Human Gene Module / Chromosome X / DDX3X

DDX3XDEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked

Score
1
High Confidence Criteria 1.1
Autism Reports / Total Reports
5 / 19
Rare Variants / Common Variants
94 / 0
Aliases
DDX3X, CAP-Rf,  DBX,  DDX14,  DDX3,  HLP2
Associated Syndromes
-
Genetic Category
Rare Single Gene Mutation, Syndromic
Chromosome Band
Xp11.4
Associated Disorders
DD/NDD, ASD, EP, EPS, ID
Relevance to Autism

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014).

Molecular Function

The protein encoded by this gene is a member of the large DEAD-box protein family, that is defined by the presence of the conserved Asp-Glu-Ala-Asp (DEAD) motif,and acts as a multifunctional ATP-dependent RNA helicase. Nuclear roles for the encoded protein include transcriptional regulation, mRNP assembly, pre-mRNA splicing, and mRNA export, while in the cytoplasm, this protein is thought to be involved in translation and cellular signaling.

Reports related to DDX3X (19 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support The contribution of de novo coding mutations to autism spectrum disorder. Iossifov I , et al. (2014) Yes -
2 Primary Mutations in DDX3X Are a Common Cause of Unexplained Intellectual Disability with Gender-Specific Effects on Wnt Signaling. Snijders Blok L , et al. (2015) No ASD
3 Support Identification of Intellectual Disability Genes in Female Patients with A Skewed X Inactivation Pattern. Fieremans N , et al. (2016) No -
4 Support Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Lelieveld SH , et al. (2016) No -
5 Support Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. C Yuen RK , et al. (2017) Yes -
6 Support Lessons learned from additional research analyses of unsolved clinical exome cases. Eldomery MK , et al. (2017) No Epilepsy/seizures, microcephaly
7 Support A clinical utility study of exome sequencing versus conventional genetic testing in pediatric neurology. Vissers LE , et al. (2017) No -
8 Support DDX3X mutations in two girls with a phenotype overlapping Toriello-Carey syndrome. Dikow N , et al. (2017) No Hypotonia, microcephaly
9 Support Genomic diagnosis for children with intellectual disability and/or developmental delay. Bowling KM , et al. (2017) No -
10 Support High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies. Hamdan FF , et al. (2017) No DD/ID
11 Support Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder. Takata A , et al. (2018) Yes -
12 Support A hypomorphic inherited pathogenic variant in DDX3X causes male intellectual disability with additional neurodevelopmental and neurodegenerative fe... Kellaris G , et al. (2018) No -
13 Support Phenotypic expansion in DDX3X - a common cause of intellectual disability in females. Wang X , et al. (2018) No -
14 Support Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model. Guo H , et al. (2018) Yes -
15 Support Three de novo DDX3X variants associated with distinctive brain developmental abnormalities and brain tumor in intellectually disabled females. Scala M , et al. (2019) No Autistic features (hand stereotypies)
16 Support Lessons Learned from Large-Scale, First-Tier Clinical Exome Sequencing in a Highly Consanguineous Population. Monies D , et al. (2019) No Autistic features, stereotypies
17 Support Increased diagnostic and new genes identification outcome using research reanalysis of singleton exome sequencing. Bruel AL , et al. (2019) No -
18 Support Expansion of phenotype of DDX3X syndrome: six new cases. Beal B , et al. (2019) No -
19 Support Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks. Ruzzo EK , et al. (2019) Yes -
Rare Variants   (94)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - stop_gained De novo NA - 30349862 Wang X , et al. (2018)
- - inframe_deletion De novo NA - 30349862 Wang X , et al. (2018)
- - inframe_deletion De novo NA - 30936465 Scala M , et al. (2019)
- - frameshift_variant De novo NA - 30349862 Wang X , et al. (2018)
- - frameshift_variant De novo NA - 31274575 Beal B , et al. (2019)
- - splice_region_variant De novo NA - 30349862 Wang X , et al. (2018)
c.-82G>A - splice_site_variant De novo NA - 30349862 Wang X , et al. (2018)
- - frameshift_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
- - splice_site_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1386C>G p.Tyr462Ter stop_gained Unknown - - 30349862 Wang X , et al. (2018)
c.284+1G>A - splice_site_variant De novo NA - 30349862 Wang X , et al. (2018)
c.874C>T p.Arg292Ter stop_gained De novo NA - 30349862 Wang X , et al. (2018)
- - frameshift_variant De novo NA Simplex 28327206 Eldomery MK , et al. (2017)
c.26C>G p.Ala9Gly missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.88G>C p.Gly30Arg missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.233C>G p.Ser78Ter stop_gained De novo NA - 28333917 Vissers LE , et al. (2017)
c.46-2A>G - splice_site_variant De novo NA Simplex 30564305 Guo H , et al. (2018)
c.-73_-72insTATA - frameshift_variant De novo NA - 30349862 Wang X , et al. (2018)
c.619C>T p.Gln207Ter stop_gained De novo NA - 28554332 Bowling KM , et al. (2017)
c.745G>T p.Glu249Ter stop_gained De novo NA - 28554332 Bowling KM , et al. (2017)
c.758C>T p.Ala253Val missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.887G>C p.Arg296Pro missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.949T>C p.Cys317Arg missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.577G>T p.Gly193Ter stop_gained De novo NA - 27159028 Fieremans N , et al. (2016)
c.865-2A>G - splice_site_variant De novo NA - 27479843 Lelieveld SH , et al. (2016)
