Alternative titles; symbols
HGNC Approved Gene Symbol: USP9X
Cytogenetic location: Xp11.4 Genomic coordinates (GRCh38): X:41,085,445-41,236,579 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| Xp11.4 | Intellectual developmental disorder, X-linked 99 | 300919 | X-linked recessive | 3 |
| Intellectual developmental disorder, X-linked 99, syndromic, female-restricted | 300968 | X-linked dominant | 3 |
The USP9X gene encodes a large substrate-specific deubiquitylating enzyme (summary by Homan et al., 2014).
Jones et al. (1996) reported that an expressed sequence tag (EST 221) derived from human adult testis shares homology with the Drosophila fat facets (faf) gene. They detected related sequences on both the human X and Y chromosomes. They used EST 221 to derive clones covering the complete open reading frame of the X-specific locus, which they termed DFFRX. Y-specific cDNA clones were derived, and they termed that locus DFFRY (400005). Over the 2 regions corresponding to nucleotides 6 to 1901 and nucleotides 5815 to 7907 of the DFFRX sequence, the X- and Y-specific sequences share 91% and 88% identity, respectively. Both putative gene products contain conserved cysteine and histidine domains that have been described in ubiquitin C-terminal hydrolases (e.g., 191342). Northern blot analysis of 16 different adult human tissues with the EST 221 revealed expression in all tissues. They also detected both DFFRX and DFFRY expression in developing human tissues.
Jones et al. (1996) determined the X inactivation status of DFFRX through use of quantitative RT-PCR with X-specific primers and found that the level of DFFRX expression rises as the copy number of the X chromosome increases, indicating that DFFRX escapes inactivation. In Drosophila the faf gene has been shown to be important in eye function and in oocyte development. The high degree of conservation between the Drosophila faf gene and the DFFRX sequence led Jones et al. (1996) to conclude that DFFRX has an important function in humans.
Proper chromosome segregation requires the attachment of sister kinetochores to microtubules from opposite spindle poles to form bioriented chromosomes on the metaphase spindle. The chromosome passenger complex containing survivin (603352) and the kinase aurora B (604970) regulates this process from the centromeres. Vong et al. (2005) reported that a deubiquitinating enzyme, FAM, also known as USP9X, regulates chromosome alignment and segregation by controlling both the dynamic association of survivin with centromeres and the proper targeting of survivin and aurora B to centromeres. Survivin is ubiquitinated in mitosis through both lys48 and lys63 ubiquitin linkages. Lys63 deubiquitination mediated by FAM is required for the dissociation of survivin from centromeres, whereas lys63 ubiquitination mediated by the ubiquitin-binding protein UFD1 (601754) is required for the association of survivin with centromeres. Thus, ubiquitination regulates dynamic protein-protein interactions and chromosome segregation independently of protein degradation.
Schwickart et al. (2010) showed that the deubiquitinase USP9X binds to and stabilizes MCL1 (159552) and removes the lys48-linked polyubiquitin chains that normally mark MCL1 for proteasomal degradation. Increased USP9X expression correlated with increased MCL1 protein in human follicular lymphomas and diffuse large B-cell lymphomas. Moreover, patients with multiple myeloma overexpressing USP9X have a poor prognosis. Knockdown of USP9X increased MCL1 polyubiquitination, which enhances MCL1 turnover and cell killing by the BH3 mimetic ABT-737. Schwickart et al. (2010) concluded that their results identified USP9X as a prognostic and therapeutic target and showed that deubiquitinases may stabilize labile oncoproteins in human malignancies.
Reijnders et al. (2016) found that endogenous USP9X localizes along the length of the ciliary axoneme in human fibroblasts. Knockdown of USP9X using siRNA in fibroblasts decreased localization to the cilia, but did not interfere with ciliogenesis, suggesting that the protein has either tissue-based specific functions or is involved in ciliary signal transduction pathways.
