Details for: PCDHB2

Gene ID: 56133

Gene Type:  Protein-coding  - A gene that serves as a template for producing a messenger RNA (mRNA) molecule, which is then translated into a functional protein.

Symbol: PCDHB2

Ensembl ID: ENSG00000112852

Description: protocadherin beta 2

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

Cell Significance Index (CSI) scores for the chosen context(s)

  • interneuron CL0000099
    CSI 4.2
    rCSI 8.43%
    PRS 98.6
  • fallopian tube secretory epithelial cell CL4030006
    CSI 2.77
    rCSI 2.67%
    PRS 99.27
  • neuroblast (sensu Vertebrata) CL0000031
    CSI 2.75
    rCSI 3.53%
    PRS 98.78
  • radial glial cell CL0000681
    CSI 2.49
    rCSI 3.46%
    PRS 99.47

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.
Network Configuration

Explore relationships of the current gene. Select an Interaction Source: 'ONTOLOGY' for shared pathways (GO/Reactome) or 'STRING' for protein-protein interactions. Further refine by selecting context genes and comparing Cell Significance Index (CSI) scores between baseline and target cell types and their specific contexts.

Comma-separated if multiple.
Comma-separated if multiple.
Legend:
  • Query Gene
  • Node Color (Target Cell CSI, relative to current network):
    • Very High
    • High
    • Medium
    • Low
    • Very Low
    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

Loading network (please wait)...

Other Information

This section provides additional information about the gene, including a description generated by an AI language model and details about associated proteins.

## Summary [PCDHB2](/details-gene/56133) is a protein-coding gene located on chromosome 5q31.3 that encodes protocadherin beta 2, a member of the cadherin superfamily. This family of proteins is known for its role in mediating calcium-dependent cell-cell adhesion, which is crucial for the formation and maintenance of tissues. The primary function of [PCDHB2](/details-gene/56133) is associated with homophilic cell adhesion, particularly within the nervous system. Expression data indicates that the gene has its highest significance in neuronal cell types, most notably [interneurons](/details-cell/CL0000099), as well as in neural progenitor cells like [neuroblasts](/details-cell/CL0000031) and [radial glial cells](/details-cell/CL0000681), suggesting a critical role in neural development, synapse formation, and the maintenance of synaptic integrity. ## Cellular Roles and Expression Landscape The expression profile of [PCDHB2](/details-gene/56133) points to a specialized function predominantly within the nervous system. **Overall**, the gene shows the highest cell significance index (CSI) in [interneurons](/details-cell/CL0000099) (CSI: 4.20), a class of neurons essential for modulating neural circuits. Its high significance is also observed in precursor cells critical for neurogenesis, including [neuroblasts (sensu Vertebrata)](/details-cell/CL0000031) (CSI: 2.75) and [radial glial cells](/details-cell/CL0000681) (CSI: 2.49). This pattern suggests that [PCDHB2](/details-gene/56133) is involved not only in the function of mature neurons but also in the foundational processes of brain development, such as neuronal migration and differentiation. Interestingly, [PCDHB2](/details-gene/56133) also shows significant expression in [fallopian tube secretory epithelial cells](/details-cell/CL4030006) (CSI: 2.77), which may indicate a less-characterized role in maintaining epithelial tissue integrity or mediating cell-cell interactions outside of the central nervous system. The protocadherin beta gene cluster, to which [PCDHB2](/details-gene/56133) belongs, is known for its complex organization and is highly conserved between humans and mice, underscoring its functional importance ([Link](https://doi.org/10.1016/s0092-8674(00)80789-8), [Link](https://doi.org/10.1016/s0014-5793(01)02372-9)). ## Pathways and Molecular Function Functionally, [PCDHB2](/details-gene/56133) is annotated as a key player in processes fundamental to neural architecture and communication. Its molecular function involves [calcium ion binding](/details-cell/GO:0005509), a characteristic feature of cadherins that enables them to mediate cell adhesion. As a [plasma membrane](/details-cell/GO:0005886) protein, it participates in biological processes such as [calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules](/details-cell/GO:0016339) and [homophilic cell adhesion via plasma membrane adhesion molecules](/details-cell/GO:0007156). These molecular activities are directly linked to its high-level roles in [nervous system development](/details-cell/GO:0007399). Consistent with its high expression in [interneurons](/details-cell/CL0000099), the gene is specifically implicated in [synapse assembly](/details-cell/GO:0007416) and [chemical synaptic transmission](/details-cell/GO:0007268). Its localization to the [synapse](/details-cell/GO:0045202) further supports a direct role in forming and stabilizing the synaptic connections that are essential for neural information processing. ## Research Directions Based on its specific expression pattern and known functions, several research avenues for [PCDHB2](/details-gene/56133) can be proposed. **Proposed Hypotheses:** 1. Given its high significance in [interneurons](/details-cell/CL0000099) and its role in homophilic adhesion, it is hypothesized that [PCDHB2](/details-gene/56133) is essential for the target recognition and specific synaptic connectivity of distinct interneuron subtypes within cortical circuits. 2. The expression of [PCDHB2](/details-gene/56133) in [neuroblasts](/details-cell/CL0000031) and [radial glial cells](/details-cell/CL0000681) suggests a hypothesis that it plays a critical role during corticogenesis, potentially mediating the migration of newly born neurons or the adhesion of neural progenitors. 3. The unexpected expression in [fallopian tube secretory epithelial cells](/details-cell/CL4030006) suggests a potential role in maintaining the structural integrity of mucosal epithelial layers or in cell-cell signaling within the reproductive tract, a function distinct from its neurological roles. **Key Experimental Approach:** To test the hypothesis that [PCDHB2](/details-gene/56133) is critical for interneuron connectivity (Hypothesis 1), a powerful approach would be to use *in vivo* CRISPR-Cas9-mediated gene editing in a mouse model. By co-electroporating guide RNAs targeting `Pcdhb2` with a fluorescent reporter into the developing mouse cortex, one could specifically label and manipulate [interneurons](/details-cell/CL0000099). Subsequent analysis using a combination of slice electrophysiology to measure synaptic currents and super-resolution microscopy to quantify synaptic density and morphology on the targeted cells would reveal deficits in synaptic formation or maintenance, thereby clarifying the gene's functional role. **Therapeutic Potential:** As a cell adhesion molecule involved in fundamental developmental processes, [PCDHB2](/details-gene/56133) is not an ideal candidate for direct therapeutic modulation (inhibition or activation) in adults, as this could have unforeseen consequences on tissue stability. However, mutations or dysregulation of [PCDHB2](/details-gene/56133) could plausibly contribute to neurodevelopmental or psychiatric disorders characterized by abnormal synaptic connectivity. Therefore, its primary clinical relevance may lie in its potential as a diagnostic biomarker or a gene associated with risk for such conditions, rather than as a direct drug target.

