Details for: PCDH20

Gene ID: 64881

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: PCDH20

Ensembl ID: ENSG00000280165

Description: protocadherin 20

Selected Context(s):  Overall

Cell Significance Landscape

Contexts:

Associated with

Significant Cells

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

  • enteroendocrine cell CL0000164
    CSI 3.64
    rCSI 4.97%
    PRS 98.57
  • neuroblast (sensu Nematoda and Protostomia) CL0000338
    CSI 2.88
    rCSI 3.33%
    PRS 98.14
  • sncg GABAergic cortical interneuron CL4023015
    CSI 1.96
    rCSI 3.15%
    PRS 97.3
  • chandelier pvalb GABAergic cortical interneuron CL4023036
    CSI 1.01
    rCSI 3.16%
    PRS 97.82

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

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  • Node Color (Target Cell CSI, relative to current network):
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    • High
    • Medium
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    • CSI N/A
  • Node Size: Proportional to Target Cell CSI magnitude
  • STRING PPI Edge
  • Shared Pathway Edge (ONTOLOGY)

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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 [PCDH20](/details-gene/64881) (Protocadherin 20) is a protein-coding gene located on chromosome 13q21.2. As a member of the cadherin superfamily, its primary function is in mediating calcium-dependent, homophilic cell-cell adhesion at the plasma membrane, as indicated by its functional annotations ([GO:0007156](https://www.ebi.ac.uk/QuickGO/term/GO:0007156), [GO:0005509](https://www.ebi.ac.uk/QuickGO/term/GO:0005509)). **Overall**, expression data reveals that [PCDH20](/details-gene/64881) is a highly specific marker for distinct neuroendocrine and neuronal cell populations. Its most significant expression is found in [enteroendocrine cell](/details-cell/CL0000164)s and developing [neuroblast](/details-cell/CL0000338)s, with notable expression also present in specific subtypes of cortical interneurons. This pattern suggests a specialized role in establishing or maintaining cellular organization and connectivity within the nervous and gastrointestinal systems. Foundational sequencing and characterization of this gene were established through large-scale cDNA projects ([Link](https://doi.org/10.1038/ng1285), [Link](https://doi.org/10.1101/gr.2596504)). ## Cellular Roles and Expression Landscape The expression profile of [PCDH20](/details-gene/64881) points to a highly specialized function in a narrow range of cell types, primarily within neurogenic and neuroendocrine lineages. **Overall**, its most significant role as a cell identity marker is in [enteroendocrine cell](/details-cell/CL0000164)s (CSI: 3.64), which are dispersed sensory hormone-secreting cells of the gut epithelium. This suggests [PCDH20](/details-gene/64881) may be critical for their positioning or interaction with neighboring cells. Furthermore, [PCDH20](/details-gene/64881) shows high significance in the developing nervous system, as evidenced by its strong marker status in [neuroblast](/details-cell/CL0000338)s (CSI: 2.88). This is consistent with a role for protocadherins in neuronal migration, differentiation, and the formation of nascent neural circuits. In the mature brain, its expression is maintained in highly specific subpopulations of inhibitory neurons, including [sncg GABAergic cortical interneuron](/details-cell/CL4023015)s (CSI: 1.96) and [chandelier pvalb GABAergic cortical interneuron](/details-cell/CL4023036)s (CSI: 1.01). This restricted expression pattern suggests that [PCDH20](/details-gene/64881) is not a general neuronal adhesion molecule but rather contributes to the precise wiring or laminar organization of specific interneuron circuits. ## Pathways and Molecular Function The