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Aliases for PCDHGB6 Gene

Aliases for PCDHGB6 Gene

  • Protocadherin Gamma Subfamily B, 6 2 3 5
  • PCDH-GAMMA-B6 3 4
  • Protocadherin Gamma-B6 3

External Ids for PCDHGB6 Gene

Previous GeneCards Identifiers for PCDHGB6 Gene

  • GC05P140589
  • GC05P141314
  • GC05P140714
  • GC05P140772
  • GC05P140793
  • GC05P140732
  • GC05P140809
  • GC05P140830
  • GC05P140847
  • GC05P140872
  • GC05P140879
  • GC05P140899
  • GC05P140933
  • GC05P140955
  • GC05P140976
  • GC05P141000
  • GC05P141027
  • GC05P141046
  • GC05P141073
  • GC05P135932
  • GC05P141111
  • GC05P141153
  • GC05P141170
  • GC05P141206
  • GC05P141246
  • GC05P141333
  • GC05P141389
  • GC05P141456
  • GC05P141534
  • GC05P141637
  • GC05P141738
  • GC05P141837
  • GC05P141940

Summaries for PCDHGB6 Gene

Entrez Gene Summary for PCDHGB6 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 PCDHGB6 Gene

PCDHGB6 (Protocadherin Gamma Subfamily B, 6) is a Protein Coding gene. GO annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHGB7.

UniProtKB/Swiss-Prot for PCDHGB6 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 PCDHGB6 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PCDHGB6 Gene

Genomics for PCDHGB6 Gene

Regulatory Elements for PCDHGB6 Gene

Enhancers for PCDHGB6 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
GH05H141506 2 FANTOM5 Ensembl ENCODE dbSUPER 16.5 +108.5 108458 20 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A FEZF1 ZNF2 YY1 ZNF207 PCDHGC4 DIAPH1 PCDHGB6 PCDHGA2 PCDHGC5 PCDHGA11 RN7SL68P PCDHGC3 PCDHGB7 PCDHGA10
GH05H141527 1.2 Ensembl ENCODE dbSUPER 16.8 +121.2 121222 2 NR2F1 HLF JUNB BATF RELA JUND POLR2A EED IKZF1 FOS PCDHGB6 PCDHGA11 PCDHGB7 PCDHGA10 PCDHGC4 LOC100505658 DIAPH1 PCDHGC5 PCDHGA7 PCDHGB4
GH05H141968 1.1 ENCODE 11.7 +561.5 561546 2 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SLC30A9 LOC102723915 HDAC3 KIAA0141 PCDHGA5 PCDHB12 RNF14 PCDHB11 PCDHB18P PCDHB4 PCDHB15
GH05H141601 2 FANTOM5 Ensembl ENCODE dbSUPER 5.7 +198.0 197966 8 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A YY1 ZNF766 CBX5 ZNF143 RELL2 HDAC3 FCHSD1 DIAPH1 LOC100505658 PCDHGA6 PCDHGB6 KIAA0141 PCDHGA1 PCDH12
GH05H141783 1.1 FANTOM5 ENCODE dbSUPER 7.9 +375.8 375766 0 MXI1 PKNOX1 KLF1 RFX1 BMI1 PCDHGB6 PCDHGA9 PCDHGC4 PCDHGC5 PCDHGC3 PCDHGB7 NDFIP1 PCDHGA3 PCDHGA6 PCDHGA7
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PCDHGB6 on UCSC Golden Path with GeneCards custom track

Promoters for PCDHGB6 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000187858 279 600 CTCF POLR2A CREM RAD21

Genomic Location for PCDHGB6 Gene

Chromosome:
5
Start:
141,408,021 bp from pter
End:
141,512,979 bp from pter
Size:
104,959 bases
Orientation:
Plus strand

Genomic View for PCDHGB6 Gene

Genes around PCDHGB6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHGB6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHGB6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHGB6 Gene

Proteins for PCDHGB6 Gene

  • Protein details for PCDHGB6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5F9-PCDGI_HUMAN
    Recommended name:
    Protocadherin gamma-B6
    Protein Accession:
    Q9Y5F9
    Secondary Accessions:
    • Q9Y5C5

    Protein attributes for PCDHGB6 Gene

    Size:
    930 amino acids
    Molecular mass:
    101043 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for PCDHGB6 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PCDHGB6 Gene

Post-translational modifications for PCDHGB6 Gene

  • Glycosylation at Asn304, Asn419, and Asn545
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHGB6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHGB6 Gene

Domains & Families for PCDHGB6 Gene

Gene Families for PCDHGB6 Gene

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

Protein Domains for PCDHGB6 Gene

Suggested Antigen Peptide Sequences for PCDHGB6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PCDHGB6: view

No data available for UniProtKB/Swiss-Prot for PCDHGB6 Gene

Function for PCDHGB6 Gene

Molecular function for PCDHGB6 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 PCDHGB6 Gene