Jones et al. (1996) mapped DFFRX to Xp11.4 by somatic cell hybrid analysis and a YAC library screen. They noted that the map location coincides with the region of the X chromosome defined by partial deletions as being critical for the major stigmata associated with Turner syndrome (163950). They raised the possibility that DFFRX plays a role in the defects of oocyte proliferation and subsequent gonadal degeneration found in Turner syndrome.
X-Linked Intellectual Developmental Disorder 99
In affected male members of 2 unrelated families with X-linked recessive nonsyndromic intellectual developmental disorder-99 (XLID99; 300919), Homan et al. (2014) identified 2 different hemizygous mutations in the USP9X gene (L2093H; 300072.0001 and c.7574delA; 300072.0003). In 1 family, unaffected females were found to be heterozygous for the mutation. A patient from a third family carried a heterozygous USP9X variant (L2157I; 300072.0002), but he also carried a deletion including the ARID1B gene (614556), which is known to cause MRD12 (135900). None of the USP9X variants affected the catalytic activity of USP9X. Isolated hippocampal neurons from Usp9x-knockout male mice (-/Y) showed a 43% reduction in axonal length and arborization compared to wildtype. The 3 USP9X variants were unable to rescue the defect, consistent with a loss of function in axonal growth. Loss of Usp9x also caused a 42% decrease in neuronal migration, which was partially rescued by the L2093H variant, but not by L2157I or c.7574delA. The variants coimmunoprecipitated normally with DCX (300121) in nonpolarized HEK293 cells, but did not localize properly to the axonal growth cone in immature polarized neurons. Overall, the findings suggested that the USP9X mutations caused changes in the neuronal cytoskeleton, which may affect neuronal migration and axonal growth, resulting in intellectual disability.
Female-Restricted X-Linked Syndromic Intellectual Developmental Disorder 99
In 17 unrelated females ranging in age from 2 to 23 years with female-restricted X-linked syndromic intellectual developmental disorder-99 (MRXS99F; 300968), Reijnders et al. (2016) identified 17 different de novo heterozygous mutations in or deletions involving the USP9X gene (see, e.g., 300072.0004-300072.0008). Most of the mutations were found by whole-exome sequencing and confirmed by Sanger sequencing; 12 of the 13 point mutations resulted in truncated proteins. Immunoblot and RT-PCR analysis of patient fibroblasts and lymphoblasts showed that the loss-of-function alleles resulted in significantly reduced USP9X protein and transcript levels compared to control females, but these levels were similar to those of normal control males. X-chromosome inactivation (XCI) was found to be skewed greater than 90% in 3 of the 5 tested patients, but skewing was not related to disease severity. In addition, there was no correlation between skewing of XCI and expression of mRNA or protein levels in studies of patient cells. Reijnders et al. (2016) suggested that there may be tissue-specific expression of USP9X that may influence the phenotype. Despite localization of wildtype USP9X to cilia, patient fibroblasts did not show any differences in ciliogenesis, ciliary length, or ciliary trafficking compared to controls.
Perez-Mancera et al. (2012) used 'Sleeping Beauty' transposon-mediated insertional mutagenesis in a mouse model of pancreatic ductal preneoplasia to identify genes that cooperate with oncogenic Kras(G12D) (190070.0003) to accelerate tumorigenesis and promote progression. This screen revealed novel candidate genes for pancreatic ductal adenocarcinoma (PDA) and confirmed the importance of many genes and pathways previously implicated in human PDA. The most commonly mutated gene was the X-linked deubiquitinase Usp9x, which was inactivated in over 50% of the tumors. Although previous work had attributed a presurvival role to USP9X in human neoplasia, Perez-Mancera et al. (2012) found instead that loss of Usp9x enhances transformation and protects pancreatic cancer cells from anoikis. Clinically, low USP9X protein and mRNA expression in PDA correlates with poor survival after surgery, and USP9X levels are inversely associated with metastatic burden in advanced disease. Furthermore, chromatin modulation with trichostatin A or 5-aza-2-prime-deoxycytidine elevates USP9X expression in human PDA cell lines, indicating a clinical approach for certain patients. The conditional deletion of Usp9x cooperated with Kras(G12D) to accelerate pancreatic tumorigenesis in mice, validating their genetic interaction. Perez-Mancera et al. (2012) proposed that USP9X is a major tumor suppressor gene with prognostic and therapeutic relevance in PDA.
