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Aliases for USP46 Gene

Aliases for USP46 Gene

  • Ubiquitin Specific Peptidase 46 2 3 5
  • Ubiquitin-Specific-Processing Protease 46 4
  • Ubiquitin Specific Protease 46 2
  • Deubiquitinating Enzyme 46 4
  • Ubiquitin Thioesterase 46 4
  • EC 4
  • EC 56

External Ids for USP46 Gene

Previous GeneCards Identifiers for USP46 Gene

  • GC04M053311
  • GC04M053376
  • GC04M053302
  • GC04M053155
  • GC04M049398

Summaries for USP46 Gene

Entrez Gene Summary for USP46 Gene

  • Modification of cellular proteins by ubiquitin is an essential regulatory mechanism controlled by the coordinated action of multiple ubiquitin-conjugating and deubiquitinating enzymes. USP46 belongs to a large family of cysteine proteases that function as deubiquitinating enzymes (Quesada et al., 2004 [PubMed 14715245]).[supplied by OMIM, Jun 2009]

GeneCards Summary for USP46 Gene

USP46 (Ubiquitin Specific Peptidase 46) is a Protein Coding gene. Among its related pathways are Ubiquitin-Proteasome Dependent Proteolysis. Gene Ontology (GO) annotations related to this gene include thiol-dependent ubiquitin-specific protease activity and obsolete ubiquitin thiolesterase activity. An important paralog of this gene is USP12.

UniProtKB/Swiss-Prot for USP46 Gene

  • Deubiquitinating enzyme that plays a role in behavior, possibly by regulating GABA action. May act by mediating the deubiquitination of GAD1/GAD67 (By similarity). Has almost no deubiquitinating activity by itself and requires the interaction with WDR48 to have a high activity (PubMed:19075014, PubMed:26388029). Not involved in deubiquitination of monoubiquitinated FANCD2 (PubMed:19075014).

Additional gene information for USP46 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP46 Gene

Genomics for USP46 Gene

GeneHancer (GH) Regulatory Elements for USP46 Gene

Promoters and enhancers for USP46 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
GH04I052657 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 562.1 +0.3 347 3.7 HDAC1 SIN3A DMAP1 YY1 ZNF335 SCRT2 ZNF143 BCLAF1 SMAD5 ZBTB11 USP46 USP46-AS1 RNU6-1252P
GH04I052656 Promoter 0.6 EPDnew 550.8 +2.8 2776 0.1 HLF USP46 RNU6-1252P
GH04I052588 Enhancer 0.8 Ensembl ENCODE 21.8 +70.2 70237 2 MEIS2 CTCF JUN ETV1 ATF2 RAD21 POLR2A SMC3 ZNF143 ZSCAN29 USP46 USP46-AS1 ENSG00000212490 ERVMER34-1 RNU6-1252P
GH04I052640 Enhancer 1 Ensembl ENCODE 11.7 +16.9 16893 3.9 PKNOX1 INSM2 BMI1 FEZF1 ZBTB40 BATF IRF4 ATF7 FOS IKZF2 USP46 DANCR SNORA26 RNU6-1252P
GH04I052721 Enhancer 1.1 Ensembl ENCODE 10.2 -63.2 -63163 1.8 HDGF PKNOX1 SIN3A BRCA1 YY1 GLIS2 ZNF143 KLF7 FOS RUNX3 ENSG00000248375 FIP1L1 ERVMER34-1 ENSG00000212490 USP46 RASL11B GC04P052749
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around USP46 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the USP46 gene promoter:

Genomic Locations for USP46 Gene

Genomic Locations for USP46 Gene
68,376 bases
Minus strand

Genomic View for USP46 Gene

Genes around USP46 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP46 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP46 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP46 Gene

Proteins for USP46 Gene

  • Protein details for USP46 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 46
    Protein Accession:
    Secondary Accessions:
    • B7Z3Y7
    • B7Z675
    • B7Z7S3
    • G8ACC7
    • Q80V95
    • Q9H7U4
    • Q9H9T8

    Protein attributes for USP46 Gene

    366 amino acids
    Molecular mass:
    42442 Da
    Quaternary structure:
    • Interacts with WDR48 (PubMed:19075014, PubMed:26388029). Interacts with WDR20 (PubMed:20147737).