c.-78del - frameshift_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1021T>C p.Cys341Arg missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.1244T>A p.Ile415Asn missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.1304T>C p.Leu435Pro missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.1438A>G p.Arg480Gly missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.1595C>T p.Thr532Met missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.1600C>T p.Arg534Cys missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.1805G>A p.Arg602Gln missense_variant De novo NA - 30349862 Wang X , et al. (2018)
c.-83A>G - splice_site_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1600C>G p.Arg534Gly missense_variant De novo NA - 28371085 Dikow N , et al. (2017)
c.1703C>T p.Pro568Leu missense_variant De novo NA - 28371085 Dikow N , et al. (2017)
c.1511G>A p.Gly504Glu missense_variant De novo NA - 30936465 Scala M , et al. (2019)
c.46-2A>G - splice_site_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.262_264del p.Arg88del inframe_deletion De novo NA - 30349862 Wang X , et al. (2018)
c.136C>T p.Arg46Ter stop_gained De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.233C>G p.Ser78Ter stop_gained De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.873C>A p.Tyr291Ter stop_gained De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.931C>T p.Arg311Ter stop_gained De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1693C>T p.Gln565Ter stop_gained De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.107G>A p.Gly36Glu missense_variant Familial Maternal - 30349862 Wang X , et al. (2018)
c.1171-2A>G - splice_site_variant De novo NA Simplex 25363768 Iossifov I , et al. (2014)
c.226dup p.Ser76LysfsTer2 splice_site_variant De novo NA - 31274575 Beal B , et al. (2019)
c.977G>A p.Arg326His missense_variant De novo NA Simplex 29346770 Takata A , et al. (2018)
c.581A>T p.Asn194Ile missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.641T>C p.Ile214Thr missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.698C>T p.Ala233Val missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.704T>C p.Leu235Pro missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.977G>A p.Arg326His missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.236_241dup p.Arg79_Gly80dup inframe_insertion De novo NA - 30349862 Wang X , et al. (2018)
c.147del p.Gly51ValfsTer170 frameshift_variant Familial - - 31231135 Bruel AL , et al. (2019)
c.833dup p.Leu278PhefsTer17 frameshift_variant Familial - - 31231135 Bruel AL , et al. (2019)
c.1126C>T p.Arg376Cys missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1175T>C p.Leu392Pro missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1250A>C p.Gln417Pro missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1423C>G p.Arg475Gly missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1440A>T p.Arg480Ser missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1463G>A p.Arg488His missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1520T>C p.Ile507Thr missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1541T>C p.Ile514Thr missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1601G>A p.Arg534His missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1703C>T p.Pro568Leu missense_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
NM_001193416.1:c.1804C>T p.Arg602Ter stop_gained De novo NA - 30349862 Wang X , et al. (2018)
c.685_687del p.Gly229del inframe_deletion Unknown - Simplex 31130284 Monies D , et al. (2019)
c.1601G>A p.Arg534His missense_variant De novo NA Simplex 29100083 Hamdan FF , et al. (2017)
c.599dup p.Tyr200Ter frameshift_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
- - frameshift_variant De novo NA Multiplex (monozygotic twins) 30349862 Wang X , et al. (2018)
c.362G>T p.Arg121Leu missense_variant Familial Maternal - 28327206 Eldomery MK , et al. (2017)
c.758C>T p.Ala253Val missense_variant De novo NA Simplex 28327206 Eldomery MK , et al. (2017)
c.426_437del p.Ser143_Leu146del frameshift_variant De novo NA - 31274575 Beal B , et al. (2019)
c.269dup p.Ser90ArgfsTer8 frameshift_variant De novo NA - 27479843 Lelieveld SH , et al. (2016)
c.734_736del p.Asp245del inframe_deletion De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1776dup p.Ser593Ter frameshift_variant De novo NA Multiplex 31398340 Ruzzo EK , et al. (2019)
c.856G>A p.Ala286Thr missense_variant Unknown Not maternal - 27159028 Fieremans N , et al. (2016)
c.160dup p.Asp54GlyfsTer2 frameshift_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.641del p.Ile214ThrfsTer7 frameshift_variant De novo NA Simplex 28263302 C Yuen RK , et al. (2017)
c.655dup p.Asp219GlyfsTer76 frameshift_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1321del p.Asp441IlefsTer3 frameshift_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1383dup p.Tyr462IlefsTer3 frameshift_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.236G>A p.Arg79Lys missense_variant Familial Maternal Multiplex 29490693 Kellaris G , et al. (2018)
c.1229_1230dup p.Thr411LeufsTer10 frameshift_variant De novo NA - 27479843 Lelieveld SH , et al. (2016)
c.439_440dup p.Gln148AsnfsTer74 frameshift_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.590_591del p.Leu197HisfsTer97 frameshift_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1535_1536del p.His512ArgfsTer5 frameshift_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.1229_1230dup p.Thr411LeufsTer10 frameshift_variant De novo NA - 26235985 Snijders Blok L , et al. (2015)
c.491_494delinsTCTC p.Asp164_Asp165delinsValSer inframe_indel De novo NA - 30936465 Scala M , et al. (2019)
c.898G>T p.Val300Phe missense_variant Familial Maternal Multiplex 26235985 Snijders Blok L , et al. (2015)
c.595A>C;c.643A>C p.Lys199Gln;p.Lys215Gln missense_variant De novo NA Simplex 28263302 C Yuen RK , et al. (2017)
c.107G>A p.Gly36Glu missense_variant Familial Maternal Multi-generational 26235985 Snijders Blok L , et al. (2015)
c.1084C>T p.Arg362Cys missense_variant Familial Maternal Multi-generational 26235985 Snijders Blok L , et al. (2015)
Common Variants  

