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PCDH10 protocadherin 10 [ Homo sapiens (human) ]

Gene ID: 57575, updated on 11-Apr-2024

Summary

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Official Symbol
PCDH10provided by HGNC
Official Full Name
protocadherin 10provided by HGNC
Primary source
HGNC:HGNC:13404
See related
Ensembl:ENSG00000138650 MIM:608286; AllianceGenome:HGNC:13404
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PCDH19; OL-PCDH
Summary
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This family member contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from those of the classical cadherins. The encoded protein is a cadherin-related neuronal receptor thought to function in the establishment of specific cell-cell connections in the brain. This gene plays a role in inhibiting cancer cell motility and cell migration. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2015]
Expression
Biased expression in brain (RPKM 21.3), placenta (RPKM 10.2) and 4 other tissues See more
Orthologs
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Genomic context

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Location:
4q28.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (133149294..133208606)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (136472535..136531845)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (134070449..134115855)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377431 Neighboring gene PCDH10 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21907 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15691 Neighboring gene R3H domain containing 2 pseudogene 1 Neighboring gene uncharacterized LOC124900863 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:134184427-134185124 Neighboring gene Sharpr-MPRA regulatory region 13606 Neighboring gene MPRA-validated peak5117 silencer Neighboring gene MPRA-validated peak5118 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:134882009-134882508 Neighboring gene Sharpr-MPRA regulatory region 7344 Neighboring gene NANOG hESC enhancer GRCh37_chr4:134933235-134933765 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:134935198-134935698 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:134935699-134936199 Neighboring gene poly(A) binding protein cytoplasmic 4 like Neighboring gene ReSE screen-validated silencer GRCh37_chr4:134981541-134981750 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:134991841-134992529

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Quantitation Analysis of PCDH10 Methylation in Adolescent Idiopathic Scoliosis Using Pyrosequencing Study. Shi B, et al. Spine (Phila Pa 1976), 2020 Apr 1. PMID 31651684
  2. High methylation levels of PCDH10 predict poor prognosis in patients with pancreatic ductal adenocarcinoma. Curia MC, et al. BMC Cancer, 2019 May 14. PMID 31088413, Free PMC Article
  3. Clinical significance of PCDH10 promoter methylation in diffuse large B-cell lymphoma. Huang W, et al. BMC Cancer, 2017 Dec 4. PMID 29202805, Free PMC Article
  4. PCDH10 gene inhibits cell proliferation and induces cell apoptosis by inhibiting the PI3K/Akt signaling pathway in hepatocellular carcinoma cells. Ye M, et al. Oncol Rep, 2017 Jun. PMID 28498423, Free PMC Article
  5. [Protocadherin 10 (PCDH10) inhibits the proliferation, invasion and migration ability of BXPC-3 pancreatic cancer cells]. Qiu C, et al. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi, 2016 Feb. PMID 26927373

