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PCDH9 protocadherin 9 [ Homo sapiens (human) ]

Gene ID: 5101, updated on 11-Apr-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
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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

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. 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
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
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

Gene LinkOut

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