No common variants reported.

SFARI Gene score
1

High Confidence

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014). A second de novo loss-of-function variant in the DDX3X gene was identified in an ASD proband from a simplex family from the ASD: Genomes to Outcome Study cohort by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in this gene, a probability of LoF intolerance rate (pLI) > 0.9, and higher-than-expected mutation rate (false discovery rate < 15%), DDX3X was classified as an ASD candidate gene in Yuen et al., 2017.

Score Delta: Score remained at 2S

1

High Confidence

See all Category 1 Genes

We considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.

10/1/2019
2S
icon
1

Decreased from 2S to 1

New Scoring Scheme
Description

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014). A second de novo loss-of-function variant in the DDX3X gene was identified in an ASD proband from a simplex family from the ASD: Genomes to Outcome Study cohort by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in this gene, a probability of LoF intolerance rate (pLI) > 0.9, and higher-than-expected mutation rate (false discovery rate < 15%), DDX3X was classified as an ASD candidate gene in Yuen et al., 2017.

Reports Added
[New Scoring Scheme]
7/1/2019
2S
icon
2S

Decreased from 2S to 2S

Description

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014). A second de novo loss-of-function variant in the DDX3X gene was identified in an ASD proband from a simplex family from the ASD: Genomes to Outcome Study cohort by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in this gene, a probability of LoF intolerance rate (pLI) > 0.9, and higher-than-expected mutation rate (false discovery rate < 15%), DDX3X was classified as an ASD candidate gene in Yuen et al., 2017.

