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Aliases for PDZRN3 Gene

Aliases for PDZRN3 Gene

  • PDZ Domain Containing Ring Finger 3 2 3 5
  • Likely Ortholog Of Mouse SemaF Cytoplasmic Domain Associated Protein 3 2 3
  • Semaphorin Cytoplasmic Domain-Associated Protein 3 3 4
  • RING-Type E3 Ubiquitin Transferase PDZRN3 3 4
  • Ligand Of Numb Protein X 3 3 4
  • SEMCAP3 3 4
  • LNX3 3 4
  • PDZ Domain-Containing RING Finger Protein 3 4
  • E3 Ubiquitin-Protein Ligase PDZRN3 3
  • Protein SEMACAP3 4
  • EC 4
  • SEMACAP3 3
  • KIAA1095 4

External Ids for PDZRN3 Gene

Previous GeneCards Identifiers for PDZRN3 Gene

  • GC03M073353
  • GC03M073514

Summaries for PDZRN3 Gene

Entrez Gene Summary for PDZRN3 Gene

  • This gene encodes a member of the LNX (Ligand of Numb Protein-X) family of RING-type ubiquitin E3 ligases. This protein may function in vascular morphogenesis and the differentiation of adipocytes, osteoblasts and myoblasts. This protein may be targeted for degradation by the human papilloma virus E6 protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]

GeneCards Summary for PDZRN3 Gene

PDZRN3 (PDZ Domain Containing Ring Finger 3) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include ligase activity and ubiquitin protein ligase activity. An important paralog of this gene is PDZRN4.

UniProtKB/Swiss-Prot for PDZRN3 Gene

  • E3 ubiquitin-protein ligase. Plays an important role in regulating the surface level of MUSK on myotubes. Mediates the ubiquitination of MUSK, promoting its endocytosis and lysosomal degradation. Might contribute to terminal myogenic differentiation.

Gene Wiki entry for PDZRN3 Gene

Additional gene information for PDZRN3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDZRN3 Gene

Genomics for PDZRN3 Gene

GeneHancer (GH) Regulatory Elements for PDZRN3 Gene

Promoters and enhancers for PDZRN3 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
GH03J073620 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 650.7 +1.4 1360 5.4 PKNOX1 SIN3A ZNF335 SCRT2 ZNF143 RCOR1 REST NR2F2 MTA1 ZSCAN16 ENSG00000278934 PDZRN3 PDZRN3-AS1 RNU7-119P
GH03J073569 Promoter/Enhancer 0.7 EPDnew dbSUPER 650.2 +55.5 55533 0.1 PDZRN3 RNU7-119P PIR59833 GC03M073571 LOC101927296
GH03J073508 Enhancer 1 Ensembl ENCODE dbSUPER 24.1 +113.2 113164 5.9 CTCF FOXA2 NANOG NFIA MZF1 YY1 OSR2 SP1 HNF1A PDZRN3 RNU7-119P LOC101927296 PIR42683
GH03J073516 Enhancer 0.7 ENCODE dbSUPER 28.9 +108.0 108034 1.4 SP1 FOXA2 RXRA FEZF1 ZNF2 NR2F2 PDZRN3 LOC101927296 PIR42683
GH03J073502 Enhancer 1.1 Ensembl ENCODE dbSUPER 17.3 +121.4 121363 2.2 CTCF ZBTB6 ZBTB21 EBF1 IRF4 RAD21 POLR2A SMC3 ZNF143 RCOR1 PDZRN3 RNU2-64P PIR42683 LOC101927296
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDZRN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDZRN3 gene promoter:
  • Bach1
  • Meis-1b
  • Meis-1
  • HOXA9B
  • HOXA9
  • Lmo2
  • Egr-2
  • Pax-6
  • FOXD1
  • HNF-4alpha1

Genomic Locations for PDZRN3 Gene

Genomic Locations for PDZRN3 Gene
242,511 bases
Minus strand
242,508 bases
Minus strand

Genomic View for PDZRN3 Gene

Genes around PDZRN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDZRN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDZRN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDZRN3 Gene

