PCDH20 protocadherin 20 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PCDH20provided by HGNC
Official Full Name: protocadherin 20provided by HGNC
Primary source: HGNC:HGNC:14257
See related: Ensembl:ENSG00000280165 MIM:614449; AllianceGenome:HGNC:14257
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: PCDH13
Summary: This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This gene encodes a protein which contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from those of the classical cadherins. Although its specific function is undetermined, the cadherin-related neuronal receptor is thought to play a role in the establishment and function of specific cell-cell connections in the brain. [provided by RefSeq, Jul 2008]
Expression: Broad expression in brain (RPKM 4.5), lung (RPKM 1.5) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q21.2

Exon count:: 2

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (61409685..61415849, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (60629962..60647554, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (61983818..61989982, complement)

Chromosome 13 - NC_000013.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Protocadherin 20 maintains intestinal barrier function to protect against Crohn's disease by targeting ATF6.
Title: Protocadherin 20 maintains intestinal barrier function to protect against Crohn's disease by targeting ATF6.
Protocadherin 20 promotes ferroptosis by suppressing the expression of Sirtuin 1 and promoting the acetylation of nuclear factor erythroid 2-related factor 2 in hepatocellular carcinoma.
Title: Protocadherin 20 promotes ferroptosis by suppressing the expression of Sirtuin 1 and promoting the acetylation of nuclear factor erythroid 2-related factor 2 in hepatocellular carcinoma.
Low PCDH20 expression is associated with hypopharyngeal squamous cell carcinoma through the Wnt/beta-catenin signalling pathway.
Title: PCDH20 acts as a tumour-suppressor gene through the Wnt/β-catenin signalling pathway in hypopharyngeal squamous cell carcinoma.
low expression of PCDH20 was found to be associated with poor OS in HCC patients; hence, this protein represents a promising potential prognostic biomarker
Title: Decreased expression of protocadherin 20 is associated with poor prognosis in hepatocellular carcinoma.
Genome-wide association analysis on normal hearing function identifies PCDH20 and SLC28A3 as good candidates for modulatory genes in the auditory system. [meta-analysis]
Title: Genome-wide association analysis on normal hearing function identifies PCDH20 and SLC28A3 as candidates for hearing function and loss.
Study shows that PCDH20 expression is downregulated in nasopharyngeal carcinoma cells (NPC) and identified it as a functional tumor suppressor and an important antagonist of Wnt/beta-catenin signaling and EMT, with frequent epigenetic inactivation in NPC.
Title: Protocadherin20 Acts as a Tumor Suppressor Gene: Epigenetic Inactivation in Nasopharyngeal Carcinoma.
In conclusion, these data here strongly suggested that PCDH20 may act as a candidate tumour suppressor in hepatocellular carcinoma.
Title: PCDH20 functions as a tumour-suppressor gene through antagonizing the Wnt/β-catenin signalling pathway in hepatocellular carcinoma.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of IL6R and chromosome 11q13.5 as risk loci for asthma. EBI GWAS Catalog EBI GWAS CatalogPubMed
Joint influence of small-effect genetic variants on human longevity. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-N34280 (e-PCR)
- UniSTS:69932

PCDH20_1029 (e-PCR)
- UniSTS:277561

1172 (e-PCR)
- UniSTS:43125

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables calcium ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in cell adhesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: protocadherin-20

Names: protocadherin 13

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_022843.4 → NP_073754.2 protocadherin-20 precursor

See identical proteins and their annotated locations for NP_073754.2

Status: VALIDATED

Source sequence(s)

AL162575, AL592490

Consensus CDS

CCDS9442.2

UniProtKB/Swiss-Prot

A8K1K9, B1AQU2, Q8N6Y1, Q8NDN4, Q9NRT9

UniProtKB/TrEMBL

B2RBD0

Related

ENSP00000387250.3, ENST00000409204.5

Conserved Domains (2) summary

cd11304
Location:540 → 635

Cadherin_repeat; Cadherin tandem repeat domain

cl09101
Location:70 → 153

E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus