Gene Gene information from NCBI Gene database.
Entrez ID 1654
Gene name DEAD-box helicase 3 X-linked
Gene symbol DDX3X
Synonyms (NCBI Gene)
CAP-RfDBXDDX14DDX3HLP2MRX102MRXSSB
Chromosome X
Chromosome location Xp11.4
Summary 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 has ATP-dependent RNA helicase activity. This protein has been reported to display a high
SNPs SNP information provided by dbSNP.
103
SNP ID Visualize variation Clinical significance Consequence
rs200427211 C>A,T Pathogenic Non coding transcript variant, coding sequence variant, missense variant, genic downstream transcript variant
rs752738546 G>A,T Pathogenic Missense variant, coding sequence variant, non coding transcript variant, stop gained, genic downstream transcript variant
rs769546741 C>G,T Likely-pathogenic Coding sequence variant, non coding transcript variant, stop gained, synonymous variant, genic downstream transcript variant, 5 prime UTR variant
rs796052226 T>C Pathogenic Missense variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs796052227 G>- Pathogenic Frameshift variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
1857
miRTarBase ID miRNA Experiments Reference
MIRT004132 hsa-miR-192-5p Microarray 16822819
MIRT016125 hsa-miR-421 Sequencing 20371350
MIRT022863 hsa-miR-124-3p Proteomics;Microarray 18668037
MIRT024813 hsa-miR-215-5p Microarray 19074876
MIRT025200 hsa-miR-181a-5p Sequencing 20371350
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
122
GO ID Ontology Definition Evidence Reference
GO:0000166 Function Nucleotide binding IEA
GO:0002376 Process Immune system process IEA
GO:0002753 Process Cytoplasmic pattern recognition receptor signaling pathway IDA 23478265
GO:0003676 Function Nucleic acid binding IEA
GO:0003677 Function DNA binding IDA 21589879
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
300160 2745 ENSG00000215301
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O00571
Protein name ATP-dependent RNA helicase DDX3X (EC 3.6.4.13) (CAP-Rf) (DEAD box protein 3, X-chromosomal) (DEAD box, X isoform) (DBX) (Helicase-like protein 2) (HLP2)
Protein function Multifunctional ATP-dependent RNA helicase (PubMed:17357160, PubMed:21589879, PubMed:31575075). The ATPase activity can be stimulated by various ribo-and deoxynucleic acids indicative for a relaxed substrate specificity (PubMed:29222110). In vit
PDB 2I4I , 2JGN , 3JRV , 4O2C , 4O2E , 4O2F , 4PX9 , 4PXA , 5E7I , 5E7J , 5E7M , 6CZ5 , 6O5F , 7LIU , 8SSW
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00270 DEAD 204 392 DEAD/DEAH box helicase Domain
PF00271 Helicase_C 426 536 Helicase conserved C-terminal domain Family
Tissue specificity TISSUE SPECIFICITY: Widely expressed (PubMed:15294876). In testis, expressed in spermatids (PubMed:15294876). Expressed in epidermis and liver (at protein level) (PubMed:16301996, PubMed:16818630). {ECO:0000269|PubMed:15294876, ECO:0000269|PubMed:16301996
Sequence
MSHVAVENALGLDQQFAGLDLNSSDNQSGGSTASKGRYIPPHLRNREATKGFYDKDSSGW
SSSKDKDAYSSFGSRSDSRGKSSFFSDRGSGSRGRFDDRGRSDYDGIGSRGDRSGFGKFE
RGGNSRWCDKSDEDDWSKPLPPSERLEQELFSGGNTGINFEKYDDIPVEATGNNCPPHIE
SFSDVEMGEIIMGNIELTRYTRPTPVQKHAIPIIKEKRDLMACAQTGSGKTAAFLLPILS
QIYSDGPGEALRAMKENGRYGRRKQYPISLVLAPTRELAVQIYEEARKFSYRSRVRPCVV
YGGADIGQQIRDLERGCHLLVATPGRLVDMMERGKIGLDFCKYLVLDEADRMLDMGFEPQ
IRRIVEQDTMPPKGVRHTMMFSATFPKEIQML
ARDFLDEYIFLAVGRVGSTSENITQKVV
WVEESDKRSFLLDLLNATGKDSLTLVFVETKKGADSLEDFLYHEGYACTSIHGDRSQRDR
EEALHQFRSGKSPILVATAVAARGLDISNVKHVINFDLPSDIEEYVHRIGRTGRVG
NLGL
ATSFFNERNINITKDLLDLLVEAKQEVPSWLENMAYEHHYKGSSRGRSKSSRFSGGFGAR
DYRQSSGASSSSFSSSRASSSRSGGGGHGSSRGFGGGGYGGFYNSDGYGGNYNSQGVDWW
GN
Sequence length 662
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  RIG-I-like receptor signaling pathway
Hepatitis B
Viral carcinogenesis
  Neutrophil degranulation
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
53
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Cerebellar vermis hypoplasia Pathogenic rs1569240005 RCV000779659
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Congenital cerebellar hypoplasia Likely pathogenic; Pathogenic rs796052231, rs1569240005 RCV001257982
RCV001257983
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
DDX3X-related disorder Pathogenic; Likely pathogenic rs1555950665, rs2519522836, rs2519518691, rs1064793796, rs1131691571, rs1555953488, rs2063876393 RCV004529158
RCV004536725
RCV004534663
RCV004535505
RCV001249289
View all (2 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
DDX3X-Related Neurodevelopmental Disorder Likely pathogenic rs2519481050 RCV003335864
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Abnormal cerebral morphology Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Acute myeloid leukemia Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CEREBELLAR HYPOPLASIA/ATROPHY, EPILEPSY, AND GLOBAL DEVELOPMENTAL DELAY Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Cervical cancer Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Adenocarcinoma Adenocarcinoma BEFREE 26294807
★☆☆☆☆
Found in Text Mining only
Adult Medulloblastoma Medulloblastoma BEFREE 22820256, 24608801, 25043297, 25724843, 27180681, 30292066, 30936465
★☆☆☆☆
Found in Text Mining only
Alzheimer Disease Alzheimer disease Pubtator 36928034 Associate
★☆☆☆☆
Found in Text Mining only
Amyotrophic Lateral Sclerosis Amyotrophic Lateral Sclerosis BEFREE 29118923
★☆☆☆☆
Found in Text Mining only
ANOPHTHALMIA AND PULMONARY HYPOPLASIA Syndromic microphthalmia BEFREE 26294807
★☆☆☆☆
Found in Text Mining only
Anxiety Anxiety disorder Pubtator 35536379 Stimulate
★☆☆☆☆
Found in Text Mining only
Aphasia Aphasia CLINVAR_DG
★☆☆☆☆
Found in Text Mining only
Apraxias Apraxia Pubtator 36117209 Associate
★☆☆☆☆
Found in Text Mining only
Astrocytoma Astrocytoma Pubtator 30936465 Associate
★☆☆☆☆
Found in Text Mining only
Attention deficit hyperactivity disorder Attention Deficit Hyperactivity Disorder CLINVAR_DG
★☆☆☆☆
Found in Text Mining only