Summary Statistics:
ASD Reports: 17
Recent Reports: 2
Annotated variants: 72
Associated CNVs: 9
Evidence score: 3
Gene Score: S
Relevance to Autism
USP9X was initially associated with X-linked intellectual disability following the identification of pathogenic USP9X variants in five affected males from three families in Homan et al., 2014. Phenotypic review of males with likely pathogenic variants in the USP9X gene (including affected individuals from Homan et al., 2014) identified a neurodevelopmental disorder characterized by developmental delay, delayed or absent speech, motor problems, brain malformations, behavioral problems (predominantly autistic and obsessive behaviors), visual system defects, growth retardation, joint hypermobility, and gastroenterological disturbances (Johnson et al., 2019). De novo loss-of-function variants in USP9X were found to cause a female-specific syndrome characterized by developmental delay/intellectual disability, dysmorphic facial features, short stature, and distinct congenital malformations in Reijnders et al., 2016.
Molecular Function
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.
References
Primary
Mutations in USP9X are associated with X-linked intellectual disability and disrupt neuronal cell migration and growth.
X-linked mental retardation-99 (MRX99)
ASD
Support
De Novo Loss-of-Function Mutations in USP9X Cause a Female-Specific Recognizable Syndrome with Developmental Delay and Congenital Malformations.
Female-restricted X-linked syndromic mental retard
Support
Clinical Targeted Panel Sequencing Analysis in Clinical Evaluation of Children with Autism Spectrum Disorder in China
ASD
Support
Seizures are regulated by ubiquitin-specific peptidase 9 X-linked (USP9X), a de-ubiquitinase.
Epilepsy/seizures
Support
Missense variant contribution to USP9X-female syndrome
Female-restricted X-linked syndromic mental retard
Epilepsy/seizures, poor eye contact
Support
Massively parallel sequencing of patients with intellectual disability, congenital anomalies and/or autism spectrum disorders with a targeted gene ...
Female-restricted X-linked syndromic mental retard
Support
Functional relationships between recessive inherited genes and genes with de novo variants in autism spectrum disorder
ASD
Support
ASD
Learning disability
Support
Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders
ASD, DD
Support
DD, ID
Autistic features
Support
Excess of de novo variants in genes involved in chromatin remodelling in patients with marfanoid habitus and intellectual disability
ID
Marfanoid habitus
Support
Integrating de novo and inherited variants in 42
ASD
Support
Novel USP9X variants in two patients with X-linked intellectual disability.
Female-restricted X-linked syndromic mental retard
Support
Comprehensive genome sequencing analyses identify novel gene mutations and copy number variations associated with infant developmental delay or intellectual disability (DD/ID)
ID
Recent Recommendation
Usp9X Controls Ankyrin-Repeat Domain Protein Homeostasis during Dendritic Spine Development.
Recent Recommendation
Partial Loss of USP9X Function Leads to a Male Neurodevelopmental and Behavioral Disorder Converging on Transforming Growth Factor Signaling.
X-linked mental retardation-99 (MRX99)
ASD
GEN1126R001
missense_variant
c.6278T>A
p.Leu2093His
Unknown
Simplex
GEN1126R002
missense_variant
c.6469C>A
p.Leu2157Ile
Familial
Maternal
Simplex
GEN1126R003
frameshift_variant
c.7574del
p.Gln2525ArgfsTer18
Familial
Maternal
Multi-generational
GEN1126R004
missense_variant
c.3034T>C
p.Ser1012Pro
De novo
GEN1126R005
missense_variant
c.5669G>A
p.Gly1890Glu
Unknown
GEN1126R006
splice_site_variant
c.1986-1G>T
De novo
Simplex
GEN1126R007
stop_gained
c.2554C>T
p.Arg852Ter
De novo
GEN1126R008
stop_gained
c.3804T>A
p.Tyr1268Ter
De novo
Simplex
GEN1126R009
splice_site_variant
c.3028-2A>G
De novo
GEN1126R010
frameshift_variant
c.2644_2645insA
p.Arg882GlnfsTer3
De novo
GEN1126R011
copy_number_loss
De novo
Simplex
GEN1126R012
