title: De Novo Loss-of-Function Mutations in USP9X Cause a Female-Specific Recognizable Syndrome with Developmental Delay and Congenital Malformations.
abstract: Mutations in more than a hundred genes have been reported to cause X-linked recessive intellectual disability (ID) mainly in males. In contrast, the number of identified X-linked genes in which de novo mutations specifically cause ID in females is limited. Here, we report 17 females with de novo loss-of-function mutations in USP9X, encoding a highly conserved deubiquitinating enzyme. The females in our study have a specific phenotype that includes ID/developmental delay (DD), characteristic facial features, short stature, and distinct congenital malformations comprising choanal atresia, anal abnormalities, post-axial polydactyly, heart defects, hypomastia, cleft palate/bifid uvula, progressive scoliosis, and structural brain abnormalities. Four females from our cohort were identified by targeted genetic testing because their phenotype was suggestive for USP9X mutations. In several females, pigment changes along Blaschko lines and body asymmetry were observed, which is probably related to differential (escape from) X-inactivation between tissues. Expression studies on both mRNA and protein level in affected-female-derived fibroblasts showed significant reduction of USP9X level, confirming the loss-of-function effect of the identified mutations. Given that some features of affected females are also reported in known ciliopathy syndromes, we examined the role of USP9X in the primary cilium and found that endogenous USP9X localizes along the length of the ciliary axoneme, indicating that its loss of function could indeed disrupt cilium-regulated processes. Absence of dysregulated ciliary parameters in affected female-derived fibroblasts, however, points toward spatiotemporal specificity of ciliary USP9X (dys-)function.
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
authors.forename: Margot R F
authors.initials: MR
authors.lastname: Reijnders
authors.affiliation: Department of Molecular Medicine and Surgery and Centre for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden.
authors.forename: Vasilios
authors.initials: V
authors.lastname: Zachariadis
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
authors.forename: Brooke
authors.initials: B
authors.lastname: Latour
authors.affiliation: Neurogenetics, School of Medicine and the Robinson Research Institute, the University of Adelaide, Adelaide, SA 5005, Australia.
authors.forename: Lachlan
authors.initials: L
authors.lastname: Jolly
authors.affiliation: Department of Clinical Genetics, Erasmus MC, Sophia Children's Hospital, 3000 CA Rotterdam, the Netherlands.
authors.forename: Grazia M
authors.initials: GM
authors.lastname: Mancini
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
authors.forename: Rolph
authors.initials: R
authors.lastname: Pfundt
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
authors.forename: Ka Man
authors.initials: KM
authors.lastname: Wu
authors.affiliation: Department of Genetics, University of Groningen, University Medical Center of Groningen, 9700 RB Groningen, the Netherlands.
authors.forename: Conny M A
authors.initials: CM
authors.lastname: van Ravenswaaij-Arts
authors.affiliation: Department of Genetics, University of Groningen, University Medical Center of Groningen, 9700 RB Groningen, the Netherlands.
authors.forename: Hermine E
authors.initials: HE
authors.lastname: Veenstra-Knol
authors.affiliation: Department of Molecular Medicine and Surgery and Centre for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden.
authors.forename: Britt-Marie M
authors.initials: BM
authors.lastname: Anderlid
authors.affiliation: The Eskitis Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Wood
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
authors.forename: Sau Wai
authors.initials: SW
authors.lastname: Cheung
authors.affiliation: Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.
authors.forename: Angela
authors.initials: A
authors.lastname: Barnicoat
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
authors.forename: Frank
authors.initials: F
authors.lastname: Probst
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
authors.forename: Pilar
authors.initials: P
authors.lastname: Magoulas
authors.affiliation: Department of Clinical Genetics, Erasmus MC, Sophia Children's Hospital, 3000 CA Rotterdam, the Netherlands.
authors.forename: Alice S
authors.initials: AS
authors.lastname: Brooks
authors.affiliation: Department of Molecular Medicine and Surgery and Centre for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden.
authors.forename: Helena
authors.initials: H
authors.lastname: Malmgren
authors.affiliation: Department of Women's and Children's Health, Karolinska University Hospital, 171 76 Stockholm, Sweden.
authors.forename: Arja
authors.initials: A
authors.lastname: Harila-Saari
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
authors.forename: Carlo M
authors.initials: CM
authors.lastname: Marcelis
authors.affiliation: Department of Clinical Genetics, Maastricht University Medical Center, 6202 AZ Maastricht, the Netherlands.
authors.forename: Maaike
authors.initials: M
authors.lastname: Vreeburg
authors.affiliation: Department of Clinical Genetics, Chapel Allerton Hospital, Leeds LS7 4SA, UK.
