USP9X ubiquitin specific peptidase 9 X-linked [Homo sapiens (human)] - Gene

Summary

Official Symbol: USP9Xprovided by HGNC
Official Full Name: ubiquitin specific peptidase 9 X-linkedprovided by HGNC
Primary source: HGNC:HGNC:12632
See related: Ensembl:ENSG00000124486 MIM:300072; AllianceGenome:HGNC:12632
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: FAF; FAM; hFAM; DFFRX; FAF-X; MRX99; XLID99; MRXS99F
Summary: This gene is a member of the peptidase C19 family and encodes a protein that is similar to ubiquitin-specific proteases. Though this gene is located on the X chromosome, it escapes X-inactivation. Mutations in this gene have been associated with Turner syndrome. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in testis (RPKM 14.2), thyroid (RPKM 14.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xp11.4

Exon count:: 46

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (41085445..41236579)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (40487470..40638605)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (40944698..41095832)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

USP9X regulates the proliferation, survival, migration and invasion of gastric cancer cells by stabilizing MTH1.
Title: USP9X regulates the proliferation, survival, migration and invasion of gastric cancer cells by stabilizing MTH1.
USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle.
Title: USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle.
Deubiquitinase USP9X stabilizes RNA m[6]A demethylase ALKBH5 and promotes acute myeloid leukemia cell survival.
Title: Deubiquitinase USP9X stabilizes RNA m(6)A demethylase ALKBH5 and promotes acute myeloid leukemia cell survival.
Deubiquitinase USP9X loss sensitizes renal cancer cells to mTOR inhibition.
Title: Deubiquitinase USP9X loss sensitizes renal cancer cells to mTOR inhibition.
USP9X mediates an acute adaptive response to MAPK suppression in pancreatic cancer but creates multiple actionable therapeutic vulnerabilities.
Title: USP9X mediates an acute adaptive response to MAPK suppression in pancreatic cancer but creates multiple actionable therapeutic vulnerabilities.
KSHV Viral Protein Kinase Interacts with USP9X to Modulate the Viral Lifecycle.
Title: KSHV Viral Protein Kinase Interacts with USP9X to Modulate the Viral Lifecycle.
USP9X promotes lipopolysaccharide-stimulated acute lung injury by deubiquitination of NLRP3.
Title: USP9X promotes lipopolysaccharide-stimulated acute lung injury by deubiquitination of NLRP3.
Ablation of EWS-FLI1 by USP9X inhibition suppresses cancer cell growth in Ewing sarcoma.
Title: Ablation of EWS-FLI1 by USP9X inhibition suppresses cancer cell growth in Ewing sarcoma.
Down-Regulation of Ubiquitin-Specific Peptidase 9X Inhibited Proliferation, Migration and Invasion of Osteosarcoma via ERK1/2 and PI3K/Akt Signaling Pathways.
Title: Down-Regulation of Ubiquitin-Specific Peptidase 9X Inhibited Proliferation, Migration and Invasion of Osteosarcoma via ERK1/2 and PI3K/Akt Signaling Pathways.
Deubiquitinating enzyme USP9X regulates metastasis and chemoresistance in triple-negative breast cancer by stabilizing Snail1.
Title: Deubiquitinating enzyme USP9X regulates metastasis and chemoresistance in triple-negative breast cancer by stabilizing Snail1.

Submit: New GeneRIF Correction See all GeneRIFs (108)

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

Associated conditions

Description	Tests
Intellectual disability, X-linked 99 MedGen: C3806746 OMIM: 300919 GeneReviews: Not available	Compare labs
Intellectual disability, X-linked 99, syndromic, female-restricted MedGen: C4225416 OMIM: 300968 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2018-03-28) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2018-03-28) ClinGen Genome Curation PagePubMed

