Human Gene Module / Chromosome X / DDX53

DDX53DEAD (Asp-Glu-Ala-Asp) box polypeptide 53

SFARI Gene Score
2
Strong Candidate Criteria 2.1
Autism Reports / Total Reports
5 / 5
Rare Variants / Common Variants
6 / 0
EAGLE Score
7.3
Moderate Learn More
Aliases
DDX53, CAGE,  CT26
Associated Syndromes
-
Chromosome Band
Xp22.11
Associated Disorders
ID
Genetic Category
Rare Single Gene Mutation
Relevance to Autism

Rare deletions involving the DDX53 gene have been identified in individuals with ASD (Pinto et al., 2010).

Molecular Function

This intronless gene encodes a protein which contains several domains found in members of the DEAD-box helicase protein family. Other members of this protein family participate in ATP-dependent RNA unwinding.

External Links
Gene CardOpen Targets PlatformgnomAD browserPubMed
Human
Entrez GeneUniProtHumanBaseVariCarta
SFARI Genomic Platforms
GPF browser SFARI genome browser
Reports related to DDX53 (5 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Primary Functional impact of global rare copy number variation in autism spectrum disorders Pinto D , et al. (2010) Yes -
2 Support A discovery resource of rare copy number variations in individuals with autism spectrum disorder Prasad A , et al. (2013) Yes -
3 Support Prospective diagnostic analysis of copy number variants using SNP microarrays in individuals with autism spectrum disorders Nava C , et al. (2013) Yes ID
4 Support - Zhou X et al. (2022) Yes -
5 Support - Hu C et al. (2023) Yes -
Rare Variants   (6)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - copy_number_loss Unknown - Unknown 23275889 Prasad A , et al. (2013)
- - copy_number_loss Familial Maternal Simplex 23632794 Nava C , et al. (2013)
- - copy_number_loss Familial Maternal Simplex 20531469 Pinto D , et al. (2010)
- - copy_number_loss Familial Maternal Multiplex 20531469 Pinto D , et al. (2010)
c.864A>C p.Pro288%3D synonymous_variant De novo - - 35982159 Zhou X et al. (2022)
c.530_549del p.Asn177SerfsTer7 frameshift_variant Familial Maternal - 37007974 Hu C et al. (2023)
Common Variants  

No common variants reported.

SFARI Gene score
2

Strong Candidate

Maternally transmitted X-linked deletions at DDX53-PTCHD1 were found in 7 males / 996 both sexes vs. 0 / 4964 both sexes (p value = 1 x 10-6). 6 of the 7 deletions here more clearly impact DDX53 than PTCHD1 but are later very strongly implicated elsewhere both via presence of PTCHD antisense transcripts and PTCHD1 point mutations (PMID 20844286). In addition, rare deletions involving the DDX53 gene have been identified in individuals with ASD (PMID 20531469).

Score Delta: Score remained at 2

criteria met
See SFARI Gene'scoring criteria
2

Strong Candidate

See all Category 2 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.

4/1/2022
3
icon
2

Decreased from 3 to 2

Description

Maternally transmitted X-linked deletions at DDX53-PTCHD1 were found in 7 males / 996 both sexes vs. 0 / 4964 both sexes (p value = 1 x 10-6). 6 of the 7 deletions here more clearly impact DDX53 than PTCHD1 but are later very strongly implicated elsewhere both via presence of PTCHD antisense transcripts and PTCHD1 point mutations (PMID 20844286). In addition, rare deletions involving the DDX53 gene have been identified in individuals with ASD (PMID 20531469).

10/1/2019
4
icon
3

Decreased from 4 to 3

New Scoring Scheme
Description

Maternally transmitted X-linked deletions at DDX53-PTCHD1 were found in 7 males / 996 both sexes vs. 0 / 4964 both sexes (p value = 1 x 10-6). 6 of the 7 deletions here more clearly impact DDX53 than PTCHD1 but are later very strongly implicated elsewhere both via presence of PTCHD antisense transcripts and PTCHD1 point mutations (PMID 20844286). In addition, rare deletions involving the DDX53 gene have been identified in individuals with ASD (PMID 20531469).

Reports Added
[New Scoring Scheme]
7/1/2014
No data
icon
4

Increased from No data to 4

Description

Maternally transmitted X-linked deletions at DDX53-PTCHD1 were found in 7 males / 996 both sexes vs. 0 / 4964 both sexes (p value = 1 x 10-6). 6 of the 7 deletions here more clearly impact DDX53 than PTCHD1 but are later very strongly implicated elsewhere both via presence of PTCHD antisense transcripts and PTCHD1 point mutations (PMID 20844286). In addition, rare deletions involving the DDX53 gene have been identified in individuals with ASD (PMID 20531469).

4/1/2014
No data
icon
4

Increased from No data to 4

Description

Maternally transmitted X-linked deletions at DDX53-PTCHD1 were found in 7 males / 996 both sexes vs. 0 / 4964 both sexes (p value = 1 x 10-6). 6 of the 7 deletions here more clearly impact DDX53 than PTCHD1 but are later very strongly implicated elsewhere both via presence of PTCHD antisense transcripts and PTCHD1 point mutations (PMID 20844286). In addition, rare deletions involving the DDX53 gene have been identified in individuals with ASD (PMID 20531469).

Krishnan Probability Score

Score 0.4816185547434

Ranking 7913/25841 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.
Original Source
ExAC Score

Score 0.82539895273504

Ranking 3782/18225 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
Original Source
Sanders TADA Score

Score 0.28487805420464

Ranking 168/18665 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).
Original Source
Larsen Cumulative Evidence Score

Score 17

Ranking 119/461 scored genes


[Show Scoring Methodology]
Larsen and colleagues generated gene scores based on the sum of evidence for all available ASD-associated variants in a gene, with assessments based on mode of inheritance, effect size, and variant frequency in the general population. The approach was first presented in Mol Autism 7:44 (2016), and scores for 461 genes can be found in column I in supplementary table 4 from that paper.
Original Source
External PIN Data
BioGRIDHuman Protein Reference Database
Interactome
Interaction Table
Interactor Symbol Interactor Name Interactor Organism Interactor Type Entrez ID Uniprot ID
DDX43 Probable ATP-dependent RNA helicase DDX43 Human Protein Binding 55510 Q9NXZ2
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