4/1/2019
2S
icon
2S

Decreased from 2S to 2S

Description

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014). A second de novo loss-of-function variant in the DDX3X gene was identified in an ASD proband from a simplex family from the ASD: Genomes to Outcome Study cohort by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in this gene, a probability of LoF intolerance rate (pLI) > 0.9, and higher-than-expected mutation rate (false discovery rate < 15%), DDX3X was classified as an ASD candidate gene in Yuen et al., 2017.

1/1/2019
2S
icon
2S

Decreased from 2S to 2S

Description

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014). A second de novo loss-of-function variant in the DDX3X gene was identified in an ASD proband from a simplex family from the ASD: Genomes to Outcome Study cohort by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in this gene, a probability of LoF intolerance rate (pLI) > 0.9, and higher-than-expected mutation rate (false discovery rate < 15%), DDX3X was classified as an ASD candidate gene in Yuen et al., 2017.

10/1/2018
2S
icon
2S

Decreased from 2S to 2S

Description

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014). A second de novo loss-of-function variant in the DDX3X gene was identified in an ASD proband from a simplex family from the ASD: Genomes to Outcome Study cohort by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in this gene, a probability of LoF intolerance rate (pLI) > 0.9, and higher-than-expected mutation rate (false discovery rate < 15%), DDX3X was classified as an ASD candidate gene in Yuen et al., 2017.

7/1/2018
3.3 + acc + S
icon
2S

Decreased from 3.3 + acc + S to 2S

Description

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014). A second de novo loss-of-function variant in the DDX3X gene was identified in an ASD proband from a simplex family from the ASD: Genomes to Outcome Study cohort by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in this gene, a probability of LoF intolerance rate (pLI) > 0.9, and higher-than-expected mutation rate (false discovery rate < 15%), DDX3X was classified as an ASD candidate gene in Yuen et al., 2017.

10/1/2017
2S
icon
2S

Increased from 2S to 2S

Description

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014). A second de novo loss-of-function variant in the DDX3X gene was identified in an ASD proband from a simplex family from the ASD: Genomes to Outcome Study cohort by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in this gene, a probability of LoF intolerance rate (pLI) > 0.9, and higher-than-expected mutation rate (false discovery rate < 15%), DDX3X was classified as an ASD candidate gene in Yuen et al., 2017.

4/1/2017
3S
icon
2S

Decreased from 3S to 2S

Description

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014). A second de novo loss-of-function variant in the DDX3X gene was identified in an ASD proband from a simplex family from the ASD: Genomes to Outcome Study cohort by whole genome sequencing as part of the MSSNG initiative in Yuen et al., 2017. Based on the discovery of two de novo LoF variants in this gene, a probability of LoF intolerance rate (pLI) > 0.9, and higher-than-expected mutation rate (false discovery rate < 15%), DDX3X was classified as an ASD candidate gene in Yuen et al., 2017.

7/1/2016
3S
icon
3S

Decreased from 3S to 3S

Description

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014).

4/1/2016
3S
icon
3S

Decreased from 3S to 3S

Description

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014).

7/1/2015
icon
3S

Increased from to 3S

Description

35 unique de novo variants (including 19 predicted loss-of-function alleles and 5 missense variants experimentally shown to be loss-of-function) in the DDX3X gene were identified in 38 female cases with intellectual disability, 20 of whom also presented with behavioral problems including autism spectrum disorder, hyperactivity, and aggression (Snijders Blok et al., 2015). A de novo splice-site variant in this gene was also identified in an ASD proband from the Simons Simplex Collection (Iossifov et al., 2014).

Krishnan Probability Score

Score 0.5862682256489

Ranking 514/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
ExAC Score

Score 0.99893006535012

Ranking 1082/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Sanders TADA Score

Score 0.47427199943605

Ranking 396/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Zhang D Score

Score 0.29074388690476

Ranking 2871/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
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SFARI Gene Update

We are pleased to announce some changes to the ongoing curation of the data in SFARI Gene. In the context of a continued effort to develop the human gene module and its manually curated list of autism risk genes, we are modifying other aspects of the site to focus on the information that is of greatest interest to the research community. The version of SFARI Gene that has been developed until now will be frozen and will remain available as “SFARI Gene Archive”. Please see the announcement for more details.
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