USP30 Gene (Protein Coding)

Ubiquitin Specific Peptidase 30

GC12P109027
GIFtS:
41
USP30, a member of the ubiquitin-specific protease family (see USP1, MIM 603478), is a novel mitochondrial deubiquitinating (DUB) enzyme (Nakamura and Hirose, 2008 [PubMed 18287522]).[supplied by OMIM, Dec 2008] See more...

Aliases for USP30 Gene

Aliases for USP30 Gene

  • Ubiquitin Specific Peptidase 30 2 3 5
  • Ubiquitin-Specific-Processing Protease 30 3 4
  • Ubiquitin Carboxyl-Terminal Hydrolase 30 3 4
  • Deubiquitinating Enzyme 30 3 4
  • Ubiquitin Thioesterase 30 3 4
  • Ub-Specific Protease 30 3 4
  • Ubiquitin-Specific Protease 30 3
  • Ubiquitin Specific Protease 30 2
  • Ubiquitin Thiolesterase 30 3
  • EC 3.4.19.12 4
  • EC 3.1.2.15 52

External Ids for USP30 Gene

Previous GeneCards Identifiers for USP30 Gene

  • GC12P109354
  • GC12P107953
  • GC12P109460
  • GC12P106508

Summaries for USP30 Gene

Entrez Gene Summary for USP30 Gene

  • USP30, a member of the ubiquitin-specific protease family (see USP1, MIM 603478), is a novel mitochondrial deubiquitinating (DUB) enzyme (Nakamura and Hirose, 2008 [PubMed 18287522]).[supplied by OMIM, Dec 2008]

GeneCards Summary for USP30 Gene

USP30 (Ubiquitin Specific Peptidase 30) is a Protein Coding gene. Diseases associated with USP30 include 3-Methylglutaconic Aciduria, Type Iii. Among its related pathways are Metabolism of proteins and Ubiquitin-Proteasome Dependent Proteolysis. Gene Ontology (GO) annotations related to this gene include cysteine-type endopeptidase activity and thiol-dependent ubiquitin-specific protease activity. An important paralog of this gene is USP32.

UniProtKB/Swiss-Prot Summary for USP30 Gene

  • Deubiquitinating enzyme tethered to the mitochondrial outer membrane that acts as a key inhibitor of mitophagy by counteracting the action of parkin (PRKN): hydrolyzes ubiquitin attached by parkin on target proteins, such as RHOT1/MIRO1 and TOMM20, thereby blocking parkin's ability to drive mitophagy (PubMed:18287522, PubMed:24896179, PubMed:25527291, PubMed:25621951). Preferentially cleaves 'Lys-6'- and 'Lys-11'-linked polyubiquitin chains, 2 types of linkage that participate to mitophagic signaling (PubMed:25621951). Does not cleave efficiently polyubiquitin phosphorylated at 'Ser-65' (PubMed:25527291). Acts as negative regulator of mitochondrial fusion by mediating deubiquitination of MFN1 and MFN2 (By similarity).

Additional gene information for USP30 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for USP30 Gene