functions of [PCDH20](/details-gene/64881) are directly related to its identity as a protocadherin. Its primary annotated biological processes are cell adhesion ([GO:0007155](https://www.ebi.ac.uk/QuickGO/term/GO:0007155)) and, more specifically, homophilic cell adhesion via plasma membrane adhesion molecules ([GO:0007156](https://www.ebi.ac.uk/QuickGO/term/GO:0007156)). This function is mediated by its molecular ability to bind calcium ions ([GO:0005509](https://www.ebi.ac.uk/QuickGO/term/GO:0005509)), a hallmark of the cadherin family that is essential for stabilizing their extracellular domains and facilitating cell-cell binding. The protein is localized to the plasma membrane ([GO:0005886](https://www.ebi.ac.uk/QuickGO/term/GO:0005886)), where it can interact with [PCDH20](/details-gene/64881) on adjacent cells. An additional annotation for RNA binding ([GO:0003723](https://www.ebi.ac.uk/QuickGO/term/GO:0003723)) is also noted, suggesting a potential intracellular function that is less characterized for protocadherins and may warrant further investigation. The established adhesion function is highly consistent with its expression in [neuroblast](/details-cell/CL0000338)s and distinct neuronal subtypes, where such molecules are known to govern cell sorting and synaptic specificity. ## Research Directions The highly specific expression pattern of [PCDH20](/details-gene/64881) provides a strong basis for investigating its precise roles in development and tissue homeostasis. ### Proposed Hypotheses 1. **Role in Cortical Interneuron Circuitry:** The specific expression of [PCDH20](/details-gene/64881) in [chandelier pvalb GABAergic cortical interneuron](/details-cell/CL4023036)s and [sncg GABAergic cortical interneuron](/details-cell/CL4023015)s suggests it is critical for the synaptic targeting or laminar positioning of these specific interneuron subtypes. Its loss may lead to aberrant connectivity and altered cortical inhibition. 2. **Function in Enteroendocrine Cell Organization:** Given its top ranking in [enteroendocrine cell](/details-cell/CL0000164)s, [PCDH20](/details-gene/64881) may be essential for mediating the proper distribution and integration of these cells within the intestinal crypt-villus axis, potentially by facilitating adhesion to specific neighboring epithelial or neuronal cells. ### Suggested Experimental Approach To test the hypothesis that [PCDH20](/details-gene/64881) is required for the correct wiring of specific interneuron circuits (Hypothesis 1), a conditional knockout mouse model could be generated. By crossing a `Pcdh20-floxed` mouse with a Cre-driver line specific to these interneurons (e.g., Pvalb-Cre), the gene can be selectively deleted. The consequences of its deletion could be assessed using a combination of techniques: patch-clamp electrophysiology to measure synaptic inputs and outputs of the targeted neurons, and advanced anatomical imaging (e.g., array tomography or expansion microscopy) to quantify changes in axonal arborization, dendritic spine density, and synaptic contact patterns. ### Therapeutic Potential As a cell surface protocadherin with a highly restricted expression pattern, [PCDH20](/details-gene/64881) could represent a valuable therapeutic target. While its role in common diseases is not yet established, its specific expression in neuronal precursors makes it a candidate for investigation in developmental brain disorders or cancers of neuronal origin, such as neuroblastoma. If a tumor type is found to specifically overexpress [PCDH20](/details-gene/64881), its location on the plasma membrane would make it an excellent target for **inhibition**-based strategies, such as antibody-drug conjugates (ADCs) or CAR-T cell therapies, which could achieve high specificity while minimizing off-target toxicity to other tissues.

