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    PCDH7 protocadherin 7 [ Homo sapiens (human) ]

    Gene ID: 5099, updated on 27-Nov-2024

    Summary

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    Official Symbol
    PCDH7provided by HGNC
    Official Full Name
    protocadherin 7provided by HGNC
    Primary source
    HGNC:HGNC:8659
    See related
    Ensembl:ENSG00000169851 MIM:602988; AllianceGenome:HGNC:8659
    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
    BHPCDH; BH-Pcdh; PPP1R120
    Summary
    This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The gene encodes a protein with an extracellular domain containing 7 cadherin repeats. The gene product is an integral membrane protein that is thought to function in cell-cell recognition and adhesion. Alternative splicing yields isoforms with unique cytoplasmic tails. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in brain (RPKM 10.8), spleen (RPKM 5.9) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PCDH7 in Genome Data Viewer
    Location:
    4p15.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (30720369..31146800)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (30709348..31135781)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (30721991..31148422)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene cathepsin B pseudogene Neighboring gene NANOG hESC enhancer GRCh37_chr4:30106274-30106775 Neighboring gene NANOG hESC enhancer GRCh37_chr4:30149486-30150025 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:30151059-30151682 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:30154558-30155155 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_78156 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_78284 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:30444783-30445382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21402 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21403 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21404 Neighboring gene uncharacterized LOC124900844 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:30722800-30723510 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:30758559-30759758 Neighboring gene NANOG hESC enhancer GRCh37_chr4:30838714-30839274 Neighboring gene MT-CYB pseudogene 43 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_78350 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_78356 Neighboring gene NANOG hESC enhancer GRCh37_chr4:31045251-31045820 Neighboring gene long intergenic non-protein coding RNA 2497 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:31235626-31236825 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr4:31238182-31239381 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:31293032-31293807 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:31462532-31463731 Neighboring gene uncharacterized LOC105374564

    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. A genome-wide screen for interactions reveals a new locus on 4p15 modifying the effect of waist-to-hip ratio on total cholesterol. Surakka I, et al. PLoS Genet, 2011 Oct. PMID 22028671, Free PMC Article
    2. Protocadherin-7 induces bone metastasis of breast cancer. Li AM, et al. Biochem Biophys Res Commun, 2013 Jul 5. PMID 23751349
    3. Global epigenomic analysis indicates protocadherin-7 activates osteoclastogenesis by promoting cell-cell fusion. Nakamura H, et al. Biochem Biophys Res Commun, 2014 Dec 12. PMID 25446128
    4. PCDH7 knockdown potentiates colon cancer cells to chemotherapy via inducing ferroptosis and changes in autophagy through restraining MEK1/2/ERK/c-Fos axis. Liu Z, et al. Biochem Cell Biol, 2022 Dec 1. PMID 35926236
    5. Low expression of protocadherin7 (PCDH7) is a potential prognostic biomarker for primary non-muscle invasive bladder cancer. Lin YL, et al. Oncotarget, 2016 May 10. PMID 27070091, Free PMC Article