In a French boy with X-linked intellectual developmental disorder-99 (XLID99; 300919), Homan et al. (2014) identified a c.6278T-A transversion in the USP9X gene, resulting in a leu2093-to-his (L2093H) substitution at a highly conserved residue. The mutation was not present in 1,129 control X chromosomes or in the dbSNP (build 137), 1000 Genomes Project, or Exome Variant Server databases. Segregation of the mutation in the family could not be established. The patient had previously been reported by Tarpey et al. (2009).
This variant is classified as a variant of unknown significance because its contribution to intellectual developmental disorder has not been confirmed.
In a boy with intellectual disability, Homan et al. (2014) identified a c.6469C-A transversion in the USP9X gene, resulting in a leu2157-to-ile (L2157I) substitution at a highly conserved residue. The patient's unaffected mother and maternal grandmother were heterozygous for the variant, which was not found in 1,129 control X chromosomes or in the dbSNP (build 137), 1000 Genomes Project, or Exome Variant Server databases. The patient was also found to carry a heterozygous 790-kb deletion at 6q23.3. The deletion included the ARID1B gene (614556), haploinsufficiency of which is known to cause mental retardation (135600). The parents could not be tested for the deletion. In addition to intellectual disability, hypotonia, and behavioral abnormalities, the patient also had complete loss of speech, short stature, poor prenatal and postnatal growth, and some congenital anomalies, including ectopic left kidney, tracheomalacia, gastroesophageal reflux, and hypospadias. Homan et al. (2014) hypothesized that the USP9X mutation aggravated the phenotype normally associated with ARID1B haploinsufficiency. The findings were consistent with multiple genetic hits contributing to the phenotype in this patient. The family had previously been reported by Tarpey et al. (2009).
In 2 half-brothers and a maternal uncle (family 383) with X-linked intellectual developmental disorder-99 (XLID99; 300919), Homan et al. (2014) identified a 1-bp deletion in the USP9X gene (c.7574delA), resulting in a frameshift and premature termination (Gln2525ArgfsTer18). The mutation was not found in 1,129 control X chromosomes or in the dbSNP (build 137), 1000 Genomes Project, or Exome Variant Server databases. The family had previously been reported by Tarpey et al. (2009).
In a 9-year-old girl with female-restricted X-linked syndromic intellectual developmental disorder-99 (MRXS99F; 300968), Reijnders et al. (2016) identified a de novo heterozygous c.2554C-T transition (c.2554C-T, NM_001039590.2) in the USP9X gene, resulting in an arg852-to-ter (R852X) substitution. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not found in the ExAC database.
In a 14-year-old girl with female-restricted X-linked syndromic intellectual developmental disorder-99 (MRXS99F; 300968), Reijnders et al. (2016) identified a de novo heterozygous c.3028-2A-G transition (c.3028-2A-G, NM_001039590.2) in the USP9X gene, resulting in a splicing defect. Analysis of patient cells showed that the mutation caused the skipping of exon 21, nonsense-mediated mRNA decay, and a loss of function. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not found in the ExAC database.
In a 7-year-old girl with female-restricted X-linked syndromic intellectual developmental disorder-99 (MRXS99F; 300968), Reijnders et al. (2016) identified a de novo heterozygous 1-bp insertion (c.2644_2645insA, NM_001039590.2) in the USP9X gene, resulting in a frameshift and premature termination (Arg882GlnfsTer3). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not found in the ExAC database.