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

DXS1454 (e-PCR)
- UniSTS:41480

RH103992 (e-PCR)
- UniSTS:98317

SHGC-34697 (e-PCR)
- UniSTS:68110

USP9X_3261 (e-PCR)
- UniSTS:462609

STS-N26828 (e-PCR)
- UniSTS:81430

PLP1 (e-PCR)
- UniSTS:480290

WI-11070 (e-PCR)
- UniSTS:19246

SGC30689 (e-PCR)
- UniSTS:68914

RH125670 (e-PCR)
- UniSTS:162451

DFFR (e-PCR)
- UniSTS:266900

DXS7601 (e-PCR)
- UniSTS:99486

G49472 (e-PCR)
- UniSTS:109214

RH70211 (e-PCR)
- UniSTS:31396

BG371737 (e-PCR)
- UniSTS:248752

RH48141 (e-PCR)
- UniSTS:52151

RH47975 (e-PCR)
- UniSTS:30142

DXS9725 (e-PCR)
- UniSTS:37847

G34982 (e-PCR)
- UniSTS:33001

D11S3316 (e-PCR)
- UniSTS:152558

D20S998 (e-PCR)
- UniSTS:154615

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables K11-linked deubiquitinase activity	IDA Inferred from Direct Assay more info	PubMed
enables K48-linked deubiquitinase activity	IDA Inferred from Direct Assay more info	PubMed
enables K63-linked deubiquitinase activity	IDA Inferred from Direct Assay more info	PubMed
enables co-SMAD binding	IPI Inferred from Physical Interaction more info	PubMed
enables cysteine-type deubiquitinase activity	EXP Inferred from Experiment more info	PubMed
enables cysteine-type deubiquitinase activity	IBA Inferred from Biological aspect of Ancestor more info
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	ISS Inferred from Sequence or Structural Similarity more info
enables cysteine-type peptidase activity	TAS Traceable Author Statement more info
enables deubiquitinase activity	IDA Inferred from Direct Assay more info	PubMed
enables deubiquitinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables molecular sequestering activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in BMP signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA alkylation repair	IDA Inferred from Direct Assay more info	PubMed
involved_in amyloid fibril formation	TAS Traceable Author Statement more info
involved_in axon extension	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromosome segregation	IEA Inferred from Electronic Annotation more info
involved_in cilium assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in cytosolic ciliogenesis	IDA Inferred from Direct Assay more info	PubMed
involved_in female gamete generation	TAS Traceable Author Statement more info	PubMed
involved_in monoubiquitinated protein deubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of proteasomal ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	TAS Traceable Author Statement more info
involved_in neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of TORC2 signaling	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein binding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein K63-linked deubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein deubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein deubiquitination	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein deubiquitination	TAS Traceable Author Statement more info
involved_in protein deubiquitination involved in ubiquitin-dependent protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein import into peroxisome matrix, receptor recycling	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization	TAS Traceable Author Statement more info
involved_in protein stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	TAS Traceable Author Statement more info
involved_in regulation of circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein stability	IBA Inferred from Biological aspect of Ancestor more info
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info
involved_in transforming growth factor beta receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytosol	IBA Inferred from Biological aspect of Ancestor more info
is_active_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in growth cone	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: ubiquitin carboxyl-terminal hydrolase 9X

Names: Drosophila fat facets related, X-linked; deubiquitinating enzyme FAF-X; fat facets in mammals; fat facets protein related, X-linked; fat facets-like, X-linked; probable ubiquitin carboxyl-terminal hydrolase FAF-X; ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila); ubiquitin thioesterase FAF-X; ubiquitin thiolesterase FAF-X; ubiquitin-specific processing protease FAF-X; ubiquitin-specific protease 9, X chromosome

NP_001034679.2

EC 3.4.19.12

NP_001034680.2

EC 3.4.19.12

NP_001397677.1

EC 3.4.19.12

NP_001397678.1

EC 3.4.19.12

XP_005272732.1

EC 3.4.19.12

XP_005272733.1

EC 3.4.19.12

XP_047298504.1

EC 3.4.19.12

XP_047298506.1

EC 3.4.19.12

XP_054183906.1

EC 3.4.19.12

XP_054183907.1

EC 3.4.19.12

XP_054183908.1

EC 3.4.19.12

XP_054183909.1

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.

Genomic

NG_012547.1 RefSeqGene

Range

4811..155945

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001039590.3 → NP_001034679.2 ubiquitin carboxyl-terminal hydrolase 9X isoform 3

See identical proteins and their annotated locations for NP_001034679.2

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents the longer transcript and encodes the longer isoform (3).

