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    PDZD2 PDZ domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 23037, updated on 10-Dec-2024

    Summary

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    Official Symbol
    PDZD2provided by HGNC
    Official Full Name
    PDZ domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:18486
    See related
    Ensembl:ENSG00000133401 MIM:610697; AllianceGenome:HGNC:18486
    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
    AIPC; PIN1; PAPIN; PDZK3
    Summary
    The protein encoded by this gene contains six PDZ domains and shares sequence similarity with pro-interleukin-16 (pro-IL-16). Like pro-IL-16, the encoded protein localizes to the endoplasmic reticulum and is thought to be cleaved by a caspase to produce a secreted peptide containing two PDZ domains. In addition, this gene is upregulated in primary prostate tumors and may be involved in the early stages of prostate tumorigenesis. [provided by RefSeq, Dec 2015]
    Expression
    Biased expression in fat (RPKM 15.3), ovary (RPKM 9.0) and 12 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PDZD2 in Genome Data Viewer
    Location:
    5p13.3
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (31639131..32110932)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (31752824..32224543)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (31639238..32111038)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22432 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22433 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22431 Neighboring gene chromosome 5 open reading frame 22 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:31618177-31618357 Neighboring gene RNA, U6 small nuclear 363, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31680333-31680851 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31680852-31681369 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:31716787-31717309 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:31753742-31754275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22434 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:31780232-31780511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31798873-31799374 Neighboring gene small nucleolar RNA U13 Neighboring gene RNA, U6 small nuclear 358, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31853436-31854109 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:31854110-31854782 Neighboring gene uncharacterized LOC124900953 Neighboring gene RNA, U6 small nuclear 760, pseudogene Neighboring gene ribosomal protein L9 pseudogene 17 Neighboring gene OCT4 hESC enhancer GRCh37_chr5:31877194-31877695 Neighboring gene ribosomal protein L21 pseudogene 56 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31878784-31879741 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:31889301-31889803 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:31889804-31890305 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31892991-31893492 Neighboring gene ribosomal protein L5 pseudogene 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:31923061-31923560 Neighboring gene mitochondrial import receptor subunit TOM7 homolog Neighboring gene NANOG hESC enhancer GRCh37_chr5:31965348-31965849 Neighboring gene TPT1 pseudogene 5 Neighboring gene microRNA 4279 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:32016671-32017172 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:32017173-32017672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22435 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22436 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:32027139-32027640 Neighboring gene NANOG hESC enhancer GRCh37_chr5:32041483-32042015 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:32092735-32093236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:32093237-32093736 Neighboring gene uncharacterized LOC105374711 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:32097810-32099009 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:32125750-32126949 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15953 Neighboring gene golgi phosphoprotein 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15954 Neighboring gene ribosomal protein L27 pseudogene 10

    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. Secreted PDZD2 exerts concentration-dependent effects on the proliferation of INS-1E cells. Ma RY, et al. Int J Biochem Cell Biol, 2006. PMID 16413998
    2. PDZ-domain containing-2 (PDZD2) is a novel factor that affects the growth and differentiation of human fetal pancreatic progenitor cells. Suen PM, et al. Int J Biochem Cell Biol, 2008. PMID 18037333
    3. PDZ-domain containing-2 (PDZD2) drives the maturity of human fetal pancreatic progenitor-derived islet-like cell clusters with functional responsiveness against membrane depolarization. Leung KK, et al. Stem Cells Dev, 2009 Sep. PMID 19046020
    4. Interaction of recombinant human cystatin C with the cysteine proteinases papain and actinidin. Lindahl P, et al. Biochem J, 1992 Jan 1. PMID 1731767, Free PMC Article
    5. Activated in prostate cancer: a PDZ domain-containing protein highly expressed in human primary prostate tumors. Chaib H, et al. Cancer Res, 2001 Mar 15. PMID 11289102

