Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
8239
Gene name Gene Name - the full gene name approved by the HGNC.
Ubiquitin specific peptidase 9 X-linked
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
USP9X
Synonyms (NCBI Gene) Gene synonyms aliases
DFFRX, FAF, FAF-X, FAM, MRX99, MRXS99F, XLID99, hFAM
Chromosome Chromosome number
X
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
Xp11.4
Summary Summary of gene provided in NCBI Entrez Gene.
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.
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.
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 information of associated ontologies with gene provided by GO database.
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 ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
300072 12632 ENSG00000124486
Protein
UniProt ID 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
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
Mental retardation intellectual disability rs2062994512 N/A
Mental Retardation, X-Linked Intellectual disability, X-linked 99, syndromic, female-restricted, Intellectual disability, X-linked 99 rs869025590, rs1601957478, rs869025591, rs869025592, rs886041595, rs1057522024, rs1555933969, rs587777317, rs1555932766, rs587777318, rs1555930128, rs869025588, rs1555917927, rs869025589 N/A
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Female Restricted Facial Dysmorphism-Short Stature-Choanal Atresia-Intellectual Disability, X-Linked X-linked female restricted facial dysmorphism-short stature-choanal atresia-intellectual disability N/A N/A GenCC
Associations from Text Mining Disease associations identified through Pubtator
Disease Name Relationship Type References
Abnormalities Drug Induced Associate 37289514
Abnormalities Multiple Associate 37289514
Adenocarcinoma Associate 29327707
Apraxias Associate 35227307
Axenfeld Rieger syndrome Associate 37895297
Brain Diseases Associate 24841553, 26833328
Breast Neoplasms Stimulate 28361952
Breast Neoplasms Associate 30689267, 31073027
Calcinosis Cutis Associate 32345963
Carcinogenesis Associate 28054945, 29721084