copy_number_loss
De novo
GEN1126R013
missense_variant
c.5078T>G
p.Leu1693Trp
De novo
Simplex
GEN1126R014
frameshift_variant
c.4086_4086+1dup
De novo
GEN1126R015
inframe_deletion
c.7495_7509del
p.Asp2499_Glu2503del
De novo
GEN1126R016
stop_gained
c.3763C>T
p.Gln1255Ter
De novo
Simplex
GEN1126R017
stop_gained
c.1111C>T
p.Arg371Ter
De novo
Simplex
GEN1126R018
frameshift_variant
c.1156del
p.Met386TrpfsTer13
De novo
Simplex
GEN1126R019
frameshift_variant
c.3709del
p.Cys1237ValfsTer2
De novo
Simplex
GEN1126R020
copy_number_loss
De novo
Simplex
GEN1126R021
frameshift_variant
c.4055dup
p.Phe1353LeufsTer18
De novo
GEN1126R022
copy_number_loss
De novo
Simplex
GEN1126R023
missense_variant
c.235A>G
p.Ile79Val
Familial
Maternal
Simplex
GEN1126R024
missense_variant
c.392T>A
p.Ile131Asn
De novo
GEN1126R025
missense_variant
c.2087C>T
p.Ala696Val
Familial
Maternal
Multiplex
GEN1126R026
missense_variant
c.2464C>T
p.Arg822Cys
De novo
GEN1126R027
missense_variant
c.2912A>G
p.Asn971Ser
De novo
GEN1126R028
missense_variant
c.4406C>T
p.Pro1469Leu
De novo
GEN1126R029
missense_variant
c.4718A>T
p.Gln1573Leu
De novo
GEN1126R030
missense_variant
c.5216C>A
p.Thr1739Asn
De novo
GEN1126R031
missense_variant
c.5603T>A
p.Val1868Glu
De novo
GEN1126R032
missense_variant
c.6034T>A
p.Phe2012Ile
De novo
GEN1126R033
missense_variant
c.6254G>A
p.Arg2085His
De novo
GEN1126R034
missense_variant
c.6697T>C
p.Ser2233Pro
Familial
Maternal
Simplex
GEN1126R035
frameshift_variant
c.4054_4058del
p.Phe1352HisfsTer17
De novo
GEN1126R036
stop_gained
c.1201C>T
p.Arg401Ter
De novo
GEN1126R037
missense_variant
c.3410C>T
p.Pro1137Leu
Familial
Maternal
Unknown
GEN1126R038
frameshift_variant
c.82dup
p.Leu28ProfsTer10
De novo
GEN1126R039
missense_variant
c.745G>A
p.Val249Ile
De novo
GEN1126R040
missense_variant
c.5975G>A
p.Arg1992Gln
De novo
GEN1126R041
frameshift_variant
c.5997_5998del
p.Met1999IlefsTer2
Unknown
GEN1126R042
missense_variant
c.461G>A
p.Arg154His
Unknown
GEN1126R043
missense_variant
c.6236G>A
p.Arg2079His
Unknown
GEN1126R044
missense_variant
c.2081G>A
p.Arg694His
Unknown
GEN1126R045
missense_variant
c.1396G>A
p.Asp466Asn
Unknown
GEN1126R046
missense_variant
c.3658C>T
p.Arg1220Cys
Unknown
GEN1126R047
missense_variant
c.10A>G
p.Thr4Ala
Familial
Maternal
Simplex
GEN1126R048
missense_variant
c.437G>A
p.Arg146Lys
Familial
Maternal
Simplex
GEN1126R049
missense_variant
c.1881G>C
p.Met627Ile
Familial
Maternal
Simplex
GEN1126R050
missense_variant
c.671T>C
p.Leu224Pro
De novo
GEN1126R051
missense_variant
c.1073T>A
p.Val358Asp
De novo
GEN1126R052
missense_variant
c.1303T>C
p.Trp435Arg
De novo
GEN1126R053
missense_variant
c.3664G>C
p.Ala1222Pro
De novo
GEN1126R054
missense_variant
c.3986G>A
p.Arg1329His
De novo
GEN1126R055
missense_variant
c.5053G>A
p.Asp1685Asn
Familial
Maternal
GEN1126R056
missense_variant
c.5053G>A
p.Asp1685Asn
De novo
GEN1126R057
missense_variant
c.5405A>G
p.Tyr1802Cys
De novo
GEN1126R058
inframe_deletion
c.5642_5644del
p.Tyr1881del
De novo
GEN1126R059
stop_gained
c.1140G>A
p.Trp380Ter
De novo
GEN1126R060
stop_gained
c.642C>T
p.Arg215Ter
Familial
Maternal
GEN1126R061
frameshift_variant
c.1603dup
p.Ile535AsnfsTer11
De novo
GEN1126R062
missense_variant
c.5290G>A
p.Glu1764Lys
Familial
Maternal
GEN1126R063
inframe_deletion
c.4147_4149del
p.Leu1383del
De novo
GEN1126R064
missense_variant
c.2902A>C
p.Ile968Leu
Familial
Maternal
GEN1126R065
missense_variant
c.2897C>A
p.Thr966Lys
Unknown
Unknown
GEN1126R066
missense_variant
c.367G>A
p.Gly123Arg
De novo
GEN1126R067
missense_variant
c.2078A>T
p.Asp693Val
De novo
Simplex
GEN1126R068
synonymous_variant
c.2445C>T
p.Phe815%3D
De novo
Simplex
GEN1126R069
stop_gained
c.3066G>A
p.Trp1022Ter
De novo
GEN1126R070
missense_variant
c.4726T>A
p.Tyr1576Asn
De novo
GEN1126R071
missense_variant
c.5686C>T
p.Arg1896Cys
Familial
Maternal
Simplex
GEN1126R072
stop_gained
c.1774C>T
p.Arg592Ter
Unknown
No Common Variants Available
X
Deletion-Duplication
31
X
Deletion-Duplication
21
No Animal Model Data Available
No Interactions Available