Genular Protein ID: 3613679210

Symbol: PCDB2_HUMAN

Name: Protocadherin beta-2

UniProtKB Accession Codes:

Q9Y5E7 Q4KMU1

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 1 CDD 1 CTD 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 3 Ensembl 2 ExpressionAtlas 1 GO 10 Gene3D 1 GeneCards 1 GeneTree 1 GeneWiki 1 GenomeRNAi 1 GlyConnect 1 GlyCosmos 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 6 KEGG 1 MANE-Select 1 MIM 2 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PRINTS 1 PRO 1 PROSITE 2 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 3 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 RNAct 1 RefSeq 1 SMART 1 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 SwissPalm 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 10380929

Title: A striking organization of a large family of human neural cadherin-like cell adhesion genes.

PubMed ID: 10380929

DOI: 10.1016/s0092-8674(00)80789-8

PubMed ID: 11322959

Title: The human and murine protocadherin-beta one-exon gene families show high evolutionary conservation, despite the difference in gene number.

PubMed ID: 11322959

DOI: 10.1016/s0014-5793(01)02372-9

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 19608861

Title: Lysine acetylation targets protein complexes and co-regulates major cellular functions.

PubMed ID: 19608861

DOI: 10.1126/science.1175371

Sequence Information:

  • Length: 798
  • Mass: 87254
  • Checksum: B2602E865378CB27
  • Sequence:
    • MEAGEGKERV PKQRQVLIFF VLLGIAQASC QPRHYSVAEE TESGSFVANL LKDLGLEIGE 
LAVRGARVVS KGKKMHLQFD RQTGDLLLNE KLDREELCGP TEPCVLPFQV LLENPLQFFQ 
AELRIRDVND HSPVFLDKEI LLKIPESITP GTTFLIERAQ DLDVGTNSLQ NYTISPNFHF 
HLNLQDSLDG IILPQLVLNR ALDREEQPEI RLTLTALDGG SPPRSGTALV RIEVVDINDN 
VPEFAKLLYE VQIPEDSPVG SQVAIVSARD LDIGTNGEIS YAFSQASEDI RKTFRLSAKS 
GELLLRQKLD FESIQTYTVN IQATDGGGLS GTCVVFVQVM DLNDNPPELT MSTLINQIPE 
NLQDTLIAVF SVSDPDSGDN GRMVCSIQDD LPFFLKPSVE NFYTLVISTA LDRETRSEYN 
ITITVTDFGT PRLKTEHNIT VLVSDVNDNA PAFTQTSYTL FVRENNSPAL HIGSVSATDR 
DSGTNAQVTY SLLPPQDPHL PLASLVSINA DNGHLFALQS LDYEALQAFE FRVGAADRGS 
PALSSEALVR VLVLDANDNS PFVLYPLQNG SAPCTELVPR AAEPGYLVTK VVAVDGDSGQ 
NAWLSYQLLK ATEPGLFGVW AHNGEVRTAR LLRERDAAKQ RLVVLVKDNG EPPRSATATL 
HVLLVDGFSQ PYLLLPEAAP AQAQADLLTV YLVVALASVS SLFLFSVLLF VAVRLCRRSR 
AASVGRCSVP EGPFPGQMVD VSGTGTLSQS YQYEVCLTGG SGTNEFKFLK PIIPNFVAQG 
AERVSEANPS FRKSFEFT

Genular Protein ID: 1249013732

Symbol: Q4KMG6_HUMAN

Name: N/A

UniProtKB Accession Codes:

Q4KMG6

Database IDs:

ARBA 6 AlphaFoldDB 1 BioGRID-ORCS 1 CDD 1 CTD 1 DNASU 1 DisGeNET 1 EMBL 2 GO 4 Gene3D 1 InterPro 6 KEGG 1 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 PRINTS 1 PROSITE 3 PROSITE-ProRule 1 PeptideAtlas 1 Pfam 3 RefSeq 1 SAM 2 SMART 1 SUPFAM 1

Citations:

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

Sequence Information:

  • Length: 798
  • Mass: 87326
  • Checksum: 984A2E865378C871
  • Sequence:
    • MEAGEGKERV PKQRQVLIFF VLLGIAQASC QPRHYSVAEE TESGSFVANL LKDLGLEIGE 
LAVRGARVVS KGKKMHLQFD RQTGDLLLNE KLDREELCGP TEPCVLPFQV LLENPLQFFQ 
AELRIRDVND HSPVFLDKEI LLKIPESITP GTTFLIERAQ DLDVGTNSLQ NYTISPNFHF 
HLNLQDSLDG IILPQLVLNR ALDREEQPEI RLTLTALDGG SPPRSGTALV RIEVVDINDN 
VPEFAKLLYE VQIPEDSPVG SQVAIVSARD LDIGTNGEIS YAFSQASEDI RKTFRLSAKS 
GELLLRQKLD FESIQTYTVN IQATDGGGLS GTCVVFVQVM DLNDNPPELT MSTLINQIPE 
NLQDTLIAVF SVSDPDSGDN GRMVCSIQDD LPFFLKPSVE NFYTLVISTA LDRETRSEYN 
ITITVTDFGT PRLKTEHNIT VLVSDVNDNA PAFTQTSYTL FVRENNSPAL HIGSVSATDR 
DSGTNAQVTY SLLPPQDPHL PLASLVSINA DNGHLFALQS LDYEALQAFE FRVGAADRGS 
PALSSEALVR VLVLDANDNS PFVLYPLQNG SAPCTELVPR AAEPGYLVTK VVAVDGDSGQ 
NAWLSYQLLK ATEPGLFGVW AHNGEVRTAR LLRERDAAKQ RLVVLVKDNG EPPRSATATL 
HVLLVDGFSQ PYLLLPEAAP AQAQADLLTV YLVVALASVS SLFLFSVLLF VAVRLCRRSR 
AASVGRCSVP EGPFPGQMVD VSGTGTLSQS YQYEVCLTGE SGTNEFKFLK PIIPNFVAQG 
AERVSEANPS FRKSFEFT