Genomics for USP30 Gene

GeneHancer (GH) Regulatory Elements for USP30 Gene

Promoters and enhancers for USP30 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
GH12J109051 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas 512.3 +30.2 30237 3.4 RXRA EP300 FOXK2 ZBTB40 ZNF217 ZSCAN5C SIN3A TCF12 POLR2G USF1 USP30 USP30-AS1 SART3 UBE3B WSCD2 TCHP piR-61945-106
GH12J109475 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 19.8 +454.3 454304 3.6 ZBTB40 ZNF217 EP300 ZSCAN5C SIN3A TCF12 POLR2G NCOR1 GTF2E2 PHF8 KCTD10 UBE3B IFT81 ALKBH2 FAM216A USP30 SART3 ARPC3 RNU4-32P ANKRD13A
GH12J108605 Enhancer 1.2 Ensembl CraniofacialAtlas dbSUPER 12 -417.0 -416989 1.8 EP300 NONO PHB2 RFX1 TSC22D4 TOE1 ZNF662 MXI1 MIER1 ARNT piR-41306-060 SART3 PWP1 ALKBH2 LOC101929162 PRDM4 UBE3B USP30 TMEM119 ISCU
GH12J108906 Enhancer 0.9 FANTOM5 ENCODE 12 -115.2 -115217 2.6 TEAD4 ZNF148 ZNF263 SPI1 ZFHX2 ZNF513 ZNF621 PKNOX1 POLR2A ZNF521 ALKBH2 SART3 USP30 DAO SVOP lnc-SVOP-1 RF00017-1252
GH12J108578 Enhancer 0.8 Ensembl ENCODE 12 -443.7 -443652 1.5 ZNF300 TSC22D4 ZNF585B SALL2 ZFHX2 YBX1 HDGF ESRRA ZNF521 ZNF785 PWP1 SART3 PRDM4 WSCD2 ALKBH2 USP30 KCTD10 UBE3B FICD TMEM119
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around USP30 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for USP30

Top Transcription factor binding sites by QIAGEN in the USP30 gene promoter:
  • AREB6
  • ATF-2
  • c-Ets-1
  • Elk-1
  • En-1
  • Hlf
  • PPAR-alpha
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for USP30 Gene

Genomic Locations for USP30 Gene
chr12:109,023,089-109,088,026
(GRCh38/hg38)
Size:
64,938 bases
Orientation:
Plus strand
chr12:109,460,894-109,525,831
(GRCh37/hg19)
Size:
64,938 bases
Orientation:
Plus strand

Genomic View for USP30 Gene

Genes around USP30 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP30 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP30 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for USP30 Gene

Proteins for USP30 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for USP30 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q70CQ3-UBP30_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 30
    Protein Accession:
    Q70CQ3
    Secondary Accessions:
    • Q8WTU7
    • Q96JX4
    • Q9BSS3

    Protein attributes for USP30 Gene

    Size:
    517 amino acids
    Molecular mass:
    58503 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH04868.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAB55392.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for USP30 Gene

neXtProt entry for USP30 Gene

Protein Expression for USP30 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for USP30 Gene

Q70CQ3:
  • HPFHGRLTS
  • AVVVHHG
  • VHHGDMHSGHF
  • GNTCFMN
  • FDSLSLSIP
  • GLVNLGN
  • AYLLFYE
  • NLGNTCF

Post-translational modifications for USP30 Gene

  • Ubiquitinated by parkin (PRKN) at Lys-235 and Lys-289, leading to its degradation.
  • Ubiquitination at Lys235 and Lys289
  • Modification sites at PhosphoSitePlus

Other Protein References for USP30 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for USP30
  • Boster Bio Antibodies for USP30
  • Santa Cruz Biotechnology (SCBT) Antibodies for USP30

Domains & Families for USP30 Gene

Gene Families for USP30 Gene

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

Protein Domains for USP30 Gene

Blocks:
  • Ubiquitin thiolesterase, family 2
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for USP30 Gene

GenScript: Design optimal peptide antigens:
  • Ubiquitin carboxyl-terminal hydrolase (B3KUS5_HUMAN)
  • Ubiquitin-specific-processing protease 30 (UBP30_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q70CQ3

UniProtKB/Swiss-Prot:

UBP30_HUMAN :
  • Belongs to the peptidase C19 family.
Family:
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP30: view

Function for USP30 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for USP30 Gene

UniProtKB/Swiss-Prot Function:
Deubiquitinating enzyme tethered to the mitochondrial outer membrane that acts as a key inhibitor of mitophagy by counteracting the action of parkin (PRKN): hydrolyzes ubiquitin attached by parkin on target proteins, such as RHOT1/MIRO1 and TOMM20, thereby blocking parkin's ability to drive mitophagy (PubMed:18287522, PubMed:24896179, PubMed:25527291, PubMed:25621951). Preferentially cleaves 'Lys-6'- and 'Lys-11'-linked polyubiquitin chains, 2 types of linkage that participate to mitophagic signaling (PubMed:25621951). Does not cleave efficiently polyubiquitin phosphorylated at 'Ser-65' (PubMed:25527291). Acts as negative regulator of mitochondrial fusion by mediating deubiquitination of MFN1 and MFN2 (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=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).; EC=3.4.19.12; Evidence=. ;.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by the diterpenoid derivative 15-oxospiramilactone (S3).

