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Aliases for PDZD4 Gene

Aliases for PDZD4 Gene

  • PDZ Domain Containing 4 2 3 5
  • PDZ Domain-Containing RING Finger Protein 4-Like Protein 3 4
  • PDZRN4L 3 4
  • PDZK4 3 4
  • PDZ Domain-Containing Protein 4 3
  • KIAA1444 4
  • LNX5 3
  • LU1 3

External Ids for PDZD4 Gene

Previous HGNC Symbols for PDZD4 Gene

  • PDZK4

Previous GeneCards Identifiers for PDZD4 Gene

  • GC0XM152589
  • GC0XM152720
  • GC0XM153067
  • GC0XM141724

Summaries for PDZD4 Gene

GeneCards Summary for PDZD4 Gene

PDZD4 (PDZ Domain Containing 4) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include ubiquitin protein ligase activity. An important paralog of this gene is PDZRN3.

Gene Wiki entry for PDZD4 Gene

Additional gene information for PDZD4 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDZD4 Gene

Genomics for PDZD4 Gene

GeneHancer (GH) Regulatory Elements for PDZD4 Gene

Promoters and enhancers for PDZD4 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ153826 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 666.2 +1.6 1592 4.1 KLF1 ZIC2 HIC1 ZNF335 ZFHX2 GLIS2 EGR1 PATZ1 PRDM10 ZNF600 PDZD4 IDH3G
GH0XJ153884 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE 13.4 -55.5 -55538 3 CTCF KLF1 MAX KLF17 ZIC2 RAD21 HIC1 ZFHX2 GATA3 GLIS2 L1CAM RENBP TMEM187 HCFC1 SNORA70 PDZD4 SSR4 IDH3G SRPK3 PLXNB3
GH0XJ153900 Enhancer 1.4 FANTOM5 Ensembl ENCODE 10.5 -71.9 -71938 4.2 HDGF GLI4 TCF12 ZNF766 GLIS2 GATA2 ZNF143 FOS REST ATF4 AVPR2 HCFC1 SNORA70 DKC1 PLXNA3 TMEM187 SNORA56 EMD ENSG00000260081 SLC10A3
GH0XJ153721 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 5.6 +105.0 104974 7.2 PKNOX1 FOXA2 ARID4B SIN3A DMAP1 IRF4 POLR2B KLF13 SP3 SP5 BCAP31 ABCD1 PNCK SLC6A8 KRT18P48 PDZD4 PLXNB3
GH0XJ154595 Enhancer 0.9 Ensembl ENCODE 10.3 -766.0 -766009 1.5 CTCF MAX SALL2 FEZF1 RAD21 SMC3 RCOR1 TCF7L2 NANOG CEBPB ENSG00000260081 GDI1 GAB3 PDZD4 L1CAM FAM3A ENSG00000232155 CTAG1A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDZD4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDZD4 gene promoter:
  • POU6F1 (c2)
  • AP-1
  • c-Fos
  • c-Jun
  • ATF-2
  • CRE-BP1
  • AML1a
  • RelA
  • NF-kappaB1
  • NF-kappaB

Genomic Locations for PDZD4 Gene

Genomic Locations for PDZD4 Gene
28,402 bases
Minus strand
28,400 bases
Minus strand

Genomic View for PDZD4 Gene

Genes around PDZD4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDZD4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDZD4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDZD4 Gene

Proteins for PDZD4 Gene

  • Protein details for PDZD4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    PDZ domain-containing protein 4
    Protein Accession:
    Secondary Accessions:
    • B3KXB1
    • B7ZKY3
    • Q8NB75
    • Q9BUH9
    • Q9P284

    Protein attributes for PDZD4 Gene

    769 amino acids
    Molecular mass:
    86171 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAC03666.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PDZD4 Gene


neXtProt entry for PDZD4 Gene

Post-translational modifications for PDZD4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PDZD4 Gene

Domains & Families for PDZD4 Gene

Gene Families for PDZD4 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted intracellular proteins

Protein Domains for PDZD4 Gene


Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PDZD4: view

No data available for UniProtKB/Swiss-Prot for PDZD4 Gene

Function for PDZD4 Gene

Gene Ontology (GO) - Molecular Function for PDZD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0061630 ubiquitin protein ligase activity IBA --
genes like me logo Genes that share ontologies with PDZD4: view
genes like me logo Genes that share phenotypes with PDZD4: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDZD4

No data available for Molecular function , Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDZD4 Gene

Localization for PDZD4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDZD4 Gene

Cytoplasm, cell cortex. Note=Mainly localized under the plasma membrane.

