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    PCDH9 protocadherin 9 [ Homo sapiens (human) ]

    Gene ID: 5101, updated on 2-May-2024

    Summary

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    Official Symbol
    PCDH9provided by HGNC
    Official Full Name
    protocadherin 9provided by HGNC
    Primary source
    HGNC:HGNC:8661
    See related
    Ensembl:ENSG00000184226 MIM:603581; AllianceGenome:HGNC:8661
    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
    Summary
    This gene encodes a member of the protocadherin family, and cadherin superfamily, of transmembrane proteins containing cadherin domains. These proteins mediate cell adhesion in neural tissues in the presence of calcium. The encoded protein may be involved in signaling at neuronal synaptic junctions. Sharing a characteristic with other protocadherin genes, this gene has a notably large exon that encodes multiple cadherin domains and a transmembrane region. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Nov 2012]
    Expression
    Biased expression in brain (RPKM 8.9), fat (RPKM 0.9) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    13q21.32
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (66302834..67230336, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (65522767..66450396, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (66876966..67804468, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:66798584-66799108 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:66799109-66799633 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:66800429-66801145 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:66804949-66805878 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:66805879-66806808 Neighboring gene uncharacterized LOC124903179 Neighboring gene microRNA 4704 Neighboring gene tripartite motif containing 60 pseudogene 19 Neighboring gene NANOG hESC enhancer GRCh37_chr13:66918798-66919386 Neighboring gene PCDH9 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr13:67104803-67105304 Neighboring gene uncharacterized LOC105370247 Neighboring gene Sharpr-MPRA regulatory region 12707 Neighboring gene RNA, U7 small nuclear 87 pseudogene Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr13:67311857-67312463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:67422445-67422946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:67422947-67423446 Neighboring gene PCDH9 antisense RNA 2 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:67507550-67508749 Neighboring gene PCDH9 antisense RNA 3 Neighboring gene PCDH9 antisense RNA 4 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:67760998-67761570 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5391 Neighboring gene uncharacterized LOC105370246 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:67832520-67833284 Neighboring gene ribosomal protein SA pseudogene 53 Neighboring gene long intergenic non-protein coding RNA 364

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. The Gene Encoding Protocadherin 9 (PCDH9), a Novel Risk Factor for Major Depressive Disorder. Xiao X, et al. Neuropsychopharmacology, 2018 Apr. PMID 28990594, Free PMC Article
    2. PCDH9 acts as a tumor suppressor inducing tumor cell arrest at G0/G1 phase and is frequently methylated in hepatocellular carcinoma. Lv J, et al. Mol Med Rep, 2017 Oct. PMID 28791409, Free PMC Article
    3. Loss of PCDH9 is associated with the differentiation of tumor cells and metastasis and predicts poor survival in gastric cancer. Chen Y, et al. Clin Exp Metastasis, 2015 Jun. PMID 25869928
    4. Downregulation of PCDH9 predicts prognosis for patients with glioma. Wang C, et al. J Clin Neurosci, 2012 Apr. PMID 22300792
    5. COP1 Acts as a Ubiquitin Ligase for PCDH9 Ubiquitination and Degradation in Human Glioma. Zhou K, et al. Mol Neurobiol, 2022 Apr. PMID 35084653

    See all (39) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. COP1 Acts as a Ubiquitin Ligase for PCDH9 Ubiquitination and Degradation in Human Glioma.
      Title: COP1 Acts as a Ubiquitin Ligase for PCDH9 Ubiquitination and Degradation in Human Glioma.
    2. This review discusses the role and potential use as biomarkers of semaphorin 3A (SEMA3A), protocadherin 9 (PCDH9), and S100 calcium binding protein A3 (S100A3) in carcinogenesis and chemoresistance of various tumors, including ovarian cancer.
      Title: Semaphorin 3A (SEMA3A), protocadherin 9 (PCdh9), and S100 calcium binding protein A3 (S100A3) as potential biomarkers of carcinogenesis and chemoresistance of different neoplasms, including ovarian cancer - review of literature.
    3. convergent lines of evidence suggest that PCDH9 is likely a novel risk gene for MDD.
      Title: The Gene Encoding Protocadherin 9 (PCDH9), a Novel Risk Factor for Major Depressive Disorder.
    4. PCDH9 acts as a potential tumor suppressor gene, and that the loss of PCDH9 expression appears be a driver in a significant fraction of hepatocarcinogenesis cases.
      Title: PCDH9 acts as a tumor suppressor inducing tumor cell arrest at G0/G1 phase and is frequently methylated in hepatocellular carcinoma.
    5. miR-215-5p up-regulation and PCDH9 down-regulation occurs in glioma samples. miR-215-5p could inhibit the mRNA and protein levels of PCDH9 in glioma cell lines by targeting its promoter and 3' UTR at the same time.
      Title: Dual inhibition of PCDH9 expression by miR-215-5p up-regulation in gliomas.
    6. Loss of PCDH9 is associated with the differentiation of tumor cells and metastasis in gastric cancer
      Title: Loss of PCDH9 is associated with the differentiation of tumor cells and metastasis and predicts poor survival in gastric cancer.
    7. Protocadherin 9 inhibits epithelial-mesenchymal transition and cell migration through activating GSK-3beta in hepatocellular carcinoma.
      Title: Protocadherin 9 inhibits epithelial-mesenchymal transition and cell migration through activating GSK-3β in hepatocellular carcinoma.
    8. Our results suggest that PCDH9 might function as a tumor suppressor during cancer development and progression
      Title: Downregulation of PCDH9 predicts prognosis for patients with glioma.
    9. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-06-07)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-06-07)