In a 16-year-old girl with female-restricted X-linked syndromic intellectual developmental disorder-99 (MRXS99F; 300968), Reijnders et al. (2016) identified a de novo heterozygous c.3763C-T transition (c.3763C-T, NM_001039590.2) in the USP9X gene, resulting in a gln1255-to-ter (Q1255X) substitution. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not found in the ExAC database.
In a 7-year-old girl with female-restricted X-linked syndromic intellectual developmental disorder-99 (MRXS99F; 300968), Reijnders et al. (2016) identified a de novo heterozygous c.1111C-T transition (c.1111C-T, NM_001039590.2) in the USP9X gene, resulting in an arg371-to-ter (R371X) substitution. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was not found in the ExAC database.
Homan, C. C., Kumar, R., Nguyen, L. S., Haan, E., Raymond, F. L., Abidi, F., Raynaud, M., Schwartz, C. E., Wood, S. A., Gecz, J., Jolly, L. A. Mutations in USP9X are associated with X-linked intellectual disability and disrupt neuronal cell migration and growth. Am. J. Hum. Genet. 94: 470-478, 2014. [PubMed: 24607389] [Full Text: https://doi.org/10.1016/j.ajhg.2014.02.004]
Jones, M. H., Furlong, R. A., Burkin, H., Chalmers, I. J., Brown, G. M., Khwaja, O., Affara, N. A. The Drosophila developmental gene fat facets has a human homologue in Xp11.4 which escapes X-inactivation and has related sequences on Yq11.2. Hum. Molec. Genet. 5: 1695-1701, 1996. Note: Erratum: Hum. Molec. Genet. 6: 334-335, 1997. [PubMed: 8922996] [Full Text: https://doi.org/10.1093/hmg/5.11.1695]
Perez-Mancera, P. A., Rust, A. G., van der Weyden, L., Kristiansen, G., Li, A., Sarver, A. L., Silverstein, K. A. T., Grutzmann, R., Aust, D., Rummele, P., Knosel, T., Herd, C., and 25 others. The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma. Nature 486: 266-270, 2012. Note: Erratum: Nature 494, 390 only, 2013. [PubMed: 22699621] [Full Text: https://doi.org/10.1038/nature11114]
Reijnders, M. R. F., Zachariadis, V., Latour, B., Jolly, L., Mancini, G. M., Pfundt, R., Wu, K. M., van Ravenswaaij-Arts, C. M. A., Veenstra-Knol, H. E., Anderlid, B.-M. M., Wood, S. A., Cheung, S. W., and 26 others. De novo loss-of-function mutations in USP9X cause a female-specific recognizable syndrome with developmental delay and congenital malformations. Am. J. Hum. Genet. 98: 373-381, 2016. [PubMed: 26833328] [Full Text: https://doi.org/10.1016/j.ajhg.2015.12.015]
Schwickart, M., Huang, X., Lill, J. R., Liu, J., Ferrando, R., French, D. M., Maecker, H., O'Rourke, K., Bazan, F., Eastham-Anderson, J., Yue, P., Dornan, D., Huang, D. C. S., Dixit, V. M. Deubiquitinase USP9X stabilizes MCL1 and promotes tumour cell survival. Nature 463: 103-107, 2010. [PubMed: 20023629] [Full Text: https://doi.org/10.1038/nature08646]
Tarpey, P. S., Smith, R., Pleasance, E., Whibley, A., Edkins, S., Hardy, C., O'Meara, S., Latimer, C., Dicks, E., Menzies, A., Stephens, P., Blow, M., and 67 others. A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Nature Genet. 41: 535-543, 2009. [PubMed: 19377476] [Full Text: https://doi.org/10.1038/ng.367]
Vong, Q. P., Cao, K., Li, H. Y., Iglesias, P. A., Zheng, Y. Chromosome alignment and segregation regulated by ubiquitination of survivin. Science 310: 1499-1504, 2005. [PubMed: 16322459] [Full Text: https://doi.org/10.1126/science.1120160]