This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail ... See more...

Aliases for PCDHB1 Gene

Aliases for PCDHB1 Gene

  • Protocadherin Beta 1 2 3 5
  • Protocadherin Beta-1 3 4
  • PCDH-Beta-1 3 4
  • PCDH-BETA1 3

External Ids for PCDHB1 Gene

Previous GeneCards Identifiers for PCDHB1 Gene

  • GC05P140247
  • GC05P141013
  • GC05P140414
  • GC05P140459
  • GC05P140411
  • GC05P135575
  • GC05P140432
  • GC05P140433
  • GC05P140452
  • GC05P141275
  • GC05P141495
  • GC05P142395
  • GC05P142500
  • GC05P142611
  • GC05P141602
  • GC05P141702
  • GC05P141804
  • GC05P141903
  • GC05P142011
  • GC05P142114
  • GC05P142217
  • GC05P142315

Summaries for PCDHB1 Gene

Entrez Gene Summary for PCDHB1 Gene

  • This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]

GeneCards Summary for PCDHB1 Gene

PCDHB1 (Protocadherin Beta 1) is a Protein Coding gene. Diseases associated with PCDHB1 include Lubs X-Linked Mental Retardation Syndrome and Gastric Diffuse Adenocarcinoma. Gene Ontology (GO) annotations related to this gene include calcium ion binding. An important paralog of this gene is PCDHB7.

UniProtKB/Swiss-Prot Summary for PCDHB1 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 PCDHB1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PCDHB1 Gene

Genomics for PCDHB1 Gene

GeneHancer (GH) Regulatory Elements for PCDHB1 Gene

Promoters and enhancers for PCDHB1 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
GH05J141051 Promoter/Enhancer 0.9 Ensembl ENCODE 500.7 +0.3 265 1.2 RFX1 PHF8 SCRT1 SIN3A E2F1 CHD7 POLR2A EZH2 RBBP5 SCRT2 PCDHB1 PCDHB@ piR-44878-011 LOC101926905 ENSG00000279047 RF00017-4954
GH05J141001 Promoter/Enhancer 1.4 FANTOM5 ENCODE CraniofacialAtlas 10.9 -47.9 -47874 4.3 ZNF217 EP300 TCF12 USF1 TEAD4 ZIC2 CLOCK CUX1 HDAC2 CTBP1 PCDHAC2 PCDHB1 PCDHA9 PCDHA8 PCDHA7 PCDHA4 PCDHA3 PCDHB2 DND1 PCDHAC1
GH05J141084 Enhancer 0.7 ENCODE 11 +33.4 33440 1.1 CTCF TCF12 POLR2G POLR2A ZNF263 ZNF184 RAD21 YY1 PHF8 ZBTB11 lnc-PCDHB2-1 piR-61945-418 PCDHAC2 PCDHB17P MALINC1 IGIP PCDHB3 PCDHGC4 PCDHA12 PCDHAC1
GH05J141085 Enhancer 0.4 FANTOM5 17.5 +34.1 34148 0.3 CUX1 E2F1 YY1 ZHX2 lnc-PCDHB2-1 piR-61945-418 PCDHB1 PCDHB10 PCDHB9 PCDHB2 ENSG00000272154 PCDHB14 PCDHB18P PCDHGB6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PCDHB1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PCDHB1

Top Transcription factor binding sites by QIAGEN in the PCDHB1 gene promoter:
  • AREB6
  • ER-alpha
  • Nkx3-1
  • Nkx3-1 v1
  • Nkx3-1 v2
  • Nkx3-1 v3
  • Nkx3-1 v4
  • NRSF form 1
  • NRSF form 2
  • p53

Genomic Locations for PCDHB1 Gene

Genomic Locations for PCDHB1 Gene
chr5:141,051,135-141,059,344
(GRCh38/hg38)
Size:
8,210 bases
Orientation:
Plus strand
chr5:140,430,979-140,433,512
(GRCh37/hg19)
Size:
2,534 bases
Orientation:
Plus strand

Genomic View for PCDHB1 Gene

Genes around PCDHB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PCDHB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PCDHB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PCDHB1 Gene

Proteins for PCDHB1 Gene

  • Protein details for PCDHB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y5F3-PCDB1_HUMAN
    Recommended name:
    Protocadherin beta-1
    Protein Accession:
    Q9Y5F3
    Secondary Accessions:
    • Q2M257

    Protein attributes for PCDHB1 Gene

    Size:
    818 amino acids
    Molecular mass:
    90491 Da
    Quaternary structure:
    No Data Available

neXtProt entry for PCDHB1 Gene

Post-translational modifications for PCDHB1 Gene

  • Glycosylation at Asn169, Asn209, Asn257, Asn419, and Asn568
  • Modification sites at PhosphoSitePlus

Other Protein References for PCDHB1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PCDHB1 Gene