    ClinGen Genome Curation Page

    EBI GWAS Catalog

    Description
    A genome-wide association study on obesity and obesity-related traits.
    EBI GWAS Catalog
    Genome-wide association study identifies candidate genes for male fertility traits in humans.
    EBI GWAS Catalog
    Genome-wide association study of lung function decline in adults with and without asthma.
    EBI GWAS Catalog
    Genome-wide meta-analysis identifies variants associated with platinating agent susceptibility across populations
    EBI GWAS Catalog
    GWAS of dental caries patterns in the permanent dentition.
    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    HIV-1 infection (VSV-G pseudotyped) of CEMT4 T cells downregulates plasma membrane expression of PCDH9 PubMed

    Go to the HIV-1, Human Interaction Database

    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
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in forebrain development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell-cell contact zone IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in growth cone IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protocadherin-9
    Names
    cadherin superfamily protein VR4-11

    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.

    Genomic

    1. NG_011876.2 RefSeqGene

      Range
      5001..932503
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001318372.2 → NP_001305301.1  protocadherin-9 isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, as compared to variant 1. It encodes a shorter isoform (3) which is missing an internal segment, as compared to isoform 1.
      Source sequence(s)
      AI300218, AL834258, BC144321, DA496130, DA497692
      Consensus CDS
      CCDS81770.1
      UniProtKB/TrEMBL
      A7E2D9, B7ZM79
      Related
      ENSP00000401699.2, ENST00000456367.5
      Conserved Domains (3) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    2. NM_001318373.2 → NP_001305302.1  protocadherin-9 isoform 4 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two in-frame exons in the coding region, as compared to variant 1. It encodes a shorter isoform (4) which is missing an internal segment, as compared to isoform 1.
      Source sequence(s)
      AI300218, AL834258, BC144321, DA353918, DA496130, DA497692
      UniProtKB/TrEMBL
      A7E2D9
      Conserved Domains (3) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    3. NM_001318374.2 → NP_001305303.1  protocadherin-9 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks several exons and its 3' terminal exon 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 a shorter isoform (5) which has a distinct C-terminus, as compared to isoform 1.
      Source sequence(s)
      AL160254, AL603863, BC144321, BC150296, DA496130, DA497692
      Consensus CDS
      CCDS81769.1
      UniProtKB/TrEMBL
      A7E2D9, Q5VT82
      Related
      ENSP00000367092.3, ENST00000377861.4
      Conserved Domains (3) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    4. NM_020403.5 → NP_065136.1  protocadherin-9 isoform 2 precursor

      See identical proteins and their annotated locations for NP_065136.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, as compared to variant 1. It encodes a shorter isoform (2) which is missing an internal segment, as compared to isoform 1.
      Source sequence(s)
      AI300218, AK054661, AL603863, AL834258, BC136627, BX537422
      Consensus CDS
      CCDS9443.1
      UniProtKB/TrEMBL
      A7E2D9
      Related
      ENSP00000442186.2, ENST00000544246.5
      Conserved Domains (3) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    5. NM_203487.3 → NP_982354.1  protocadherin-9 isoform 1 precursor

      See identical proteins and their annotated locations for NP_982354.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AI300218, AK054661, AL834258, BX537422, DA278856
      Consensus CDS
      CCDS9444.1
      UniProtKB/Swiss-Prot
      A2A6U1, Q5VT83, Q7Z3U0, Q8N3K7, Q9HC56
      UniProtKB/TrEMBL
      A7E2D9, X5D7N0
      Related
      ENSP00000367096.2, ENST00000377865.7
      Conserved Domains (2) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin

    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_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      66302834..67230336 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017020619.3 → XP_016876108.1  protocadherin-9 isoform X1

      UniProtKB/Swiss-Prot
      A2A6U1, Q5VT83, Q7Z3U0, Q8N3K7, Q9HC56
      UniProtKB/TrEMBL
      A7E2D9, X5D7N0
      Conserved Domains (2) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin

    2. XM_017020620.3 → XP_016876109.1  protocadherin-9 isoform X2

      UniProtKB/TrEMBL
      A7E2D9

    3. XM_011535099.2 → XP_011533401.1  protocadherin-9 isoform X3

      UniProtKB/TrEMBL
      A7E2D9
      Conserved Domains (3) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    4. XM_017020621.3 → XP_016876110.1  protocadherin-9 isoform X4

      UniProtKB/TrEMBL
      A7E2D9
      Conserved Domains (3) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    5. XM_005266408.5 → XP_005266465.1  protocadherin-9 isoform X4

      UniProtKB/TrEMBL
      A7E2D9
      Conserved Domains (3) summary
      cd11304
      Location:576 → 671
      Cadherin_repeat; Cadherin tandem repeat domain
      pfam08374
      Location:777 → 997
      Protocadherin; Protocadherin
      cl09101
      Location:28 → 117
      E_set; Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      65522767..66450396 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054374591.1 → XP_054230566.1  protocadherin-9 isoform X1

      UniProtKB/Swiss-Prot
      A2A6U1, Q5VT83, Q7Z3U0, Q8N3K7, Q9HC56
      UniProtKB/TrEMBL
      X5D7N0

    2. XM_054374592.1 → XP_054230567.1  protocadherin-9 isoform X2

    3. XM_054374593.1 → XP_054230568.1  protocadherin-9 isoform X3

    4. XM_054374595.1 → XP_054230570.1  protocadherin-9 isoform X4

    5. XM_054374594.1 → XP_054230569.1  protocadherin-9 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HC56.2 GenPept UniProtKB/Swiss-Prot:Q9HC56

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