authors.forename: Emma
authors.initials: E
authors.lastname: Hobson
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
authors.forename: V Reid
authors.initials: VR
authors.lastname: Sutton
authors.affiliation: Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia.
authors.forename: Zornitza
authors.initials: Z
authors.lastname: Stark
authors.affiliation: West Midlands Regional Genetics Service, Clinical Genetics Unit, Birmingham Women's Hospital, Birmingham B15 2TG, UK.
authors.forename: Julie
authors.initials: J
authors.lastname: Vogt
authors.affiliation: Clinical Genetics Unit, Birmingham Women's NHS Foundation Trust, Mindelsohn Way, Edgbaston, Birmingham B15 2G, UK.
authors.forename: Nicola
authors.initials: N
authors.lastname: Cooper
authors.affiliation: KK Women's and Children's Hospital, 229899 Singapore, Singapore.
authors.forename: Jiin Ying
authors.initials: JY
authors.lastname: Lim
authors.affiliation: Department of Clinical Genetics, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK.
authors.forename: Sue
authors.initials: S
authors.lastname: Price
authors.affiliation: KK Women's and Children's Hospital, 229899 Singapore, Singapore.
authors.forename: Angeline Hwei Meeng
authors.initials: AH
authors.lastname: Lai
authors.affiliation: School of Biological Sciences, The University of Adelaide, Adelaide 5000, Australia.
authors.forename: Deepti
authors.initials: D
authors.lastname: Domingo
authors.affiliation: Institute of Medical Biology, A(∗)STAR, 138648 Singapore, Singapore; Amsterdam Reproduction & Development, Academic Medical Centre & VU University Medical Center, Reproductive Biology Laboratory (Q3-119), Meibergdreef 9, 1105 AZ Amsterdam, the Netherlands.
authors.forename: Bruno
authors.initials: B
authors.lastname: Reversade
authors.affiliation: Neurogenetics, School of Medicine and the Robinson Research Institute, the University of Adelaide, Adelaide, SA 5005, Australia.
authors.forename: Jozef
authors.initials: J
authors.lastname: Gecz
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
authors.forename: Christian
authors.initials: C
authors.lastname: Gilissen
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Department of Clinical Genetics, Maastricht University Medical Center, 6202 AZ Maastricht, the Netherlands.
authors.forename: Han G
authors.initials: HG
authors.lastname: Brunner
authors.affiliation: Department of Clinical Genetics, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK.
authors.forename: Usha
authors.initials: U
authors.lastname: Kini
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands. Electronic address: ronald.roepman@radboudumc.nl.
authors.forename: Ronald
authors.initials: R
authors.lastname: Roepman
authors.affiliation: Department of Molecular Medicine and Surgery and Centre for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden; Department of Clinical Genetics, Karolinska University Hospital, 171 76 Stockholm, Sweden.
authors.forename: Ann
authors.initials: A
authors.lastname: Nordgren
authors.affiliation: Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands. Electronic address: tjitske.kleefstra@radboudumc.nl.
authors.forename: Tjitske
authors.initials: T
authors.lastname: Kleefstra
mesh_terms: D000293:Adolescent; D001483:Base Sequence; D002648:Child; D002675:Child, Preschool; D002754:Choanal Atresia / Q000175:diagnosis / Q000235:genetics; D002658:Developmental Disabilities / Q000175:diagnosis / Q000235:genetics*; D005260:Female; D050172:Genes, X-Linked; D005820:Genetic Testing; D006801:Humans; D008607:Intellectual Disability / Q000175:diagnosis / Q000235:genetics*; D008969:Molecular Sequence Data; D009154:Mutation; D010641:Phenotype; D043222:Ubiquitin Thiolesterase / Q000235:genetics* / Q000378:metabolism; D049951:X Chromosome Inactivation; D055815:Young Adult
chemical_list: C506234:USP9X protein, human; D043222:Ubiquitin Thiolesterase
references.citation: PLoS Genet. 2015 Mar;11(3):e1005022
references.pmid: 25763846
references.citation: Biochem J. 2008 Apr 15;411(2):249-60
