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 inv... See more...

Aliases for PDZD2 Gene

Aliases for PDZD2 Gene

  • PDZ Domain Containing 2 2 3 5
  • Activated In Prostate Cancer Protein 3 4
  • PDZ Domain-Containing Protein 2 3 4
  • PDZ Domain-Containing Protein 3 3 4
  • KIAA0300 2 4
  • PDZK3 3 4
  • AIPC 3 4
  • Plakophilin-Related Armadillo Repeat Protein-Interactive PDZ Protein 3
  • PDZ Domain Containing 3 2
  • PAPIN 3
  • PDZD2 5
  • PIN1 3

External Ids for PDZD2 Gene

Previous HGNC Symbols for PDZD2 Gene

  • PDZK3

Previous GeneCards Identifiers for PDZD2 Gene

  • GC05P031584
  • GC05P031834

Summaries for PDZD2 Gene

Entrez Gene Summary for PDZD2 Gene

  • 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]

GeneCards Summary for PDZD2 Gene

PDZD2 (PDZ Domain Containing 2) is a Protein Coding gene. Diseases associated with PDZD2 include Motility-Related Diarrhea and Prostate Cancer. An important paralog of this gene is IL16.

Gene Wiki entry for PDZD2 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PDZD2 Gene

Genomics for PDZD2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PDZD2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J031638 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +0.5 469 2.4 TEAD4 PRDM10 ZNF629 KDM1A CTCF TARDBP ZHX2 LARP7 ZNF143 MTA2 PDZD2 hsa-miR-5096-021 RF00017-4549 GOLPH3
GH05J032108 Promoter 0.4 EPDnew 600 +468.2 468199 0.1 RBM22 PDZD2 HSALNG0040978 NONHSAG040135.2 piR-55985-152 ENSG00000250764 GOLPH3
GH05J031790 Promoter 0.3 EPDnew 600.1 +151.6 151581 0.1 piR-61945-402 PDZD2 RF00026-853 RNU6-358P RF00017-4552 RF00017-4549 GOLPH3
GH05J031810 Enhancer 0.9 Ensembl ENCODE 16.7 +172.2 172180 1 ZNF629 JUND ZNF501 SOX6 ZNF341 CEBPB SP1 ZNF639 ZXDB CTBP1 PDZD2 DROSHA RNU6-760P RNU6-358P RF00026-853 piR-61945-402 RF00017-4552 GOLPH3
GH05J031935 Promoter/Enhancer 1.2 Ensembl ENCODE CraniofacialAtlas dbSUPER 9.6 +297.6 297627 2.5 PRDM10 CEBPB KLF9 POLR2A ZBTB17 GATA3 ZNF558 MZF1 MIR4279 PDZD2 piR-32214-537 GOLPH3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDZD2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PDZD2

Top Transcription factor binding sites by QIAGEN in the PDZD2 gene promoter:
  • AP-1
  • ATF-2
  • c-Fos
  • c-Jun
  • USF-1

Genomic Locations for PDZD2 Gene

Genomic Locations for PDZD2 Gene
chr5:31,639,131-32,110,932
(GRCh38/hg38)
Size:
471,802 bases
Orientation:
Plus strand
chr5:31,639,517-32,111,038
(GRCh37/hg19)
Size:
471,522 bases
Orientation:
Plus strand

Genomic View for PDZD2 Gene

Genes around PDZD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDZD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDZD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDZD2 Gene

Proteins for PDZD2 Gene

  • Protein details for PDZD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15018-PDZD2_HUMAN
    Recommended name:
    PDZ domain-containing protein 2
    Protein Accession:
    O15018
    Secondary Accessions:
    • Q9BXD4

    Protein attributes for PDZD2 Gene

    Size:
    2839 amino acids
    Molecular mass:
    301641 Da
    Quaternary structure:
    • Interacts with SCN10A, CTNND2 and PKP4.
    SequenceCaution:
    • Sequence=BAA20760.2; Type=Erroneous initiation; Evidence={ECO:0000305};
    Miscellaneous:
    • [Isoform 2]: May be due to aberrant splicing.