Proteins for PDZRN3 Gene

  • Protein details for PDZRN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    E3 ubiquitin-protein ligase PDZRN3
    Protein Accession:
    Secondary Accessions:
    • A7MCZ6
    • Q8N2N7
    • Q96CC2
    • Q9NSQ2

    Protein attributes for PDZRN3 Gene

    1066 amino acids
    Molecular mass:
    119596 Da
    Quaternary structure:
    • Interacts with NLGN1 and EFNB2. Interacts with UBE2D2 and with MUSK via the first PDZ domain.
    • Sequence=BAA83047.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC11068.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PDZRN3 Gene

    Alternative splice isoforms for PDZRN3 Gene


neXtProt entry for PDZRN3 Gene

Post-translational modifications for PDZRN3 Gene

No data available for DME Specific Peptides for PDZRN3 Gene

Domains & Families for PDZRN3 Gene

Gene Families for PDZRN3 Gene

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

Protein Domains for PDZRN3 Gene

Graphical View of Domain Structure for InterPro Entry



  • The RING-type zinc finger domain is required for E3 ligase activity.
  • The RING-type zinc finger domain is required for E3 ligase activity.
genes like me logo Genes that share domains with PDZRN3: view

Function for PDZRN3 Gene

Molecular function for PDZRN3 Gene

UniProtKB/Swiss-Prot Function:
E3 ubiquitin-protein ligase. Plays an important role in regulating the surface level of MUSK on myotubes. Mediates the ubiquitination of MUSK, promoting its endocytosis and lysosomal degradation. Might contribute to terminal myogenic differentiation.
UniProtKB/Swiss-Prot CatalyticActivity:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.

Enzyme Numbers (IUBMB) for PDZRN3 Gene

Phenotypes From GWAS Catalog for PDZRN3 Gene

Gene Ontology (GO) - Molecular Function for PDZRN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004842 ubiquitin-protein transferase activity ISS --
GO:0005515 protein binding IEA --
GO:0008270 zinc ion binding IEA --
GO:0016740 transferase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PDZRN3: view
genes like me logo Genes that share phenotypes with PDZRN3: view

Animal Model Products

miRNA for PDZRN3 Gene

miRTarBase miRNAs that target PDZRN3

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDZRN3 Gene

Localization for PDZRN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDZRN3 Gene

Cell junction, synapse. Cytoplasm. Note=Localizes to the postsynaptic region of neuromuscular junctions. {ECO:0000250 UniProtKB:Q69ZS0}.

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 PDZRN3 gene
Compartment Confidence
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PDZRN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IDA --
GO:0030054 cell junction IEA --
genes like me logo Genes that share ontologies with PDZRN3: view

Pathways & Interactions for PDZRN3 Gene

SuperPathways for PDZRN3 Gene

No Data Available

UniProtKB/Swiss-Prot Q9UPQ7-PZRN3_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for PDZRN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007528 neuromuscular junction development IBA --
GO:0016567 protein ubiquitination ISS --
genes like me logo Genes that share ontologies with PDZRN3: view

No data available for Pathways by source and SIGNOR curated interactions for PDZRN3 Gene

Drugs & Compounds for PDZRN3 Gene

No Compound Related Data Available

Transcripts for PDZRN3 Gene

Unigene Clusters for PDZRN3 Gene

PDZ domain containing ring finger 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDZRN3 Gene

No ASD Table

Relevant External Links for PDZRN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PDZRN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDZRN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDZRN3 Gene

This gene is overexpressed in Gallbladder (43.3) and Adipocyte (16.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PDZRN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of PDZRN3 Gene:


SOURCE GeneReport for Unigene cluster for PDZRN3 Gene:


mRNA Expression by UniProt/SwissProt for PDZRN3 Gene:

Tissue specificity: Widely expressed, including in the heart, skeletal muscle and liver and, at lower levels, in the brain, colon, small intestine, placenta and lung. Down-regulated in ovarian serous papillary tumors.

