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

Gene ID: 8239, updated on 11-May-2025
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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See USP9X in Genome Data Viewer
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_000023.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:40809037-40809720 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:40809721-40810402 Neighboring gene ribosomal protein S2 pseudogene 55 Neighboring gene Sharpr-MPRA regulatory region 12561 Neighboring gene Sharpr-MPRA regulatory region 13807 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20771 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:40944771-40945308 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20772 Neighboring gene chloride intracellular channel 4 pseudogene 3 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:40973903-40974035 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29553 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:40991170-40991670 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:41070375-41071092 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:41135078-41135578 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chrX:41135579-41136079 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chrX:41150473-41151037 Neighboring gene long intergenic non-protein coding RNA 2601 Neighboring gene RNA, 5S ribosomal pseudogene 502

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Usp9X Regulates Cell Death in Malignant Peripheral Nerve Sheath Tumors. Bianchetti E, et al. Sci Rep, 2018 Nov 26. PMID 30478285, Free PMC Article
  2. Down-Regulation of Ubiquitin-Specific Peptidase 9X Inhibited Proliferation, Migration and Invasion of Osteosarcoma via ERK1/2 and PI3K/Akt Signaling Pathways. Zheng W, et al. Biol Pharm Bull, 2022. PMID 36047196
  3. Genetic disruption of USP9X sensitizes colorectal cancer cells to 5-fluorouracil. Harris DR, et al. Cancer Biol Ther, 2012 Nov. PMID 22895071, Free PMC Article
  4. Context-dependent function of the deubiquitinating enzyme USP9X in pancreatic ductal adenocarcinoma. Cox JL, et al. Cancer Biol Ther, 2014 Aug. PMID 24841553, Free PMC Article
  5. Exome and RNA-Seq analyses of an incomplete penetrance variant in USP9X in female-specific syndromic intellectual disability. Li D, et al. Am J Med Genet A, 2022 Jun. PMID 35253988

See all (339) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. Deubiquitinase USP9X loss sensitizes renal cancer cells to mTOR inhibition.
    Title: Deubiquitinase USP9X loss sensitizes renal cancer cells to mTOR inhibition.
  5. 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.
  6. 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.
  7. USP9X promotes lipopolysaccharide-stimulated acute lung injury by deubiquitination of NLRP3.
    Title: USP9X promotes lipopolysaccharide-stimulated acute lung injury by deubiquitination of NLRP3.
  8. 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.
  9. 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.
  10. 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)

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 2024-11-27)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2024-11-27)

ClinGen Genome Curation PagePubMed

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

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 IEA
Inferred from Electronic Annotation
more info
  
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 endopeptidase activity TAS
Traceable Author Statement
more info
 PubMed 
enables cysteine-type peptidase activity IEA
Inferred from Electronic Annotation
more info
  
enables cysteine-type peptidase activity TAS
Traceable Author Statement
more info
 PubMed 
enables deubiquitinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables deubiquitinase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables molecular sequestering activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables peptidase activity IEA
Inferred from Electronic Annotation
more info
  
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 IEA
Inferred from Electronic Annotation
more info
  
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 proteolysis IEA
Inferred from Electronic Annotation
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
located_in cell projection IEA
Inferred from Electronic Annotation
more info
  
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 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
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 IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in growth cone IDA
Inferred from Direct Assay
more info
 PubMed 
located_in growth cone IEA
Inferred from Electronic Annotation
more info
  
located_in membrane HDA PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
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
NP_001034680.2
NP_001397677.1
NP_001397678.1
XP_005272732.1
XP_005272733.1
XP_047298504.1
XP_047298506.1
XP_054183906.1
XP_054183907.1
XP_054183908.1
XP_054183909.1

NEW Try the new Transcript table

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

  1. NG_012547.1 RefSeqGene

    Range
    4811..155945
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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 ...

  2. 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

  3. 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, A0A994J4T3

  4. 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
    A0A994J4T3, A0A994J6S4

  5. NM_001437534.1 → NP_001424463.1  ubiquitin carboxyl-terminal hydrolase 9X isoform 6

    Status: REVIEWED

    Source sequence(s)
    AL109797, AL391259
    UniProtKB/TrEMBL
    A0A994J4T3, 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

  1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

    Range
    41085445..41236579
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A994J4T3

  2. XM_047442550.1 → XP_047298506.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X4

    UniProtKB/Swiss-Prot
    O75550, Q8WWT3, Q8WX12, Q93008
    UniProtKB/TrEMBL
    A0A994J4T3

  3. 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

  4. XM_005272676.5 → XP_005272733.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X3

    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

  1. NC_060947.1 Alternate T2T-CHM13v2.0

    Range
    40487470..40638605
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A994J4T3

  2. XM_054327934.1 → XP_054183909.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X4

    UniProtKB/Swiss-Prot
    O75550, Q8WWT3, Q8WX12, Q93008
    UniProtKB/TrEMBL
    A0A994J4T3

  3. XM_054327931.1 → XP_054183906.1  ubiquitin carboxyl-terminal hydrolase 9X isoform X1

    UniProtKB/TrEMBL
    A0A994J4R6, A0A994J4T3

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

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_004652.3: Suppressed sequence

    Description
    NM_004652.3: This RefSeq was temporarily suppressed because currently there is insufficient data to support this transcript.

  2. NM_021906.2: Suppressed sequence

    Description
    NM_021906.2: This RefSeq was temporarily suppressed because currently there is insufficient data to support this transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q93008.4 GenPept UniProtKB/Swiss-Prot:Q93008

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