    Alternative splice isoforms for PDZD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDZD2 Gene

Post-translational modifications for PDZD2 Gene

  • A secreted form is produced by caspase-mediated proteolytic cleavage.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PDZD2 Gene

Domains & Families for PDZD2 Gene

Gene Families for PDZD2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PDZD2 Gene

InterPro:
Blocks:
  • PDZ/DHR/GLGF domain
ProtoNet:

Suggested Antigen Peptide Sequences for PDZD2 Gene

GenScript: Design optimal peptide antigens:
  • PDZ domain-containing protein 3 (PDZD2_HUMAN)
genes like me logo Genes that share domains with PDZD2: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for PDZD2 Gene

Function for PDZD2 Gene

Phenotypes From GWAS Catalog for PDZD2 Gene

Gene Ontology (GO) - Molecular Function for PDZD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with PDZD2: view
genes like me logo Genes that share phenotypes with PDZD2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PDZD2

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDZD2

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDZD2 Gene

Localization for PDZD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDZD2 Gene

Nucleus. Cytoplasm. Endoplasmic reticulum. Note=At cell-cell contacts in lung epithelial cells. {ECO:0000250 UniProtKB:Q9QZR8}.
[Processed PDZ domain-containing protein 2]: Secreted.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDZD2 gene
Compartment Confidence
nucleus 5
extracellular 4
endoplasmic reticulum 4
plasma membrane 3
cytosol 3
cytoskeleton 1
mitochondrion 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PDZD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region ISS 12671685
GO:0005634 nucleus ISS 12671685
GO:0005737 cytoplasm IEA,IDA 11289102
GO:0005783 endoplasmic reticulum ISS 12671685
GO:0005911 cell-cell junction ISS 12671685
genes like me logo Genes that share ontologies with PDZD2: view

Pathways & Interactions for PDZD2 Gene

PathCards logo

SuperPathways for PDZD2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PDZD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007155 cell adhesion IEA --
genes like me logo Genes that share ontologies with PDZD2: view

No data available for Pathways by source and SIGNOR curated interactions for PDZD2 Gene

Drugs & Compounds for PDZD2 Gene

No Compound Related Data Available

Transcripts for PDZD2 Gene

mRNA/cDNA for PDZD2 Gene

2 REFSEQ mRNAs :
13 NCBI additional mRNA sequence :
12 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDZD2

Alternative Splicing Database (ASD) splice patterns (SP) for PDZD2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: - -
SP2:
SP3:
SP4:
SP5: -
SP6:
SP7:
SP8: - -

ExUns: 23 ^ 24 ^ 25 ^ 26 ^ 27a · 27b ^ 28a · 28b ^ 29 ^ 30 ^ 31a · 31b · 31c
SP1: - - -
SP2: - -
SP3: -
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for PDZD2 Gene

GeneLoc Exon Structure for
PDZD2

Expression for PDZD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PDZD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDZD2 Gene

This gene is overexpressed in Plasma (28.4), Frontal cortex (13.8), Placenta (10.3), and Heart (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PDZD2 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PDZD2

SOURCE GeneReport for Unigene cluster for PDZD2 Gene:

Hs.481819

mRNA Expression by UniProt/SwissProt for PDZD2 Gene:

O15018-PDZD2_HUMAN
Tissue specificity: Isoform 2 is expressed (at protein level) in prostate and many prostate tumors.

Evidence on tissue expression from TISSUES for PDZD2 Gene

  • Nervous system(4.8)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with PDZD2: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDZD2 Gene

Orthologs for PDZD2 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDZD2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PDZD2 30 31
  • 98.86 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia -- 31
  • 90 (a)
OneToMany
PDZD2 30
  • 79.09 (n)
-- 31
  • 70 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 87 (a)
OneToMany
-- 31
  • 49 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia PDZD2 30 31
  • 78.74 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Pdzd2 30 17 31
  • 76.67 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pdzd2 30
  • 76.48 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia PDZD2 31
  • 62 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PDZD2 30 31
  • 61.35 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PDZD2 31
  • 41 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pdzd2 30
  • 57.01 (n)
Zebrafish
(Danio rerio)
Actinopterygii LOC569088 30
  • 56.36 (n)
pdzd2 31
  • 37 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG15803 31
  • 17 (a)
ManyToMany
Species where no ortholog for PDZD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for PDZD2 Gene

ENSEMBL:
Gene Tree for PDZD2 (if available)
TreeFam:
Gene Tree for PDZD2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PDZD2: view image

Paralogs for PDZD2 Gene

Paralogs for PDZD2 Gene

(5) SIMAP similar genes for PDZD2 Gene using alignment to 3 proteins:

  • PDZD2_HUMAN
  • D6RF66_HUMAN
  • L8E9S3_HUMAN
genes like me logo Genes that share paralogs with PDZD2: view

