USP30 ubiquitin specific peptidase 30 [Homo sapiens (human)] - Gene

Summary

Official Symbol: USP30provided by HGNC
Official Full Name: ubiquitin specific peptidase 30provided by HGNC
Primary source: HGNC:HGNC:20065
See related: Ensembl:ENSG00000135093 MIM:612492; AllianceGenome:HGNC:20065
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary: 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]
Expression: Ubiquitous expression in testis (RPKM 5.7), ovary (RPKM 5.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q24.11

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (109023089..109088023)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (108997903..109062835)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (109460894..109525828)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

LncRNA USP30-AS1 promotes the survival of acute myeloid leukemia cells by cis-regulating USP30 and ANKRD13A.
Title: LncRNA USP30-AS1 promotes the survival of acute myeloid leukemia cells by cis-regulating USP30 and ANKRD13A.
USP30 sets a trigger threshold for PINK1-PARKIN amplification of mitochondrial ubiquitylation.
Title: USP30 sets a trigger threshold for PINK1-PARKIN amplification of mitochondrial ubiquitylation.
The IKKbeta-USP30-ACLY Axis Controls Lipogenesis and Tumorigenesis.
Title: The IKKβ-USP30-ACLY Axis Controls Lipogenesis and Tumorigenesis.
Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues.
Title: Probing the Active Site of Deubiquitinase USP30 with Noncanonical Tryptophan Analogues.
Define the primary specificity of endogenous Parkin action on mitochondria, the abundance of ubiquitin proteoforms, the role of p97 in remodeling the mitochondrial proteome downstream of Parkin, and the target specificity of USP30 during mitophagic signaling.
Title: Global Landscape and Dynamics of Parkin and USP30-Dependent Ubiquitylomes in iNeurons during Mitophagic Signaling.
USP30 can rescue the peroxisome loss observed in some disease-causing peroxisome mutations, pointing to a potential therapeutic target.
Title: Deubiquitinating enzyme USP30 maintains basal peroxisome abundance by regulating pexophagy.
GNPAT and USP30-mediated stabilization of DRP1 play a critical role in the development of hepatocellular carcinoma
Title: Amplification of Glyceronephosphate O-Acyltransferase and Recruitment of USP30 Stabilize DRP1 to Promote Hepatocarcinogenesis.
we use two distinct mitophagy reporter systems to reveal tonic suppression by USP30, of a PINK1-dependent component of basal mitophagy in cells lacking detectable Parkin.
Title: Dual role of USP30 in controlling basal pexophagy and mitophagy.
the role of USP30 in the dynamic networks of mitochondrial quality control and its physiological implications.
Title: Beyond Deubiquitylation: USP30-Mediated Regulation of Mitochondrial Homeostasis.
Here the authors report crystal structures of human USP30 bound to monoubiquitin and Lys6-linked diubiquitin, which explain how USP30 achieves Lys6-linkage preference through unique ubiquitin binding interfaces.
Title: Mechanism and regulation of the Lys6-selective deubiquitinase USP30.

Submit: New GeneRIF Correction See all GeneRIFs (15)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH48223 (e-PCR)
- UniSTS:13588