Evidence on tissue expression from TISSUES for PDZRN3 Gene

  • Nervous system(4.6)
  • Skin(4.2)
genes like me logo Genes that share expression patterns with PDZRN3: 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 PDZRN3 Gene

Orthologs for PDZRN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDZRN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PDZRN3 34 33
  • 99.59 (n)
(Bos Taurus)
Mammalia PDZRN3 34 33
  • 90.6 (n)
(Mus musculus)
Mammalia Pdzrn3 16 34 33
  • 88.61 (n)
(Rattus norvegicus)
Mammalia Pdzrn3 33
  • 88.58 (n)
(Monodelphis domestica)
Mammalia PDZRN3 34
  • 85 (a)
(Canis familiaris)
Mammalia PDZRN3 34
  • 83 (a)
(Ornithorhynchus anatinus)
Mammalia PDZRN3 34
  • 71 (a)
(Gallus gallus)
Aves PDZRN3 34 33
  • 78.07 (n)
(Anolis carolinensis)
Reptilia PDZRN3 34
  • 81 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pdzrn3 33
  • 72.96 (n)
(Danio rerio)
Actinopterygii pdzrn3b 34 33
  • 70.13 (n)
pdzrn3a 34
  • 50 (a)
Dr.5264 33
fruit fly
(Drosophila melanogaster)
Insecta Slip1 34
  • 16 (a)
(Caenorhabditis elegans)
Secernentea C50F7.6 34
  • 22 (a)
Species where no ortholog for PDZRN3 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)
  • 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 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 PDZRN3 Gene

Gene Tree for PDZRN3 (if available)
Gene Tree for PDZRN3 (if available)
Evolutionary constrained regions (ECRs) for PDZRN3: view image

Paralogs for PDZRN3 Gene

Paralogs for PDZRN3 Gene

(6) SIMAP similar genes for PDZRN3 Gene using alignment to 9 proteins:

  • B7Z2I8_HUMAN
  • F5H8I9_HUMAN
  • H7C566_HUMAN
  • L8E852_HUMAN
genes like me logo Genes that share paralogs with PDZRN3: view

Variants for PDZRN3 Gene

Sequence variations from dbSNP and Humsavar for PDZRN3 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs748809996 likely-pathogenic, Childhood-Onset Schizophrenia 73,602,452(-) C/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs1000037222 -- 73,579,565(-) G/C genic_upstream_transcript_variant, intron_variant
rs1000042584 -- 73,463,864(-) T/G genic_upstream_transcript_variant, intron_variant
rs1000090224 -- 73,517,165(-) T/A genic_upstream_transcript_variant, intron_variant
rs1000094196 -- 73,573,009(-) G/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PDZRN3 Gene

Variant ID Type Subtype PubMed ID
esv24230 CNV loss 19812545
esv3310131 CNV mobile element insertion 20981092
esv3381647 CNV insertion 20981092
esv3596558 CNV loss 21293372
nsv236186 CNV deletion 16902084
nsv3878 CNV insertion 18451855
nsv520326 CNV loss 19592680
nsv525749 CNV loss 19592680
nsv526832 CNV gain 19592680
nsv590636 CNV gain 21841781
nsv590637 CNV gain+loss 21841781
nsv590638 CNV loss 21841781
nsv590639 CNV gain 21841781
nsv834730 CNV loss 17160897
nsv834731 CNV gain 17160897

Variation tolerance for PDZRN3 Gene

Residual Variation Intolerance Score: 18% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.23; 81.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDZRN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDZRN3 Gene

Disorders for PDZRN3 Gene

Additional Disease Information for PDZRN3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PDZRN3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PDZRN3 Gene

Publications for PDZRN3 Gene

  1. PDZRN3 (LNX3, SEMCAP3) is required for the differentiation of C2C12 myoblasts into myotubes. (PMID: 17118964) Ko JA … Inui M (Journal of cell science 2006) 3 4 22 58
  2. Identification and characterization of PDZRN3 and PDZRN4 genes in silico. (PMID: 15010864) Katoh M … Katoh M (International journal of molecular medicine 2004) 3 4 22 58
  3. Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10470851) Kikuno R … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1999) 2 3 4 58
  4. Genome-wide association scan for survival on dialysis in African-Americans with type 2 diabetes. (PMID: 21546767) Murea M … Freedman BI (American journal of nephrology 2011) 3 44 58
  5. 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 44 58

Products for PDZRN3 Gene

Sources for PDZRN3 Gene

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