Enzyme Numbers (IUBMB) for USP30 Gene

Phenotypes From GWAS Catalog for USP30 Gene

Gene Ontology (GO) - Molecular Function for USP30 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004197 cysteine-type endopeptidase activity IMP 24896179
GO:0004843 thiol-dependent ubiquitin-specific protease activity IBA,IDA 14715245
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 USP30: view
genes like me logo Genes that share phenotypes with USP30: view

Animal Model Products

miRNA for USP30 Gene

miRTarBase miRNAs that target USP30

Clone Products

  • Addgene plasmids for USP30

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for USP30 Gene

Localization for USP30 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP30 Gene

Mitochondrion outer membrane.

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 USP30 gene
Compartment Confidence
mitochondrion 5
plasma membrane 2
peroxisome 2
nucleus 2
endoplasmic reticulum 2
cytosol 2
lysosome 2
extracellular 1
cytoskeleton 1
endosome 1

Gene Ontology (GO) - Cellular Components for USP30 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion ISS --
GO:0005741 mitochondrial outer membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with USP30: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for USP30 Gene

Pathways & Interactions for USP30 Gene

genes like me logo Genes that share pathways with USP30: view

Pathways by source for USP30 Gene

1 KEGG pathway for USP30 Gene
1 Qiagen pathway for USP30 Gene
  • Ubiquitin-Proteasome Dependent Proteolysis

Gene Ontology (GO) - Biological Process for USP30 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000422 autophagy of mitochondrion IMP 24896179
GO:0006508 proteolysis IEA --
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0008053 mitochondrial fusion ISS --
GO:0016579 protein deubiquitination IEA,TAS --
genes like me logo Genes that share ontologies with USP30: view

No data available for SIGNOR curated interactions for USP30 Gene

Drugs & Compounds for USP30 Gene

Products:

  1. Drug

(1) Drugs for USP30 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 USP30: view

Transcripts for USP30 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for USP30 Gene

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

Clone Products

  • Addgene plasmids for USP30

Alternative Splicing Database (ASD) splice patterns (SP) for USP30 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16a · 16b · 16c
SP1: - - - - -
SP2: - -
SP3:
SP4:
SP5: -
SP6:

Relevant External Links for USP30 Gene

GeneLoc Exon Structure for
USP30

Expression for USP30 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for USP30 Gene

mRNA expression in normal human tissues for USP30 Gene
mRNA expression by GTEx for USP30 GenemRNA expression by BioGPS for USP30 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for USP30 Gene

This gene is overexpressed in Fetal ovary (13.4), Frontal cortex (13.3), Testis (11.5), and Peripheral blood mononuclear cells (10.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for USP30 Gene



Protein tissue co-expression partners for USP30 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for USP30

SOURCE GeneReport for Unigene cluster for USP30 Gene:

Hs.486434

mRNA Expression by UniProt/SwissProt for USP30 Gene:

Q70CQ3-UBP30_HUMAN
Tissue specificity: Expressed in skeletal muscle, pancreas, liver and kidney.

Evidence on tissue expression from TISSUES for USP30 Gene

  • Lung(4.2)
  • Skin(4.1)
  • Nervous system(2.4)
genes like me logo Genes that share expression patterns with USP30: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for USP30 Gene

Orthologs for USP30 Gene

This gene was present in the common ancestor of animals.