RH45029 (e-PCR)
- UniSTS:8755

WI-20815 (e-PCR)
- UniSTS:1668

D20S1119 (e-PCR)
- UniSTS:40845

RH45951 (e-PCR)
- UniSTS:11230

STS-D60111 (e-PCR)
- UniSTS:57312

Homology

Homologs of the USP30 gene: The USP30 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, and frog.
Orthologs from Annotation Pipeline: 337 organisms have orthologs with human gene USP30
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables cysteine-type deubiquitinase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables cysteine-type deubiquitinase activity	IDA Inferred from Direct Assay more info	PubMed
enables cysteine-type deubiquitinase activity	TAS Traceable Author Statement more info
enables cysteine-type endopeptidase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables cysteine-type endopeptidase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables deubiquitinase activity	TAS Traceable Author Statement more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in autophagy of mitochondrion	IDA Inferred from Direct Assay more info	PubMed
involved_in autophagy of mitochondrion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrial fusion	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of mitophagy	IEA Inferred from Electronic Annotation more info
involved_in pexophagy	TAS Traceable Author Statement more info
involved_in protein K11-linked deubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein K6-linked deubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein deubiquitination	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in protein deubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein deubiquitination	TAS Traceable Author Statement more info
involved_in ubiquitin-dependent protein catabolic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in mitochondrial outer membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial outer membrane	TAS Traceable Author Statement more info
located_in mitochondrion	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in peroxisomal membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: ubiquitin carboxyl-terminal hydrolase 30

Names: deubiquitinating enzyme 30; ub-specific protease 30; ubiquitin thioesterase 30; ubiquitin thiolesterase 30; ubiquitin-specific protease 30; ubiquitin-specific-processing protease 30

NP_001288104.1

EC 3.4.19.12

NP_116052.2

EC 3.4.19.12

XP_005254019.1

EC 3.4.19.12

XP_005254022.1

EC 3.4.19.12

XP_016875537.1

EC 3.4.19.12

XP_016875538.1

EC 3.4.19.12

XP_016875539.1

EC 3.4.19.12

XP_016875540.1

EC 3.4.19.12

XP_016875541.1

EC 3.4.19.12

XP_016875542.1

EC 3.4.19.12

XP_047285688.1

EC 3.4.19.12

XP_047285689.1

EC 3.4.19.12

XP_047285690.1

EC 3.4.19.12

XP_047285691.1

EC 3.4.19.12

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001301175.2 → NP_001288104.1 ubiquitin carboxyl-terminal hydrolase 30 isoform 2

See identical proteins and their annotated locations for NP_001288104.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) has a different 5' structure, resulting in the use of a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AC011596, AK097830, AL834278, BX095894

Consensus CDS

CCDS76599.1

UniProtKB/Swiss-Prot

Q70CQ3

UniProtKB/TrEMBL

B3KUS5

Related

ENSP00000376535.2, ENST00000392784.6

Conserved Domains (2) summary

cd02662
Location:38 → 469

Peptidase_C19F; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

cl02553
Location:38 → 234

Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
NM_032663.5 → NP_116052.2 ubiquitin carboxyl-terminal hydrolase 30 isoform 1

See identical proteins and their annotated locations for NP_116052.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AC011596, AL834278, BC004868, BX095894, HY127211

Consensus CDS

CCDS9123.2

UniProtKB/Swiss-Prot

Q70CQ3, Q9BSS3

UniProtKB/TrEMBL

A0A024RBM3

Related

ENSP00000257548.5, ENST00000257548.10

Conserved Domains (2) summary

COG5560
Location:69 → 265

UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

cd02662
Location:69 → 500

Peptidase_C19F; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

109023089..109088023

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047429732.1 → XP_047285688.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X3
XM_017020052.3 → XP_016875541.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X3
XM_017020051.3 → XP_016875540.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X3
XM_017020048.2 → XP_016875537.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X1
XM_017020049.2 → XP_016875538.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X2
XM_005253962.4 → XP_005254019.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X4

See identical proteins and their annotated locations for XP_005254019.1

Conserved Domains (2) summary

COG5560
Location:69 → 264

UBP12; Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]

cd02662
Location:69 → 499

Peptidase_C19F; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
XM_017020053.2 → XP_016875542.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X5
XM_005253965.5 → XP_005254022.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X7

See identical proteins and their annotated locations for XP_005254022.1

Conserved Domains (1) summary

cd02662
Location:97 → 439

Peptidase_C19F; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
XM_047429734.1 → XP_047285690.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X8
XM_047429735.1 → XP_047285691.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X9
XM_047429733.1 → XP_047285689.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X6
XM_017020050.2 → XP_016875539.1 ubiquitin carboxyl-terminal hydrolase 30 isoform X3