Domains & Families for PCDHB1 Gene

Gene Families for PCDHB1 Gene

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

Protein Domains for PCDHB1 Gene

Suggested Antigen Peptide Sequences for PCDHB1 Gene

GenScript: Design optimal peptide antigens:
  • Protocadherin beta-1 (PCDB1_HUMAN)
genes like me logo Genes that share domains with PCDHB1: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PCDHB1 Gene

Function for PCDHB1 Gene

Molecular function for PCDHB1 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 PCDHB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005509 calcium ion binding IEA --
genes like me logo Genes that share ontologies with PCDHB1: view
genes like me logo Genes that share phenotypes with PCDHB1: view

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PCDHB1 Gene

Localization for PCDHB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PCDHB1 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 PCDHB1 gene
Compartment Confidence
plasma membrane 4
extracellular 1
peroxisome 1
nucleus 1
endoplasmic reticulum 0
cytosol 0

Gene Ontology (GO) - Cellular Components for PCDHB1 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 PCDHB1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PCDHB1 Gene

Pathways & Interactions for PCDHB1 Gene

PathCards logo

SuperPathways for PCDHB1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PCDHB1 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 PCDHB1: view

No data available for Pathways by source and SIGNOR curated interactions for PCDHB1 Gene

Drugs & Compounds for PCDHB1 Gene

(1) Drugs for PCDHB1 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 PCDHB1: view

Transcripts for PCDHB1 Gene

mRNA/cDNA for PCDHB1 Gene

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

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PCDHB1 Gene

No ASD Table

Relevant External Links for PCDHB1 Gene

GeneLoc Exon Structure for
PCDHB1

Expression for PCDHB1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PCDHB1 Gene

mRNA differential expression in normal tissues according to GTEx for PCDHB1 Gene

This gene is overexpressed in Testis (x12.5) and Pituitary (x8.5).

Protein differential expression in normal tissues from HIPED for PCDHB1 Gene

This gene is overexpressed in Bone (58.1) and Heart (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PCDHB1 Gene



Protein tissue co-expression partners for PCDHB1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PCDHB1

SOURCE GeneReport for Unigene cluster for PCDHB1 Gene:

Hs.278950

Evidence on tissue expression from TISSUES for PCDHB1 Gene

  • Nervous system(4)
genes like me logo Genes that share expression patterns with PCDHB1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PCDHB1 Gene

Orthologs for PCDHB1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PCDHB1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PCDHB1 31 30
  • 99.39 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PCDHB1 31 30
  • 88.26 (n)
OneToOne
dog
(Canis familiaris)
Mammalia PCDHB1 31
  • 87 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pcdhb1 17 31 30
  • 85.04 (n)
rat
(Rattus norvegicus)
Mammalia Pcdhb1 30
  • 84.39 (n)
oppossum
(Monodelphis domestica)
Mammalia PCDHB1 31
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PCDHB1 31
  • 71 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Cad89D 32
  • 26 (a)
Species where no ortholog for PCDHB1 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)
  • 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)
  • 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 PCDHB1 Gene

ENSEMBL:
Gene Tree for PCDHB1 (if available)
TreeFam:
Gene Tree for PCDHB1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PCDHB1: view image

Paralogs for PCDHB1 Gene

genes like me logo Genes that share paralogs with PCDHB1: view

Variants for PCDHB1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PCDHB1 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs193920928 Uncertain Significance: Malignant tumor of prostate 141,053,125(+) T/C MISSENSE_VARIANT
rs10476822 - p.Thr611Ile
rs17208383 - p.Ala524Val
rs2233591 - p.Phe385Leu
rs2233592 - p.Leu390Phe

Additional dbSNP identifiers (rs#s) for PCDHB1 Gene

Structural Variations from Database of Genomic Variants (DGV) for PCDHB1 Gene

Variant ID Type Subtype PubMed ID
esv2759382 CNV gain 17122850
nsv428127 CNV loss 18775914
nsv818387 CNV gain 17921354

Variation tolerance for PCDHB1 Gene

Residual Variation Intolerance Score: 70.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.91; 67.70% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PCDHB1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PCDHB1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PCDHB1 Gene

Disorders for PCDHB1 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PCDHB1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
lubs x-linked mental retardation syndrome
  • mrxsl
gastric diffuse adenocarcinoma
  • adenocarcinoma of linitis plastica type
kleefstra syndrome 1
  • klefs1
immunodeficiency-centromeric instability-facial anomalies syndrome
  • immune deficiency, variable, with centromeric instability of chromosomes 1, 9, and 16
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PCDHB1

genes like me logo Genes that share disorders with PCDHB1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PCDHB1 Gene

Publications for PCDHB1 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. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3 54
  3. 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
  4. 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 54
  5. Comparative DNA sequence analysis of mouse and human protocadherin gene clusters. (PMID: 11230163) Wu Q … Maniatis T (Genome research 2001) 3 54

Products for PCDHB1 Gene

Sources for PCDHB1 Gene