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

Gene ID: 23037, updated on 5-Mar-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
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Genomic context

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Location:
5p13.3
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (31639131..32110932)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (31752824..32224543)
105.20220307 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. 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
  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. 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
  4. miR-363 acts as a tumor suppressor in osteosarcoma cells by inhibiting PDZD2. He F, et al. Oncol Rep, 2019 May. PMID 30896877, Free PMC Article
  5. Germline genetic variations in PDZD2 and ITPR2 genes are associated with clear cell renal cell carcinoma in Chinese population. Zhang N, et al. Oncotarget, 2017 Apr 11. PMID 26918600, Free PMC Article

See all (36) 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)

Genotypes

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_2023_10

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

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