Gene Gene information from NCBI Gene database.
Entrez ID 8239
Gene name Ubiquitin specific peptidase 9 X-linked
Gene symbol USP9X
Synonyms (NCBI Gene)
DFFRXFAFFAF-XFAMMRX99MRXS99FXLID99hFAM
Chromosome X
Chromosome location Xp11.4
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 sy
SNPs SNP information provided by dbSNP.
33
SNP ID Visualize variation Clinical significance Consequence
rs587777317 T>A Pathogenic Missense variant, coding sequence variant
rs587777318 A>- Pathogenic Frameshift variant, coding sequence variant
rs757903212 A>G Likely-pathogenic Missense variant, coding sequence variant
rs774054468 A>-,AA Uncertain-significance, not-provided, pathogenic Frameshift variant, coding sequence variant, intron variant
rs869025588 C>T Pathogenic Stop gained, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
667
miRTarBase ID miRNA Experiments Reference
MIRT031499 hsa-miR-16-5p Proteomics 18668040
MIRT048997 hsa-miR-92a-3p CLASH 23622248
MIRT046739 hsa-miR-222-3p CLASH 23622248
MIRT045086 hsa-miR-186-5p CLASH 23622248
MIRT043839 hsa-miR-330-3p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
70
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II TAS
GO:0001764 Process Neuron migration IMP 24607389
GO:0004197 Function Cysteine-type endopeptidase activity ISS
GO:0004197 Function Cysteine-type endopeptidase activity TAS 9827704
GO:0004843 Function Cysteine-type deubiquitinase activity EXP 22371489, 26235645
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
300072 12632 ENSG00000124486
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q93008
Protein name Ubiquitin carboxyl-terminal hydrolase 9X (EC 3.4.19.12) (Deubiquitinating enzyme FAF-X) (Fat facets in mammals) (hFAM) (Fat facets protein-related, X-linked) (Ubiquitin thioesterase FAF-X) (Ubiquitin-specific protease 9, X chromosome) (Ubiquitin-specific-
Protein function Deubiquitinase involved both in the processing of ubiquitin precursors and of ubiquitinated proteins (PubMed:18254724, PubMed:19135894, PubMed:22371489, PubMed:25944111, PubMed:29626158, PubMed:30914461, PubMed:37454738). May therefore play an i
PDB 5VBD , 5WCH , 7YXX , 7YXY
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00443 UCH 1557 1953 Ubiquitin carboxyl-terminal hydrolase Family
PF12030 DUF3517 2097 2476 Domain of unknown function (DUF3517) Family
Tissue specificity TISSUE SPECIFICITY: Widely expressed in embryonic and adult tissues. {ECO:0000269|PubMed:8922996}.
Sequence
MTATTRGSPVGGNDNQGQAPDGQSQPPLQQNQTSSPDSSNENSPATPPDEQGQGDAPPQL
EDEEPAFPHTDLAKLDDMINRPRWVVPVLPKGELEVLLEAAIDLSKKGLDVKSEACQRFF
RDGLTISFTKILTDEAVSGWKFEIHRCIINNTHRLVELCVAKLSQDWFPLLELLAMALNP
HCKFHIYNGTRPCESVSSSVQLPEDELFARSPDPRSPKGWLVDLLNKFGTLNGFQILHDR
FINGSALNVQIIAALIKPFGQCYEFLTLHTVKKYFLPIIEMVPQFLENLTDEELKKEAKN
EAKNDALSMIIKSLKNLASRVPGQEETVKNLEIFRLKMILRLLQISSFNGKMNALNEVNK
VISSVSYYTHRHGNPEEEEWLTAERMAEWIQQNNILSIVLRDSLHQPQYVEKLEKILRFV
IKEKALTLQDLDNIWAAQAGKHEAIVKNVHDLLAKLAWDFSPEQLDHLFDCFKASWTNAS
KKQREKLLELIRRLAEDDKDGVMAHKVLNLLWNLAHSDDVPVDIMDLALSAHIKILDYSC
SQDRDTQKIQWIDRFIEELRTNDKWVIPALKQIREICSLFGEAPQNLSQTQRSPHVFYRH
DLINQLQHNHALVTLVAENLATYMESMRLYARDHEDYDPQTVRLGSRYSHVQEVQERLNF
LRFLLKDGQLWLCAPQAKQIWKCLAENAVYLCDREACFKWYSKLMGDEPDLDPDINKDFF
ESNVLQLDPSLLTENGMKCFERFFKAVNCREGKLVAKRRAYMMDDLELIGLDYLWRVVIQ
SNDDIASRAIDLLKEIYTNLGPRLQVNQVVIHEDFIQSCFDRLKASYDTLCVLDGDKDSV
NCARQEAVRMVRVLTVLREYINECDSDYHEERTILPMSRAFRGKHLSFVVRFPNQGRQVD
DLEVWSHTNDTIGSVRRCILNRIKANVAHTKIELFVGGELIDPADDRKLIGQLNLKDKSL
ITAKLTQISSNMPSSPDSSSDSSTGSPGNHGNHYSDGPNPEVESCLPGVIMSLHPRYISF
LWQVADLGSSLNMPPLRDGARVLMKLMPPDSTTIEKLRAICLDHAKLGESSLSPSLDSLF
FGPSASQVLYLTEVVYALLMPAGAPLADDSSDFQFHFLKSGGLPLVLSMLTRNNFLPNAD
METRRGAYLNALKIAKLLLTAIGYGHVRAVAEACQPGVEGVNPMTQINQVTHDQAVVLQS
ALQSIPNPSSECMLRNVSVRLAQQISDEASRYMPDICVIRAIQKIIWASGCGSLQLVFSP
NEEITKIYEKTNAGNEPDLEDEQVCCEALEVMTLCFALIPTALDALSKEKAWQTFIIDLL