    See all (37) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Study results revealed that MG-63 osteosarcoma cells contained low levels of miR-363, and that overexpression of miR-363 in MG-63 cells significantly inhibited the vitality, proliferation, and colony formation ability of the cells. Bioinformatics analysis and luciferase reporter assay indicated that PDZD2 was a direct target of miR-363. In vivo xenograft model further confirmed that miR-363 functioned as tumor suppressor.
      Title: miR-363 acts as a tumor suppressor in osteosarcoma cells by inhibiting PDZD2.
    2. we systematically evaluating RCC risk-associated SNPs indentified from previous GWAS in a Chinese population, finding that one SNP located in PDZD2 and two SNPs located in ITPR2 were ccRCC-risk associated in Chinese population.
      Title: Germline genetic variations in PDZD2 and ITPR2 genes are associated with clear cell renal cell carcinoma in Chinese population.
    3. The DNA copy number variations disrupt PDZD2 and GOLPH3 genes predominantly expressed in placenta, and it may represent a novel risk factor for recurrent miscarriage.
      Title: Structural genomic variation as risk factor for idiopathic recurrent miscarriage.
    4. This study does not support the association of PDZD2, GOLPH3, and MTMR12 genes with schizophrenia.
      Title: Mutation screening of PDZD2, GOLPH3, and MTMR12 genes in patients with schizophrenia.
    5. Observational study and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Genome-wide association study of genetic predictors of anti-tumor necrosis factor treatment efficacy in rheumatoid arthritis identifies associations with polymorphisms at seven loci.
    6. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: New genetic associations detected in a host response study to hepatitis B vaccine.
    8. PDZ-domain containing-2 (PDZD2) drives the maturity of human fetal pancreatic progenitor-derived islet-like cell clusters with functional responsiveness against membrane depolarization.
      Title: PDZ-domain containing-2 (PDZD2) drives the maturity of human fetal pancreatic progenitor-derived islet-like cell clusters with functional responsiveness against membrane depolarization.
    9. sPDZD2 sensitized mutant p53-positive DU145 cells and wild-type p53-positive MCF-7 cells to apoptosis induction through genotoxic stress imposed by sub-lethal concentration of hydrogen peroxide
      Title: The autocrine human secreted PDZ domain-containing protein 2 (sPDZD2) induces senescence or quiescence of prostate, breast and liver cancer cells via transcriptional activation of p53.
    10. Results show that a novel pancreatic developmental factor, PDZD2, is sufficient to promote the proliferation of human fetal PPCs while limiting differentiation of ICCs into islet/endocrine cells.
      Title: PDZ-domain containing-2 (PDZD2) is a novel factor that affects the growth and differentiation of human fetal pancreatic progenitor cells.
    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
    Citalopram and escitalopram plasma drug and metabolite concentrations: genome-wide associations.
    EBI GWAS Catalog
    Common variation at 2q22.3 (ZEB2) influences the risk of renal cancer.
    EBI GWAS Catalog
    Genome-wide association study of bipolar disorder accounting for effect of body mass index identifies a new risk allele in TCF7L2.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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

    • KIAA0300

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell-cell junction ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in centriolar satellite IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in endoplasmic reticulum ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in extracellular region ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    PDZ domain-containing protein 2
    Names
    PDZ domain-containing protein 3
    activated in prostate cancer protein
    plakophilin-related armadillo repeat protein-interactive PDZ protein

    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_033962.2 RefSeqGene

      Range
      4722..476523
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_178140.4 → NP_835260.2  PDZ domain-containing protein 2

      See identical proteins and their annotated locations for NP_835260.2

      Status: REVIEWED

      Source sequence(s)
      AB002298, AC022447, AC025178, CA503068
      Consensus CDS
      CCDS34137.1
      UniProtKB/Swiss-Prot
      O15018, Q9BXD4
      Related
      ENSP00000402033.1, ENST00000438447.2
      Conserved Domains (2) summary
      smart00228
      Location:2751 → 2833
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:589 → 670
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      31639131..32110932
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005248269.5 → XP_005248326.1  PDZ domain-containing protein 2 isoform X1

      See identical proteins and their annotated locations for XP_005248326.1

      Conserved Domains (2) summary
      smart00228
      Location:2785 → 2867
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:589 → 670
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    2. XM_011513992.3 → XP_011512294.1  PDZ domain-containing protein 2 isoform X1

      See identical proteins and their annotated locations for XP_011512294.1

      Conserved Domains (2) summary
      smart00228
      Location:2785 → 2867
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:589 → 670
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    3. XM_011513994.3 → XP_011512296.1  PDZ domain-containing protein 2 isoform X2

      Conserved Domains (2) summary
      smart00228
      Location:2773 → 2855
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:589 → 670
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    4. XM_011513996.3 → XP_011512298.1  PDZ domain-containing protein 2 isoform X3

      Conserved Domains (2) summary
      smart00228
      Location:2693 → 2775
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:497 → 578
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    5. XM_011513993.3 → XP_011512295.1  PDZ domain-containing protein 2 isoform X1

      See identical proteins and their annotated locations for XP_011512295.1

      Conserved Domains (2) summary
      smart00228
      Location:2785 → 2867
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:589 → 670
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    6. XM_006714460.3 → XP_006714523.1  PDZ domain-containing protein 2 isoform X4

      Conserved Domains (2) summary
      smart00228
      Location:2454 → 2536
      PDZ; Domain present in PSD-95, Dlg, and ZO-1/2
      cd00992
      Location:258 → 339
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    7. XM_047416965.1 → XP_047272921.1  PDZ domain-containing protein 2 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      31752824..32224543
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054352108.1 → XP_054208083.1  PDZ domain-containing protein 2 isoform X1

    2. XM_054352110.1 → XP_054208085.1  PDZ domain-containing protein 2 isoform X2

    3. XM_054352107.1 → XP_054208082.1  PDZ domain-containing protein 2 isoform X1

    4. XM_054352111.1 → XP_054208086.1  PDZ domain-containing protein 2 isoform X3

    5. XM_054352109.1 → XP_054208084.1  PDZ domain-containing protein 2 isoform X1

    6. XM_054352112.1 → XP_054208087.1  PDZ domain-containing protein 2 isoform X4

    7. XM_054352113.1 → XP_054208088.1  PDZ domain-containing protein 2 isoform X5

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_015022.2: Suppressed sequence

      Description
      NM_015022.2: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O15018.4 GenPept UniProtKB/Swiss-Prot:O15018

    Gene LinkOut

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