Variants for PDZD2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PDZD2 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
708923 Likely Benign: not provided 32,089,263(+) G/A MISSENSE_VARIANT
710960 Benign: not provided 32,089,010(+) G/A SYNONYMOUS_VARIANT
717441 Benign: not provided 32,088,107(+) C/T SYNONYMOUS_VARIANT
720336 Benign: not provided 32,074,566(+) G/C MISSENSE_VARIANT
737653 Likely Benign: not provided 32,074,076(+) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for PDZD2 Gene

Structural Variations from Database of Genomic Variants (DGV) for PDZD2 Gene

Variant ID Type Subtype PubMed ID
dgv1086e214 CNV gain 21293372
dgv1087e214 CNV gain 21293372
dgv1591e212 CNV gain 25503493
dgv201e55 CNV gain 17911159
dgv208n111 CNV duplication 26073780
dgv3068n106 CNV deletion 24896259
dgv3249e59 CNV duplication 20981092
dgv54n64 CNV gain 17921354
dgv5620n100 CNV gain 25217958
dgv5621n100 CNV gain 25217958
dgv5622n100 CNV gain 25217958
dgv5623n100 CNV gain 25217958
dgv698n27 CNV gain 19166990
dgv941n67 CNV gain 20364138
dgv9714n54 CNV gain 21841781
dgv9715n54 CNV gain 21841781
esv1011293 CNV deletion 20482838
esv1533065 CNV insertion 17803354
esv22226 CNV loss 19812545
esv2662404 CNV deletion 23128226
esv2668094 CNV deletion 23128226
esv2671710 CNV deletion 23128226
esv2675462 CNV deletion 23128226
esv2730024 CNV deletion 23290073
esv2759337 CNV gain 17122850
esv2763905 CNV gain 21179565
esv33235 CNV gain 17666407
esv34132 CNV loss 18971310
esv3442350 CNV duplication 20981092
esv3575833 CNV gain 25503493
esv3584528 CNV gain 24956385
esv3604580 CNV gain 21293372
esv3604589 CNV loss 21293372
esv3604590 CNV loss 21293372
esv3604591 CNV loss 21293372
esv3604592 CNV loss 21293372
esv3604593 CNV loss 21293372
esv3604594 CNV gain 21293372
esv3604595 CNV gain 21293372
esv3604597 CNV loss 21293372
esv3604598 CNV loss 21293372
esv3894170 CNV gain 25118596
nsv1021781 CNV gain 25217958
nsv1027907 CNV gain 25217958
nsv1114675 CNV deletion 24896259
nsv1117410 CNV tandem duplication 24896259
nsv1123936 CNV deletion 24896259
nsv441947 CNV gain 18776908
nsv514301 CNV gain 21397061
nsv517387 CNV gain 19592680
nsv597766 CNV loss 21841781
nsv597771 CNV gain 21841781
nsv597780 CNV gain 21841781
nsv830250 CNV gain 17160897
nsv830251 CNV loss 17160897
nsv950664 CNV deletion 24416366
nsv964828 CNV duplication 23825009
nsv964829 CNV duplication 23825009
nsv968159 CNV duplication 23825009
nsv980628 CNV duplication 23825009

Variation tolerance for PDZD2 Gene

Residual Variation Intolerance Score: 38.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.20; 84.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDZD2 Gene

Human Gene Mutation Database (HGMD)
PDZD2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDZD2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDZD2 Gene

Disorders for PDZD2 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PDZD2 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
motility-related diarrhea
prostate cancer
  • prostate cancer, somatic
- elite association - COSMIC cancer census association via MalaCards
Search PDZD2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PDZD2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with PDZD2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDZD2 Gene

Publications for PDZD2 Gene

  1. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9205841) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  3. Proteolytic cleavage of PDZD2 generates a secreted peptide containing two PDZ domains. (PMID: 12671685) Yeung ML … Yao KM (EMBO reports 2003) 3 23
  4. Localization of p0071-interacting proteins, plakophilin-related armadillo-repeat protein-interacting protein (PAPIN) and ERBIN, in epithelial cells. (PMID: 12370826) Ohno H … Hata Y (Oncogene 2002) 3 23
  5. Activated in prostate cancer: a PDZ domain-containing protein highly expressed in human primary prostate tumors. (PMID: 11289102) Chaib H … Macoska JA (Cancer research 2001) 3 4

Products for PDZD2 Gene

Sources for PDZD2 Gene