Gene Ontology (GO) - Molecular Function for PCDHGB6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHGB6: view

Phenotypes for PCDHGB6 Gene

GenomeRNAi human phenotypes for PCDHGB6:
genes like me logo Genes that share phenotypes with PCDHGB6: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PCDHGB6
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHGB6 Gene

Localization for PCDHGB6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHGB6 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 PCDHGB6 gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for PCDHGB6 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 --
genes like me logo Genes that share ontologies with PCDHGB6: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDHGB6 Gene

Pathways & Interactions for PCDHGB6 Gene

SuperPathways for PCDHGB6 Gene

No Data Available

Interacting Proteins for PCDHGB6 Gene

Gene Ontology (GO) - Biological Process for PCDHGB6 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 PCDHGB6: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHGB6 Gene

Drugs & Compounds for PCDHGB6 Gene

(1) Drugs for PCDHGB6 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 PCDHGB6: view

Transcripts for PCDHGB6 Gene

mRNA/cDNA for PCDHGB6 Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PCDHGB6
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHGB6 Gene

No ASD Table

Relevant External Links for PCDHGB6 Gene

GeneLoc Exon Structure for
PCDHGB6
ECgene alternative splicing isoforms for
PCDHGB6

Expression for PCDHGB6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PCDHGB6 Gene

Protein differential expression in normal tissues from HIPED for PCDHGB6 Gene

This gene is overexpressed in Islet of Langerhans (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PCDHGB6 Gene



Protein tissue co-expression partners for PCDHGB6 Gene

NURSA nuclear receptor signaling pathways regulating expression of PCDHGB6 Gene:

PCDHGB6

Evidence on tissue expression from TISSUES for PCDHGB6 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHGB6: 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 PCDHGB6 Gene

Orthologs for PCDHGB6 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PCDHGB6 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHGB6 33
  • 99.53 (n)
cow
(Bos Taurus)
Mammalia PCDHGB6 33
  • 86.21 (n)
dog
(Canis familiaris)
Mammalia PCDHGB6 33
  • 84.39 (n)
mouse
(Mus musculus)
Mammalia Pcdhgb6 33 16
  • 82.19 (n)
rat
(Rattus norvegicus)
Mammalia LOC102552497 33
  • 80.5 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 60 (a)
ManyToMany
-- 34
  • 59 (a)
ManyToMany
-- 34
  • 59 (a)
ManyToMany
-- 34
  • 58 (a)
ManyToMany
-- 34
  • 56 (a)
ManyToMany
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 59 (a)
ManyToMany
-- 34
  • 58 (a)
ManyToMany
-- 34
  • 56 (a)
ManyToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 53 (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
  • 50 (a)
ManyToMany
-- 34
  • 50 (a)
ManyToMany
-- 34
  • 49 (a)
ManyToMany
-- 34
  • 49 (a)
ManyToMany
-- 34
  • 49 (a)
ManyToMany
-- 34
  • 49 (a)
ManyToMany
-- 34
  • 49 (a)
ManyToMany
-- 34
  • 49 (a)
ManyToMany
Species where no ortholog for PCDHGB6 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)
  • 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 PCDHGB6 Gene

ENSEMBL:
Gene Tree for PCDHGB6 (if available)
TreeFam:
Gene Tree for PCDHGB6 (if available)

Paralogs for PCDHGB6 Gene

Variants for PCDHGB6 Gene

Sequence variations from dbSNP and Humsavar for PCDHGB6 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 PCDHGB6 Gene

Variant ID Type Subtype PubMed ID
esv25744 CNV gain 19812545
esv2730847 CNV deletion 23290073
esv2759382 CNV gain 17122850
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
nsv980740 CNV duplication 23825009

Variation tolerance for PCDHGB6 Gene

Residual Variation Intolerance Score: 55.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.75; 66.47% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PCDHGB6 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHGB6

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHGB6 Gene

Disorders for PCDHGB6 Gene

Relevant External Links for PCDHGB6

Genetic Association Database (GAD)
PCDHGB6
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PCDHGB6

No disorders were found for PCDHGB6 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PCDHGB6 Gene

Publications for PCDHGB6 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 60
  2. A prognostic DNA methylation signature for stage I non-small-cell lung cancer. (PMID: 24081945) Sandoval J … Esteller M (Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2013) 3 60
  3. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q … Maniatis T (Genome research 2001) 3 60
  4. Large exons encoding multiple ectodomains are a characteristic feature of protocadherin genes. (PMID: 10716726) Wu Q … Maniatis T (Proceedings of the National Academy of Sciences of the United States of America 2000) 3 60
  5. Cadherin superfamily genes: functions, genomic organization, and neurologic diversity. (PMID: 10817752) Yagi T … Takeichi M (Genes & development 2000) 3 60

Products for PCDHGB6 Gene

Sources for PCDHGB6 Gene

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