Source sequence(s)

AA261797, AF070645, AL109797, AL391259, AW183065, BC063645, BE925861, BX956755, CD619095, DA854185, X98296

Consensus CDS

CCDS43930.1

UniProtKB/TrEMBL

A0A994J4T3

Related

ENSP00000316357.6, ENST00000324545.9

Conserved Domains (1) summary

cd02659
Location:1555 → 1958

peptidase_C19C; 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 ...
NM_001039591.3 → NP_001034680.2 ubiquitin carboxyl-terminal hydrolase 9X isoform 4

See identical proteins and their annotated locations for NP_001034680.2

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses an alternate in-frame splice site at the 3' end of an exon compared to variant 3. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 3.

Source sequence(s)

AA261797, AL109797, AL391259, AW183065, BC046205, BC063645, BE925861, BX956755, CD619095, DA854185, X98296

Consensus CDS

CCDS55403.1

UniProtKB/Swiss-Prot

O75550, Q8WWT3, Q8WX12, Q93008

UniProtKB/TrEMBL

A0A994J4T3

Related

ENSP00000367558.2, ENST00000378308.7

Conserved Domains (3) summary

cd02659
Location:1555 → 1958

peptidase_C19C; 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 ...

pfam12030
Location:2097 → 2476

DUF3517; Domain of unknown function (DUF3517)

cl28922
Location:900 → 964

Ubiquitin_like_fold; Beta-grasp ubiquitin-like fold
NM_001410748.1 → NP_001397677.1 ubiquitin carboxyl-terminal hydrolase 9X isoform 5

Status: REVIEWED

Source sequence(s)

AL109797, AL391259

Consensus CDS

CCDS94594.1

UniProtKB/TrEMBL

A0A994J4R6
NM_001410749.1 → NP_001397678.1 ubiquitin carboxyl-terminal hydrolase 9X isoform 6

Status: REVIEWED

Source sequence(s)

AL109797, AL391259

Consensus CDS

CCDS94593.1

UniProtKB/TrEMBL

A0A994J6S4

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

41085445..41236579

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047442548.1 → XP_047298504.1 ubiquitin carboxyl-terminal hydrolase 9X isoform X2
XM_047442550.1 → XP_047298506.1 ubiquitin carboxyl-terminal hydrolase 9X isoform X4

UniProtKB/Swiss-Prot

O75550, Q8WWT3, Q8WX12, Q93008
XM_005272675.5 → XP_005272732.1 ubiquitin carboxyl-terminal hydrolase 9X isoform X1

See identical proteins and their annotated locations for XP_005272732.1

UniProtKB/TrEMBL

A0A994J4R6, A0A994J4T3

Related

ENSP00000515604.1, ENST00000703987.1

Conserved Domains (2) summary

cd02659
Location:1560 → 1963

peptidase_C19C; 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 ...

pfam00443
Location:1562 → 1958

UCH; Ubiquitin carboxyl-terminal hydrolase
XM_005272676.5 → XP_005272733.1 ubiquitin carboxyl-terminal hydrolase 9X isoform X3

See identical proteins and their annotated locations for XP_005272733.1

UniProtKB/TrEMBL

A0A994J4T3, A0A994J6S4

Related

ENSP00000515603.1, ENST00000703986.1

Conserved Domains (2) summary

cd02659
Location:1560 → 1963

peptidase_C19C; 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 ...

pfam00443
Location:1562 → 1958

UCH; Ubiquitin carboxyl-terminal hydrolase

Alternate T2T-CHM13v2.0

Genomic

NC_060947.1 Alternate T2T-CHM13v2.0

Range

40487470..40638605

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054327932.1 → XP_054183907.1 ubiquitin carboxyl-terminal hydrolase 9X isoform X2
XM_054327934.1 → XP_054183909.1 ubiquitin carboxyl-terminal hydrolase 9X isoform X4

UniProtKB/Swiss-Prot

O75550, Q8WWT3, Q8WX12, Q93008
XM_054327931.1 → XP_054183906.1 ubiquitin carboxyl-terminal hydrolase 9X isoform X1

UniProtKB/TrEMBL

A0A994J4R6
XM_054327933.1 → XP_054183908.1 ubiquitin carboxyl-terminal hydrolase 9X isoform X3

UniProtKB/TrEMBL

A0A994J6S4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_004652.3: Suppressed sequence

Description

NM_004652.3: This RefSeq was temporarily suppressed because currently there is insufficient data to support this transcript.
NM_021906.2: Suppressed sequence

Description

NM_021906.2: This RefSeq was temporarily suppressed because currently there is insufficient data to support this transcript.