references.pmid: 18254724
references.citation: J Cell Biol. 1982 Jun;93(3):938-49
references.pmid: 7119006
references.citation: Mol Cell Neurosci. 2005 Jan;28(1):153-64
references.pmid: 15607950
references.citation: Mol Psychiatry. 2016 Jan;21(1):133-48
references.pmid: 25644381
references.citation: Nature. 2005 Mar 17;434(7031):400-4
references.pmid: 15772666
references.citation: Hum Mutat. 2013 Dec;34(12):1679-87
references.pmid: 24038936
references.citation: Zebrafish. 2007 Summer;4(2):95-101
references.pmid: 18041927
references.citation: Mol Biol Cell. 2009 Apr;20(7):2015-29
references.pmid: 19176755
references.citation: Development. 1992 Dec;116(4):985-1000
references.pmid: 1295747
references.citation: Bioessays. 2014 Aug;36(8):746-56
references.pmid: 24913292
references.citation: Eur J Hum Genet. 2014 Jan;22(1):79-87
references.pmid: 23695279
references.citation: PLoS One. 2014;9(4):e93409
references.pmid: 24690944
references.citation: Proc Am Thorac Soc. 2011 Sep;8(5):444-50
references.pmid: 21926397
references.citation: J Biol Chem. 2006 Dec 15;281(50):38738-47
references.pmid: 17038327
references.citation: Nature. 2014 Nov 13;515(7526):216-21
references.pmid: 25363768
references.citation: Trends Biochem Sci. 1998 Jun;23(6):198-9
references.pmid: 9644970
references.citation: BMC Med Genet. 2014;15:14
references.pmid: 24451042
references.citation: Hum Mol Genet. 1996 Nov;5(11):1695-701
references.pmid: 8922996
references.citation: Am J Hum Genet. 2014 Mar 6;94(3):470-8
references.pmid: 24607389
references.citation: Nat Genet. 2009 May;41(5):535-43
references.pmid: 19377476
references.citation: Eur J Neurosci. 2005 Jun;21(11):3017-22
references.pmid: 15978012
references.citation: N Engl J Med. 2012 Nov 15;367(20):1921-9
references.pmid: 23033978
references.citation: Cell. 1979 Jul;17(3):527-35
references.pmid: 476831
references.citation: Am J Hum Genet. 2010 Aug 13;87(2):173-88
references.pmid: 20655035
references.citation: Hum Genet. 2011 Aug;130(2):237-45
references.pmid: 21614513
references.citation: Mech Dev. 1997 Apr;63(1):29-38
references.pmid: 9178254
references.citation: Genomics. 2006 Dec;88(6):675-81
references.pmid: 16949791
references.citation: Hum Mol Genet. 2015 Mar 15;24(6):1528-39
references.pmid: 25381334
references.citation: Proc Natl Acad Sci U S A. 2003 Jan 7;100(1):189-92
references.pmid: 12502788
references.citation: Hum Genet. 2011 Aug;130(2):175-85
references.pmid: 21553122
references.citation: Am J Hum Genet. 2015 Aug 6;97(2):343-52
references.pmid: 26235985
references.citation: Nature. 2010 Jan 7;463(7277):103-7
references.pmid: 20023629
references.citation: J Biol Chem. 2012 Jun 15;287(25):21164-75
references.pmid: 22544753
references.citation: J Cell Biol. 1998 Aug 24;142(4):1053-62
references.pmid: 9722616
references.citation: Nat Rev Genet. 2014 Jun;15(6):367-78
references.pmid: 24733023
references.citation: Lancet. 2015 Apr 4;385(9975):1305-14
references.pmid: 25529582
references.citation: Cell Mol Life Sci. 2015 Jun;72(11):2075-89
references.pmid: 25672900
references.citation: Mol Cytogenet. 2014 Jan 09;7(1):3
references.pmid: 24401281
references.citation: J Biol Chem. 2013 Feb 1;288(5):2976-85
references.pmid: 23184937
references.citation: J Med Genet. 2013 Dec;50(12):838-47
references.pmid: 24092917
references.citation: J Med Genet. 2008 Jul;45(7):401-8
references.pmid: 18463129
references.citation: Genes Cells. 1999 Dec;4(12):757-67
references.pmid: 10620020
references.citation: PLoS One. 2013;8(7):e68287
references.pmid: 23861879
references.citation: Am J Hum Genet. 2012 Apr 6;90(4):579-90
references.pmid: 22482801
references.citation: PLoS One. 2011;6(1):e15891
references.pmid: 21283576
references.citation: Am J Hum Genet. 2013 Aug 8;93(2):368-83
references.pmid: 23871722
references.citation: Cell. 2009 Jan 9;136(1):123-35
references.pmid: 19135894
references.citation: Biochem Soc Trans. 2012 Jun 1;40(3):539-45
references.pmid: 22616864
references.citation: Mol Biol Cell. 2004 Apr;15(4):1591-9
references.pmid: 14742711