    Three dimensional structures from OCA and Proteopedia for USP46 Gene

    Alternative splice isoforms for USP46 Gene


neXtProt entry for USP46 Gene

Selected DME Specific Peptides for USP46 Gene


Post-translational modifications for USP46 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for USP46 Gene

Gene Families for USP46 Gene

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

Protein Domains for USP46 Gene

Suggested Antigen Peptide Sequences for USP46 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase C19 family. USP12/USP46 subfamily.
  • Belongs to the peptidase C19 family. USP12/USP46 subfamily.
genes like me logo Genes that share domains with USP46: view

Function for USP46 Gene

Molecular function for USP46 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
UniProtKB/Swiss-Prot EnzymeRegulation:
Activated by interaction with WDR48.
UniProtKB/Swiss-Prot Function:
Deubiquitinating enzyme that plays a role in behavior, possibly by regulating GABA action. May act by mediating the deubiquitination of GAD1/GAD67 (By similarity). Has almost no deubiquitinating activity by itself and requires the interaction with WDR48 to have a high activity (PubMed:19075014, PubMed:26388029). Not involved in deubiquitination of monoubiquitinated FANCD2 (PubMed:19075014).

Enzyme Numbers (IUBMB) for USP46 Gene

Phenotypes From GWAS Catalog for USP46 Gene

Gene Ontology (GO) - Molecular Function for USP46 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004843 thiol-dependent ubiquitin-specific protease activity IDA 14715245
GO:0005515 protein binding IPI 19075014
GO:0008233 peptidase activity IEA --
GO:0008234 cysteine-type peptidase activity IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with USP46: view
genes like me logo Genes that share phenotypes with USP46: view

Clone Products

  • Addgene plasmids for USP46

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for USP46 Gene

Localization for USP46 Gene

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 USP46 gene
Compartment Confidence
cytosol 2
mitochondrion 1
nucleus 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for USP46 Gene

Pathways & Interactions for USP46 Gene

genes like me logo Genes that share pathways with USP46: view

Pathways by source for USP46 Gene

1 Qiagen pathway for USP46 Gene

Gene Ontology (GO) - Biological Process for USP46 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001662 behavioral fear response IEA --
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0007610 behavior IEA --
GO:0008343 adult feeding behavior IEA --
genes like me logo Genes that share ontologies with USP46: view

No data available for SIGNOR curated interactions for USP46 Gene

Drugs & Compounds for USP46 Gene

(1) Drugs for USP46 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
genes like me logo Genes that share compounds with USP46: view

Transcripts for USP46 Gene

Unigene Clusters for USP46 Gene

Ubiquitin specific peptidase 46:
Representative Sequences:

Clone Products

  • Addgene plasmids for USP46

Alternative Splicing Database (ASD) splice patterns (SP) for USP46 Gene

ExUns: 1 ^ 2a · 2b · 2c · 2d ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c · 7d ^ 8a · 8b · 8c ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b
SP1: -
SP3: - - - - - - - -
SP5: - - - - -
SP6: - - -
SP7: - - - -

Relevant External Links for USP46 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for USP46 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for USP46 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for USP46 Gene

This gene is overexpressed in Spinal cord (16.8), Retina (12.2), and Frontal cortex (11.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for USP46 Gene

Protein tissue co-expression partners for USP46 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of USP46 Gene:


SOURCE GeneReport for Unigene cluster for USP46 Gene:


mRNA Expression by UniProt/SwissProt for USP46 Gene:

Tissue specificity: Broadly expressed.

