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PCDH17 protocadherin 17 [ Homo sapiens (human) ]

Gene ID: 27253, updated on 2-Nov-2024

Summary

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Official Symbol
PCDH17provided by HGNC
Official Full Name
protocadherin 17provided by HGNC
Primary source
HGNC:HGNC:14267
See related
Ensembl:ENSG00000118946 MIM:611760; AllianceGenome:HGNC:14267
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
PCH68; PCDH68
Summary
This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein contains six extracellular cadherin domains, a transmembrane domain, and a cytoplasmic tail differing from those of the classical cadherins. The encoded protein may 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 spleen (RPKM 10.8), brain (RPKM 7.3) and 14 other tissues See more
Orthologs
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Genomic context

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See PCDH17 in Genome Data Viewer
Location:
13q21.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (57630108..57729311)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (56846361..56945624)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (58205878..58303445)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein L31 pseudogene 53 Neighboring gene uncharacterized LOC105370217 Neighboring gene Sharpr-MPRA regulatory region 8499 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:58203841-58204426 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:58206385-58207064 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:58361242-58361742 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:58361743-58362243 Neighboring gene tRNA-Glu (CTC) 4-1 Neighboring gene RNA, 5S ribosomal pseudogene 30

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 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. Aberrant methylation of PCDH17 gene in high-grade serous ovarian carcinoma. Baranova I, et al. Cancer Biomark, 2018. PMID 29991130
  2. PCDH17 gene promoter demethylation and cell cycle arrest by genistein in gastric cancer. Yang Y, et al. Histol Histopathol, 2012 Feb. PMID 22207556
  3. Protocadherin 17 acts as a tumour suppressor inducing tumour cell apoptosis and autophagy, and is frequently methylated in gastric and colorectal cancers. Hu X, et al. J Pathol, 2013 Jan. PMID 22926751
  4. Protocadherin-17 promoter methylation in serum-derived DNA is associated with poor prognosis of bladder cancer. Luo ZG, et al. J Int Med Res, 2014 Feb. PMID 24366498
  5. Protocadherin 17 promoter methylation in tumour tissue from patients with bladder transitional cell carcinoma. Wang XB, et al. J Int Med Res, 2014 Apr. PMID 24567353

See all (58) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Ubiquitin ligase NEDD4 promotes the proliferation of hepatocellular carcinoma cells through targeting PCDH17 protein for ubiquitination and degradation.
    Title: Ubiquitin ligase NEDD4 promotes the proliferation of hepatocellular carcinoma cells through targeting PCDH17 protein for ubiquitination and degradation.
  2. PCDH17 gene promoter methylation status in a cohort of Egyptian women with epithelial ovarian cancer.
    Title: PCDH17 gene promoter methylation status in a cohort of Egyptian women with epithelial ovarian cancer.
  3. Repression of protocadherin 17 is correlated with elevated angiogenesis and hypoxia markers in female patients with breast cancer.
    Title: Repression of protocadherin 17 is correlated with elevated angiogenesis and hypoxia markers in female patients with breast cancer.
  4. MiR-23a-3p promoted G1/S cell cycle transition by targeting protocadherin17 in hepatocellular carcinoma.
    Title: MiR-23a-3p promoted G1/S cell cycle transition by targeting protocadherin17 in hepatocellular carcinoma.
  5. PCDH17 gene was silenced by DNA methylation in acute myeloid leukemia (AML). Low PCDH17 expression is associated with distinct clinical and biological features and improves risk stratification in patients with AML.
    Title: Reduced protocadherin17 expression in leukemia stem cells: the clinical and biological effect in acute myeloid leukemia.
  6. PCDH17 is downregulated in laryngeal squamous cell carcinoma.
    Title: MiR-196b affects the progression and prognosis of human LSCC through targeting PCDH-17.
  7. Aberrant hypermethylation in the promoter might be the explanation of PCDH17 downregulated in PCDH17 and promoted the development of nasopharyngeal cancer(NPC).
    Title: Aberrant promoter methylation reduced the expression of protocadherin 17 in nasopharyngeal cancer.
  8. 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.
  9. PCDH17 methylation is detectable in serum of cancer patients.
    Title: Recurrent transcriptional loss of the PCDH17 tumor suppressor in laryngeal squamous cell carcinoma is partially mediated by aberrant promoter DNA methylation.
  10. We report a genetic association with mood disorders within the genomic region spanning PCDH17. A consistent pattern of allelic association, involving cognition, neuroticism as personality trait, structural and functional imaging, was found in independent samples and in expression of the PCDH17 gene in brain tissues.
    Title: The protocadherin 17 gene affects cognition, personality, amygdala structure and function, synapse development and risk of major mood disorders.
Submit: New GeneRIF Correction See all GeneRIFs (27)

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 for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
EBI GWAS Catalog

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in adult behavior IEA
Inferred from Electronic Annotation
more info
  
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 negative regulation of synaptic transmission IEA
Inferred from Electronic Annotation
more info
  
involved_in presynaptic active zone assembly IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of synaptic vesicle clustering IEA
Inferred from Electronic Annotation
more info
  
involved_in synaptic membrane adhesion IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in GABA-ergic synapse IEA
Inferred from Electronic Annotation
more info
  
located_in glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in postsynaptic membrane IEA
Inferred from Electronic Annotation
more info
  
located_in presynaptic membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protocadherin-17
Names
protocadherin 68

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)

  1. NM_001040429.3 → NP_001035519.1  protocadherin-17 precursor

    See identical proteins and their annotated locations for NP_001035519.1

    Status: REVIEWED

    Source sequence(s)
    AL445216, AL445288, BC028165
    Consensus CDS
    CCDS31986.1
    UniProtKB/Swiss-Prot
    A8K1R5, O14917, Q5VVW9, Q5VVX0
    Related
    ENSP00000367151.3, ENST00000377918.8
    Conserved Domains (2) summary
    cd11304
    Location:247 → 347
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:21 → 112
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    57630108..57729311
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005266357.3 → XP_005266414.1  protocadherin-17 isoform X1

    See identical proteins and their annotated locations for XP_005266414.1

    UniProtKB/Swiss-Prot
    A8K1R5, O14917, Q5VVW9, Q5VVX0
    Conserved Domains (2) summary
    cd11304
    Location:247 → 347
    Cadherin_repeat; Cadherin tandem repeat domain
    cl09101
    Location:21 → 112
    E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

  2. XM_047430276.1 → XP_047286232.1  protocadherin-17 isoform X2

  3. XM_017020547.2 → XP_016876036.1  protocadherin-17 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    56846361..56945624
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054374466.1 → XP_054230441.1  protocadherin-17 isoform X1

    UniProtKB/Swiss-Prot
    A8K1R5, O14917, Q5VVW9, Q5VVX0

  2. XM_054374467.1 → XP_054230442.1  protocadherin-17 isoform X2

  3. XM_054374468.1 → XP_054230443.1  protocadherin-17 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_014459.2: Suppressed sequence

    Description
    NM_014459.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O14917.2 GenPept UniProtKB/Swiss-Prot:O14917

Gene LinkOut

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