    See all (59) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PCDH7 knockdown potentiates colon cancer cells to chemotherapy via inducing ferroptosis and changes in autophagy through restraining MEK1/2/ERK/c-Fos axis.
      Title: PCDH7 knockdown potentiates colon cancer cells to chemotherapy via inducing ferroptosis and changes in autophagy through restraining MEK1/2/ERK/c-Fos axis.
    2. Effect of aberrantly methylated androgen receptor target gene PCDH7 on the development of androgen-independent prostate cancer cells.
      Title: Effect of aberrantly methylated androgen receptor target gene PCDH7 on the development of androgen-independent prostate cancer cells.
    3. Authors demonstrated that enforced PCDH7 expression significantly accelerates Kras(G12D) -driven lung tumorigenesis and potentiates MAPK pathway activation.
      Title: Modulation of Mutant Kras(G12D) -Driven Lung Tumorigenesis In Vivo by Gain or Loss of PCDH7 Function.
    4. The findings indicate that low PCDH7 expression is a potential prognostic biomarker for primary non-muscle invasive bladder cancer
      Title: Low expression of protocadherin7 (PCDH7) is a potential prognostic biomarker for primary non-muscle invasive bladder cancer.
    5. we report that the PROTOCADHERIN PCDH7 is overexpressed frequently in Non-small cell lung cancer tumors where this event is associated with poor clinical outcome
      Title: PROTOCADHERIN 7 Acts through SET and PP2A to Potentiate MAPK Signaling by EGFR and KRAS during Lung Tumorigenesis.
    6. protocadherin 7 may play important roles in the invasion and metastasis of gastric cancer.
      Title: Protocadherin 7 inhibits cell migration and invasion through E-cadherin in gastric cancer.
    7. Two SNPs rs13146789 and rs13109270 of PCDH7 showed strong association with musical aptitude and inner ear development and neurocognitive functions.
      Title: A genome-wide linkage and association study of musical aptitude identifies loci containing genes related to inner ear development and neurocognitive functions.
    8. Pcdh7 plays a key role in osteoclastogenesis by promoting cell-cell fusion
      Title: Global epigenomic analysis indicates protocadherin-7 activates osteoclastogenesis by promoting cell-cell fusion.
    9. PCDH7 is up-regulation in bone metastatic breast cancer tissues.
      Title: Protocadherin-7 induces bone metastasis of breast cancer.
    10. Methylation of polycomb groups target genes is an early event in urothelial carcinogenesis in young patients.
      Title: Hypermethylation of the polycomb group target gene PCDH7 in bladder tumors from patients of all ages.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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
    A genome-wide screen for interactions reveals a new locus on 4p15 modifying the effect of waist-to-hip ratio on total cholesterol.
    EBI GWAS Catalog
    Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies.
    EBI GWAS Catalog
    Genetic Loci Associated with Circulating Levels of Very Long-Chain Saturated Fatty Acids.
    EBI GWAS Catalog
    Genome-wide association studies and heritability estimates of body mass index related phenotypes in bangladeshi adults.
    EBI GWAS Catalog
    Genome-wide association study for refractive astigmatism reveals genetic co-determination with spherical equivalent refractive error: the CREAM consortium.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ97161

    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
    		  
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in platelet alpha granule membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin-7
    Names
    BH-protocadherin (brain-heart)
    brain-heart protocadherin
    protein phosphatase 1, regulatory subunit 120

    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_001173523.2 → NP_001166994.1  protocadherin-7 isoform d precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (d) represents the longest transcript and encodes the longest isoform (d).
      Source sequence(s)
      AC098595, AC107394, AC110766
      UniProtKB/TrEMBL
      A0A087X2C4, A0A8Q3SI70
      Related
      ENSP00000512266.1, ENST00000695919.1
      Conserved Domains (2) summary
      cd11304
      Location:541 → 635
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:842 → 1053
      Protocadherin; Protocadherin

    2. NM_002589.4 → NP_002580.2  protocadherin-7 isoform a precursor

      See identical proteins and their annotated locations for NP_002580.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (a) uses an alternate splice pattern in the 3' CDS and 3' UTR, compared to variant d. The resulting isoform (a) has a shorter and distinct C-terminus, compared to isoform d.
      Source sequence(s)
      AC098595
      Consensus CDS
      CCDS33971.1
      UniProtKB/Swiss-Prot
      O60245, O60246, O60247, Q4W5C4
      UniProtKB/TrEMBL
      A0A8Q3SIA5
      Related
      ENSP00000355243.2, ENST00000361762.3
      Conserved Domains (2) summary
      cd11304
      Location:541 → 635
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:842 → 1053
      Protocadherin; Protocadherin

    3. NM_032457.4 → NP_115833.2  protocadherin-7 isoform c precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (c) uses an alternate in-frame splice site in the 3' coding region, compared to variant d. The resulting isoform (c) lacks an internal segment near the C-terminus, compared to isoform d.
      Source sequence(s)
      AC098595, AC107394, AC110766
      Consensus CDS
      CCDS93490.1
      UniProtKB/TrEMBL
      A0A087X2C4, A0A8V8TM73
      Related
      ENSP00000513121.1, ENST00000511884.7
      Conserved Domains (2) summary
      cd11304
      Location:541 → 635
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:842 → 1053
      Protocadherin; Protocadherin

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      30720369..31146800
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      30709348..31135781
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_032456.4: Suppressed sequence

      Description
      NM_032456.4: This RefSeq was removed because currently there is support for the transcript but not for the protein.

    2. NR_172626.1: Suppressed sequence

      Description
      NR_172626.1: This RefSeq was removed because currently there is insufficient support for the transcript.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O60245.2 GenPept UniProtKB/Swiss-Prot:O60245

    Gene LinkOut

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

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