Evidence on tissue expression from TISSUES for USP46 Gene

  • Nervous system(4.9)
genes like me logo Genes that share expression patterns with USP46: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for USP46 Gene

Orthologs for USP46 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for USP46 Gene

Organism Taxonomy Gene Similarity Type Details
(Monodelphis domestica)
Mammalia USP46 34
  • 100 (a)
(Pan troglodytes)
Mammalia USP46 33 34
  • 99.64 (n)
(Ornithorhynchus anatinus)
Mammalia USP46 34
  • 97 (a)
(Bos Taurus)
Mammalia USP46 33 34
  • 93.99 (n)
(Canis familiaris)
Mammalia USP46 33 34
  • 93.52 (n)
(Mus musculus)
Mammalia Usp46 33 16 34
  • 93.08 (n)
(Rattus norvegicus)
Mammalia Usp46 33
  • 92.9 (n)
(Gallus gallus)
Aves USP46 33 34
  • 87.61 (n)
(Anolis carolinensis)
Reptilia USP46 34
  • 97 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia usp46 33
  • 78.72 (n)
(Danio rerio)
Actinopterygii usp46 33 34
  • 79.36 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG7023 33 34
  • 69.2 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012139 33
  • 68.08 (n)
(Caenorhabditis elegans)
Secernentea usp-46 33 34
  • 66.67 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AGR370W 33
  • 53.33 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E20351g 33
  • 52.49 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP9 33 34
  • 51.94 (n)
UBP13 34
  • 18 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons UBP3 33
  • 62.37 (n)
(Glycine max)
eudicotyledons Gma.2460 33
(Oryza sativa)
Liliopsida Os04g0452400 33
  • 61.96 (n)
(Zea mays)
Liliopsida Zm.8954 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 55 (a)
Species where no ortholog for USP46 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for USP46 Gene

Gene Tree for USP46 (if available)
Gene Tree for USP46 (if available)

Paralogs for USP46 Gene

Paralogs for USP46 Gene

(1) SIMAP similar genes for USP46 Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with USP46: view

Variants for USP46 Gene

Sequence variations from dbSNP and Humsavar for USP46 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000025493 -- 52,629,409(-) TCTCT/TCT intron_variant
rs10000311 -- 52,641,778(-) T/C intron_variant
rs1000092592 -- 52,622,400(-) T/A/C intron_variant
rs10001370 -- 52,597,564(-) G/A 3_prime_UTR_variant
rs10001387 -- 52,627,743(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for USP46 Gene

Variant ID Type Subtype PubMed ID
esv2105142 CNV deletion 18987734
esv2727602 CNV deletion 23290073
nsv1074712 CNV deletion 25765185
nsv1109610 CNV deletion 24896259
nsv1117091 CNV deletion 24896259
nsv475935 CNV novel sequence insertion 20440878
nsv478096 CNV novel sequence insertion 20440878
nsv524494 CNV loss 19592680
nsv594201 CNV loss 21841781

Variation tolerance for USP46 Gene

Residual Variation Intolerance Score: 36.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.28; 6.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for USP46 Gene

Human Gene Mutation Database (HGMD)
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 USP46 Gene

Disorders for USP46 Gene

Additional Disease Information for USP46

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

No disorders were found for USP46 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP46 Gene

Publications for USP46 Gene

  1. A conserved two-step binding for the UAF1 regulator to the USP12 deubiquitinating enzyme. (PMID: 27650958) Dharadhar S … Sixma TK (Journal of structural biology 2016) 3 4 58
  2. Structural Insights into WD-Repeat 48 Activation of Ubiquitin-Specific Protease 46. (PMID: 26388029) Yin J … Harris SF (Structure (London, England : 1993) 2015) 3 4 58
  3. Lysine 92 amino acid residue of USP46, a gene associated with 'behavioral despair' in mice, influences the deubiquitinating enzyme activity. (PMID: 22043315) Zhang W … Wang MW (PloS one 2011) 3 4 58
  4. Association study of ubiquitin-specific peptidase 46 (USP46) with bipolar disorder and schizophrenia in a Japanese population. (PMID: 20111060) Kushima I … Ozaki N (Journal of human genetics 2010) 3 44 58
  5. WDR20 regulates activity of the USP12 x UAF1 deubiquitinating enzyme complex. (PMID: 20147737) Kee Y … D'Andrea AD (The Journal of biological chemistry 2010) 3 4 58

Products for USP46 Gene

  • Addgene plasmids for USP46

Sources for USP46 Gene

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