGB4 34 35
  • 99.42 (n)
cow
(Bos Taurus)
Mammalia PCDHGB4 34
  • 86.86 (n)
dog
(Canis familiaris)
Mammalia PCDHGB4 34
  • 85.13 (n)
mouse
(Mus musculus)
Mammalia Pcdhgb4 34 16
  • 83.17 (n)
rat
(Rattus norvegicus)
Mammalia LOC102552705 34
  • 81.38 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 35
  • 60 (a)
ManyToMany
-- 35
  • 60 (a)
ManyToMany
-- 35
  • 59 (a)
ManyToMany
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 57 (a)
ManyToMany
-- 35
  • 57 (a)
ManyToMany
-- 35
  • 57 (a)
ManyToMany
-- 35
  • 57 (a)
ManyToMany
-- 35
  • 56 (a)
ManyToMany
chicken
(Gallus gallus)
Aves -- 35
  • 44 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 35
  • 52 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 51 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 50 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
-- 35
  • 49 (a)
ManyToMany
Species where no ortholog for PCDHGB4 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)
  • 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)
  • zebrafish (Danio rerio)

Evolution for PCDHGB4 Gene

ENSEMBL:
Gene Tree for PCDHGB4 (if available)
TreeFam:
Gene Tree for PCDHGB4 (if available)

Paralogs for PCDHGB4 Gene

genes like me logo Genes that share paralogs with PCDHGB4: view

Variants for PCDHGB4 Gene

Sequence variations from dbSNP and Humsavar for PCDHGB4 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type
rs386352347 Uncertain significance 141,485,635(+) CCGTT(A/G)GAAAA intron-variant, reference, synonymous-codon
rs1000014772 -- 141,409,727(+) TGAGC(A/G)CGCAG intron-variant, reference, missense
rs1000022316 -- 141,472,751(+) GAGGC(A/G)GAGGC intron-variant
rs1000136303 -- 141,452,887(+) TTATT(C/T)CACTT intron-variant
rs1000138324 -- 141,499,091(+) GGCAC(A/C)TGCTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PCDHGB4 Gene

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

Variation tolerance for PCDHGB4 Gene

Residual Variation Intolerance Score: 55.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.10; 61.06% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHGB4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGB4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGB4 Gene

Disorders for PCDHGB4 Gene

Relevant External Links for PCDHGB4

Genetic Association Database (GAD)
PCDHGB4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHGB4

No disorders were found for PCDHGB4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGB4 Gene

Publications for PCDHGB4 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 64
  2. Multiple cadherins are expressed in human fibroblasts. (PMID: 9199196) Matsuyoshi N. … Imamura S. (Biochem. Biophys. Res. Commun. 1997) 3 4 22 64
  3. Cadherin-19 expression is restricted to myelin-forming cells in the chicken embryo. (PMID: 19850111) Lin J. … Redies C. (Neuroscience 2010) 22 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 4 64
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PMID: 12477932) Strausberg R.L. … Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3 64

Products for PCDHGB4 Gene

Sources for PCDHGB4 Gene

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