Orthologs for USP30 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia USP30 31 30
  • 99.87 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia USP30 31 30
  • 89.93 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia USP30 31 30
  • 88.14 (n)
 OneToOne
mouse
(Mus musculus)
 Mammalia Usp30 17 31 30
  • 85.62 (n)
rat
(Rattus norvegicus)
 Mammalia Usp30 30
  • 85.56 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia USP30 31
  • 81 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia USP30 31
  • 70 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves USP30 31 30
  • 74.38 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia USP30 31
  • 78 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia usp30 30
  • 66.88 (n)
zebrafish
(Danio rerio)
 Actinopterygii LOC100537262 30
  • 62.85 (n)
USP30 (3 of 3) 31
  • 62 (a)
 OneToMany
usp30 31
  • 58 (a)
 OneToMany
USP30 (2 of 3) 31
  • 55 (a)
 OneToMany
fruit fly
(Drosophila melanogaster)
 Insecta CG3016 31 30
  • 48.95 (n)
 OneToOne
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP000269 30
  • 46.92 (n)
worm
(Caenorhabditis elegans)
 Secernentea Y67D2.2 31 30
  • 41.4 (n)
 OneToOne
Species where no ortholog for USP30 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 USP30 Gene

ENSEMBL:
Gene Tree for USP30 (if available)
TreeFam:
Gene Tree for USP30 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for USP30: view image

Paralogs for USP30 Gene

Paralogs for USP30 Gene

(7) SIMAP similar genes for USP30 Gene using alignment to 7 proteins:

  • UBP30_HUMAN
  • B3KUS5_HUMAN
  • F5GXG2_HUMAN
  • F5H3L3_HUMAN
  • F5H8D3_HUMAN
  • S4R354_HUMAN
  • S4R3D1_HUMAN
genes like me logo Genes that share paralogs with USP30: view

Variants for USP30 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for USP30 Gene

SNP ID Clinical significance and condition Chr 12 pos Variation AA Info Type
770233 Benign: not provided 109,067,525(+) C/A SYNONYMOUS_VARIANT
rs16939904 - p.His357Arg

Additional dbSNP identifiers (rs#s) for USP30 Gene

Structural Variations from Database of Genomic Variants (DGV) for USP30 Gene

Variant ID Type Subtype PubMed ID
dgv1553n100 CNV gain 25217958
esv1340901 CNV insertion 17803354
esv2422361 CNV duplication 17116639
nsv472373 CNV novel sequence insertion 20440878
nsv474986 CNV novel sequence insertion 20440878
nsv478748 CNV novel sequence insertion 20440878
nsv479881 CNV novel sequence insertion 20440878
nsv53822 CNV insertion 16902084

Variation tolerance for USP30 Gene

Residual Variation Intolerance Score: 32.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.40; 63.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for USP30 Gene

Human Gene Mutation Database (HGMD)
USP30
SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP30

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP30 Gene

Disorders for USP30 Gene

MalaCards: The human disease database

(1) MalaCards diseases for USP30 Gene - From: DISEASES

Disorder Aliases PubMed IDs
3-methylglutaconic aciduria, type iii
  • mgca3
- elite association - COSMIC cancer census association via MalaCards
Search USP30 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for USP30

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with USP30: view

No data available for UniProtKB/Swiss-Prot and Genatlas for USP30 Gene

Publications for USP30 Gene

  1. Regulation of mitochondrial morphology by USP30, a deubiquitinating enzyme present in the mitochondrial outer membrane. (PMID: 18287522) Nakamura N … Hirose S (Molecular biology of the cell 2008) 3 4 23 54
  2. Ubiquitin Ser65 phosphorylation affects ubiquitin structure, chain assembly and hydrolysis. (PMID: 25527291) Wauer T … Komander D (The EMBO journal 2015) 3 4 54
  3. USP30 and parkin homeostatically regulate atypical ubiquitin chains on mitochondria. (PMID: 25621951) Cunningham CN … Corn JE (Nature cell biology 2015) 3 4 54
  4. The mitochondrial deubiquitinase USP30 opposes parkin-mediated mitophagy. (PMID: 24896179) Bingol B … Sheng M (Nature 2014) 3 4 54
  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 54

ExternalLinks

View latest publications for USP30 gene in Mastermind

Products for USP30 Gene

  • Addgene plasmids for USP30

Sources for USP30 Gene