Subcellular locations from

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 PDZD4 gene
Compartment Confidence
nucleus 2
cytosol 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PDZD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005938 cell cortex IEA --
genes like me logo Genes that share ontologies with PDZD4: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PDZD4 Gene

Pathways & Interactions for PDZD4 Gene

SuperPathways for PDZD4 Gene

No Data Available

Interacting Proteins for PDZD4 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
Selected Interacting proteins: Q76G19-PDZD4_HUMAN ENSP00000164640 for PDZD4 Gene via IID STRING

Gene Ontology (GO) - Biological Process for PDZD4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016567 protein ubiquitination IBA --
genes like me logo Genes that share ontologies with PDZD4: view

No data available for Pathways by source and SIGNOR curated interactions for PDZD4 Gene

Drugs & Compounds for PDZD4 Gene

No Compound Related Data Available

Transcripts for PDZD4 Gene

Unigene Clusters for PDZD4 Gene

PDZ domain containing 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDZD4

Alternative Splicing Database (ASD) splice patterns (SP) for PDZD4 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4a · 4b · 4c · 4d · 4e ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12a · 12b
SP1: - - - - - - - - - - - - - -
SP2: - - - - - - - - - -
SP3: - - - - - - - - - - -
SP5: - -
SP6: - - - - - - - - - - - - -
SP7: -
SP8: - - - - - - - - -
SP9: - - - - -
SP10: - - -
SP11: - - - - - -
SP12: - - -

Relevant External Links for PDZD4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PDZD4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDZD4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDZD4 Gene

This gene is overexpressed in Brain - Cortex (x5.4), Brain - Frontal Cortex (BA9) (x4.7), Brain - Hippocampus (x4.4), Brain - Anterior cingulate cortex (BA24) (x4.3), and Brain - Amygdala (x4.1).

Protein differential expression in normal tissues from HIPED for PDZD4 Gene

This gene is overexpressed in Liver (30.7), Fetal Brain (22.2), and Adipocyte (16.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PDZD4 Gene

Protein tissue co-expression partners for PDZD4 Gene

NURSA nuclear receptor signaling pathways regulating expression of PDZD4 Gene:


SOURCE GeneReport for Unigene cluster for PDZD4 Gene:


mRNA Expression by UniProt/SwissProt for PDZD4 Gene:

Tissue specificity: Brain-specific. Expressed in fetal and adult brain. Up-regulated in synovial carcinomas.

Evidence on tissue expression from TISSUES for PDZD4 Gene

  • Nervous system(4.8)
genes like me logo Genes that share expression patterns with PDZD4: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for PDZD4 Gene

Orthologs for PDZD4 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDZD4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PDZD4 34
  • 99 (a)
(Canis familiaris)
Mammalia PDZD4 34 33
  • 90.95 (n)
(Bos Taurus)
Mammalia PDZD4 34 33
  • 88.95 (n)
(Mus musculus)
Mammalia Pdzd4 16 34 33
  • 86.68 (n)
(Rattus norvegicus)
Mammalia Pdzd4 33
  • 86.55 (n)
(Monodelphis domestica)
Mammalia PDZD4 34
  • 84 (a)
(Anolis carolinensis)
Reptilia PDZD4 34
  • 71 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pdzd4 33
  • 68.76 (n)
(Danio rerio)
Actinopterygii pdzd4 34 33
  • 59.39 (n)
PDZD4 (2 of 2) 34
  • 51 (a)
fruit fly
(Drosophila melanogaster)
Insecta Slip1 34
  • 18 (a)
(Caenorhabditis elegans)
Secernentea C50F7.6 34
  • 22 (a)
Species where no ortholog for PDZD4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • chicken (Gallus gallus)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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)

Evolution for PDZD4 Gene

Gene Tree for PDZD4 (if available)
Gene Tree for PDZD4 (if available)
Evolutionary constrained regions (ECRs) for PDZD4: view image

Paralogs for PDZD4 Gene

Paralogs for PDZD4 Gene

(3) SIMAP similar genes for PDZD4 Gene using alignment to 5 proteins:

  • Q17RL8_HUMAN
genes like me logo Genes that share paralogs with PDZD4: view

Variants for PDZD4 Gene

Sequence variations from dbSNP and Humsavar for PDZD4 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs782272149 A breast cancer sample 153,808,541(-) G/A 5_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant
rs1000424478 -- 153,806,194(-) C/A intron_variant
rs1000643431 -- 153,814,331(-) G/A intron_variant
rs1000796004 -- 153,832,469(-) C/T upstream_transcript_variant
rs1000912027 -- 153,832,054(-) G/C upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PDZD4 Gene

Variant ID Type Subtype PubMed ID
dgv4325n106 CNV deletion 24896259
esv33199 CNV gain+loss 17666407
esv3575025 CNV loss 25503493
nsv469867 CNV loss 16826518
nsv7159 CNV deletion 18451855

Variation tolerance for PDZD4 Gene

Residual Variation Intolerance Score: 6.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.48; 28.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDZD4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDZD4 Gene

Disorders for PDZD4 Gene

Additional Disease Information for PDZD4

No disorders were found for PDZD4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PDZD4 Gene

Publications for PDZD4 Gene

  1. Identification and characterization of human PDZRN4L gene and mouse Pdzrn4l gene in silico. (PMID: 15138636) Katoh M … Katoh M (International journal of molecular medicine 2004) 3 4 22 58
  2. Identification of PDZK4, a novel human gene with PDZ domains, that is upregulated in synovial sarcomas. (PMID: 15077175) Nagayama S … Nakamura Y (Oncogene 2004) 2 3 4 58
  3. Prediction of the coding sequences of unidentified human genes. XVII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10819331) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for PDZD4 Gene

Sources for PDZD4 Gene

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