See all (71) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The role of Pcdh10 in neurological disease and cancer.
    Title: The role of Pcdh10 in neurological disease and cancer.
  2. E3 ubiquitin ligase RNF180 prevents excessive PCDH10 methylation to suppress the proliferation and metastasis of gastric cancer cells by promoting ubiquitination of DNMT1.
    Title: E3 ubiquitin ligase RNF180 prevents excessive PCDH10 methylation to suppress the proliferation and metastasis of gastric cancer cells by promoting ubiquitination of DNMT1.
  3. Miz1 promotes KRAS-driven lung tumorigenesis by repressing the protocadherin Pcdh10.
    Title: Miz1 promotes KRAS-driven lung tumorigenesis by repressing the protocadherin Pcdh10.
  4. PCDH10 exerts tumor-suppressor functions through modulation of EGFR/AKT axis in colorectal cancer.
    Title: PCDH10 exerts tumor-suppressor functions through modulation of EGFR/AKT axis in colorectal cancer.
  5. HOTAIR Induces Methylation of PCDH10, a Tumor Suppressor Gene, by Regulating DNMT1 and Sponging with miR-148b in Gastric Adenocarcinoma.
    Title: HOTAIR Induces Methylation of PCDH10, a Tumor Suppressor Gene, by Regulating DNMT1 and Sponging with miR-148b in Gastric Adenocarcinoma.
  6. PCDH10 inhibits invasion of lymphoma cells by regulating beta-catenin.
    Title: PCDH10 inhibits invasion of lymphoma cells by regulating β-catenin.
  7. Disruption of PCDH10 and TNRC18 Genes due to a Balanced Translocation.
    Title: Disruption of PCDH10 and TNRC18 Genes due to a Balanced Translocation.
  8. Quantitation Analysis of PCDH10 Methylation in Adolescent Idiopathic Scoliosis Using Pyrosequencing Study.
    Title: Quantitation Analysis of PCDH10 Methylation in Adolescent Idiopathic Scoliosis Using Pyrosequencing Study.
  9. Study found elevated promoter methylation and decreased expression of PCDH10 and PCDH17 in advanced gastric lesions, suggesting that elevated PCDH10 and PCDH17 methylation may be an early event in gastric carcinogenesis.
    Title: Methylation and Expression of Nonclustered Protocadherins Encoding Genes and Risk of Precancerous Gastric Lesions in a High-Risk Population.
  10. Study shows for that the methylation status of PCDH10 can predict prognosis in pancreatic ductal adenocarcinoma (PDAC) patients with a significant impact on the outcome in terms of progression-free survival. High levels of PCDH10 promoter methylation could be useful to identify patients at high risk of PDAC disease progression.
    Title: High methylation levels of PCDH10 predict poor prognosis in patients with pancreatic ductal adenocarcinoma.
Submit: New GeneRIF Correction See all GeneRIFs (51)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1400, MGC133344, DKFZp761O2023

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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
  
involved_in nervous system development 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
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protocadherin-10

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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)

  1. NM_020815.3 → NP_065866.1  protocadherin-10 isoform 2 precursor

    See identical proteins and their annotated locations for NP_065866.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) is intronless, and its 3' terminal end extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2 which is shorter, and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC105383, AI479918, AW007480, AY013874, CX760781, DA318338
    Consensus CDS
    CCDS75192.1
    UniProtKB/TrEMBL
    Q14DV7
    Related
    ENSP00000480512.1, ENST00000618019.1
    Conserved Domains (3) summary
    cd11304
    Location:254 → 354
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:19 → 101
    Cadherin_2; Cadherin-like
    pfam16492
    Location:713 → 838
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

  2. NM_032961.3 → NP_116586.1  protocadherin-10 isoform 1 precursor

    See identical proteins and their annotated locations for NP_116586.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB037821, AC105383, AL157470, BC039411, CB052787, DA318338
    Consensus CDS
    CCDS34063.1
    UniProtKB/Swiss-Prot
    Q4W5F6, Q96SF0, Q9P2E7
    UniProtKB/TrEMBL
    Q14DV7, X5D999
    Related
    ENSP00000264360.4, ENST00000264360.7
    Conserved Domains (3) summary
    cd11304
    Location:254 → 354
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:19 → 101
    Cadherin_2; Cadherin-like
    pfam16492
    Location:713 → 838
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    133149294..133208606
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532150.2 → XP_011530452.1  protocadherin-10 isoform X1

    UniProtKB/TrEMBL
    Q14DV7
    Conserved Domains (3) summary
    cd11304
    Location:254 → 354
    Cadherin_repeat; Cadherin tandem repeat domain
    pfam08266
    Location:19 → 101
    Cadherin_2; Cadherin-like
    pfam16492
    Location:713 → 838
    Cadherin_C_2; Cadherin cytoplasmic C-terminal

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    136472535..136531845
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350597.1 → XP_054206572.1  protocadherin-10 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9P2E7.2 GenPept UniProtKB/Swiss-Prot:Q9P2E7

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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