LHCHSKTVRQVAQEQFFLMCTRCCMGHRPLLFFITLLFTVLGSTARERAKHSGDYFTLLR
HLLNYAYNSNINVPNAEVLLNNEIDWLKRIRDDVKRTGETGIEETILEGHLGVTKELLAF
QTSEKKFHIGCEKGGANLIKELIDDFIFPASNVYLQYMRNGELPAEQAIPVCGSPPTINA
GFELLVALAVGCVRNLKQIVDSLTEMYYIGTAITTCEALTEWEYLPPVGPRPPKGFVGLK
NAGATCYMNSVIQQLYMIPSIRNGILAIEGTGSDVDDDMSGDEKQDNESNVDPRDDVFGY
PQQFEDKPALSKTEDRKEYNIGVLRHLQVIFGHLAASRLQYYVPRGFWKQFRLWGEPVNL
REQHDALEFFNSLVDSLDEALKALGHPAMLSKVLGGSFADQKICQGCPHRYECEESFTTL
NVDIRNHQNLLDSLEQYVKGDLLEGANAYHCEKCNKKVDTVKRLLIKKLPPVLAIQLKRF
DYDWERECAIKFNDYFEFPRELDMEPYTVAGVAKLEGDNVNPESQLIQQSEQSESETAGS
TKYRLVGVLVHSGQASGGHYYSYIIQRNGGDGERNRWYKFDDGDVTECKMDDDEEMKNQC
FGGEYMGEVFDHMMKRMSYRRQKRWWNAYILFY
ERMDTIDQDDELIRYISELAITTRPHQ
IIMPSAIERSVRKQNVQFMHNRMQYSMEYFQFMKKLLTCNGVYLNPPPGQDHLLPEAEEI
TMISIQLAARFLFTTGFHTKKVVRGSASDWYDALCILLRHSKNVRFWFAHNVLFNVSNRF
SEYLLECPSAEVRGAFAKLIVFIAHFSLQDGPCPSPFASPGPSSQAYDNLSLSDHLLRAV
LNLLRREVSEHGRHLQQYFNLFVMYANLGVAEKTQLLKLSVPATFMLVSLDEGPGPPIKY
QYAELGKLYSVVSQLIRCCNVSSRMQSSINGNPPLPNPFGDPNLSQPIMPIQQNVADILF
VRTSYVKKIIEDCSNSEETVKLLRFCCWENPQFSSTVLSELLWQVAYSYTYELRPYLDLL
LQILLIEDSWQTHRIHNALKGIPDDRDGLFDTIQRSKNHYQKRAYQCIKCMVALFSNCPV
AYQILQGNGDLKRKWTWAVEWLGDELERRPYTGNPQYTYNNWSPPVQSNETSNGYFLERS
HSARMTLAKACELCPE
EEPDDQDAPDEHESPPPEDAPLYPHSPGSQYQQNNHVHGQPYTG
PAAHHMNNPQRTGQRAQENYEGSEEVSPPQTKDQ
Sequence length 2554
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Downregulation of SMAD2/3:SMAD4 transcriptional activity
Ub-specific processing proteases
Synthesis of active ubiquitin: roles of E1 and E2 enzymes
Peroxisomal protein import
Amyloid fiber formation
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
40
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Intellectual disability Pathogenic rs2062994512 RCV001030991
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability, X-linked 99 Pathogenic; Likely pathogenic rs2062675453, rs2147163808, rs2147251154, rs587777317, rs587777318, rs2147171235, rs2519156202, rs2519371283, rs5918118, rs2519366750, rs1431284689, rs1057522024, rs1569165417, rs1601957478 RCV001337114
RCV001733820
RCV001804241
RCV000114949
RCV000114950
View all (9 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Intellectual disability, X-linked 99, syndromic, female-restricted Pathogenic; Likely pathogenic rs2062209732, rs2147080766, rs2147118205, rs2147080697, rs2147230302, rs2147123290, rs2147262405, rs2147266578, rs2519213433, rs869025588, rs869025589, rs869025590, rs869025591, rs869025592, rs5918118
View all (13 more)
RCV001729975
RCV001733426
RCV001808064
RCV001823055
RCV001823056
View all (24 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neurodevelopmental disorder Likely pathogenic rs2147006012 RCV001375035
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Benign; Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Developmental delay Conflicting classifications of pathogenicity ClinVar
Disgenet
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
2-3 toe syndactyly Syndactyly Of The Toes HPO_DG
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma Adenocarcinoma BEFREE 29327707
★☆☆☆☆
Found in Text Mining only
Ankylosing spondylitis Ankylosing Spondylitis BEFREE 31287414
★☆☆☆☆
Found in Text Mining only
ANOPHTHALMIA AND PULMONARY HYPOPLASIA Syndromic microphthalmia BEFREE 24841553, 29130109, 29844826, 30553134
★☆☆☆☆
Found in Text Mining only
Anus, Imperforate Imperforate anus HPO_DG
★☆☆☆☆
Found in Text Mining only
Apraxias Apraxia Pubtator 35227307 Associate
★☆☆☆☆
Found in Text Mining only
Astigmatism Astigmatism HPO_DG
★☆☆☆☆
Found in Text Mining only
Astrocytoma Astrocytoma BEFREE 26775694
★☆☆☆☆
Found in Text Mining only
Atrial Fibrillation Atrial Fibrillation BEFREE 12821245
★☆☆☆☆
Found in Text Mining only
Atrial Septal Defects Atrial Septal Defect HPO_DG
★☆☆☆☆
Found in Text Mining only