Genular Protein ID: 3672285168

Symbol: PCD20_HUMAN

Name: Protocadherin-20

UniProtKB Accession Codes:

Q8N6Y1 A8K1K9 B1AQU2 Q8NDN4 Q9NRT9

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 6 Ensembl 1 GO 5 Gene3D 1 GeneCards 1 GeneTree 1 GeneWiki 1 GenomeRNAi 1 GlyCosmos 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 4 KEGG 1 MANE-Select 1 MIM 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 2 OrthoDB 1 PANTHER 2 PRINTS 1 PRO 1 PROSITE 2 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 RNAct 1 RefSeq 2 SMART 1 SMR 1 STRING 1 SUPFAM 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 neXtProt 1

Citations:

PubMed ID: 17974005

Title: The full-ORF clone resource of the German cDNA consortium.

PubMed ID: 17974005

DOI: 10.1186/1471-2164-8-399

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 15057823

Title: The DNA sequence and analysis of human chromosome 13.

PubMed ID: 15057823

DOI: 10.1038/nature02379

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: 16959974

Title: The consensus coding sequences of human breast and colorectal cancers.

PubMed ID: 16959974

DOI: 10.1126/science.1133427

Sequence Information:

  • Length: 951
  • Mass: 104919
  • Checksum: E8506B94A686A591
  • Sequence:
    • MRGRGNARSS QALGVSWCPA TWHPRLDMGR LHRPRSSTSY RNLPHLFLFF LFVGPFSCLG 
SYSRATELLY SLNEGLPAGV LIGSLAEDLR LLPRSAGRPD PQSQLPERTG AEWNPPLSFS 
LASRGLSGQY VTLDNRSGEL HTSAQEIDRE ALCVEGGGGT AWSGSVSISS SPSDSCLLLL 
DVLVLPQEYF RFVKVKIAIR DINDNAPQFP VSQISVWVPE NAPVNTRLAI EHPAVDPDVG 
INGVQTYRLL DYHGMFTLDV EENENGERTP YLIVMGALDR ETQDQYVSII IAEDGGSPPL 
LGSATLTIGI SDINDNCPLF TDSQINVTVY GNATVGTPIA AVQAVDKDLG TNAQITYSYS 
QKVPQASKDL FHLDENTGVI KLFSKIGGSV LESHKLTILA NGPGCIPAVI TALVSIIKVI 
FRPPEIVPRY IANEIDGVVY LKELEPVNTP IAFFTIRDPE GKYKVNCYLD GEGPFRLSPY 
KPYNNEYLLE TTKPMDYELQ QFYEVAVVAW NSEGFHVKRV IKVQLLDDND NAPIFLQPLI 
ELTIEENNSP NAFLTKLYAT DADSEERGQV SYFLGPDAPS YFSLDSVTGI LTVSTQLDRE 
EKEKYRYTVR AVDCGKPPRE SVATVALTVL DKNDNSPRFI NKDFSFFVPE NFPGYGEIGV 
ISVTDADAGR NGWVALSVVN QSDIFVIDTG KGMLRAKVSL DREQQSSYTL WVEAVDGGEP 
ALSSTAKITI LLLDINDNPP LVLFPQSNMS YLLVLPSTLP GSPVTEVYAV DKDTGMNAVI 
AYSIIGRRGP RPESFRIDPK TGNITLEEAL LQTDYGLHRL LVKVSDHGYP EPLHSTVMVN 
LFVNDTVSNE SYIESLLRKE PEINIEEKEP QISIEPTHRK VESVSCMPTL VALSVISLGS 
ITLVTGMGIY ICLRKGEKHP REDENLEVQI PLKGKIDLHM RERKPMDISN I

Genular Protein ID: 3907203471

Symbol: B3KSZ7_HUMAN

Name: N/A

UniProtKB Accession Codes:

B3KSZ7

Database IDs:

ARBA 5 AlphaFoldDB 1 BioGRID-ORCS 1 CDD 1 CTD 1 DNASU 1 DisGeNET 1 EMBL 2 GO 3 Gene3D 1 InterPro 4 KEGG 1 NCBI Taxonomy 1 OrthoDB 1 PANTHER 2 PRINTS 1 PROSITE 3 PROSITE-ProRule 1 PeptideAtlas 1 Pfam 1 PharmGKB 1 RefSeq 1 SAM 1 SMART 1 SUPFAM 1

Citations:

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

Sequence Information:

  • Length: 697
  • Mass: 77140
  • Checksum: A556F156239ADAEB
  • Sequence:
    • MFTLDVEENE NGERTPYLIV MGALDRETQD QYVSIIIAED GGSPPLLGSA TLTIGISDIN 
DNCPLFTDSQ INVTVYGNAT VGTPIAAVQA VDKDLGTNAQ ITYSYSQKVP QASKDLFHLD 
ENTGVIKLFS KIGGSVLESH KLTILANGPG CIPAVITALV SIIKVIFRPP EIVPRYIANE 
IDGVVYLKEL EPVNTPIAFF TIRDPEGKYK VNCYLDGEGP FRLSPYKPYN NEYLLETTKP 
MDYELQQFYE VAVVAWNSEG FHVKRVIKVQ LLDDNDNAPI FLQPLIELTI EENNSPNAFL 
TKLYATDADS EERGQVSYFL GPDAPSYFSL DSVTGILTVS TQLDREEKEK YRYTVRAVDC 
GKPPRESVAT VALTVLDKND NSPRFINKDF SFFVPENFPG YGEIGVISVT DADAGRNGWV 
ALSVVNQSDI FVIDTGKGML RAKVSLDREQ QSSYTLWVEA VDGGEPALSS TAKITILLLD 
INDNPPLVLF PQSNMSYLLV LPSTLPGSPV TEVYAVDKDT GMNAVIAYSI IGRRGPRPES 
FRIDPKTGNI TLEEALLQTD YGLHRLLVKV SDHGYPEPLH STVMVNLFVN DTVSNESYIE 
SLLRKEPEIN IEEKEPQISI EPTHRKVESV SCMPTLVALS VISLGSITLV TGMGIYICLR 
KGEKHPREDE NLEVQIPLKG KIDLHMRERK PMDISNI