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Gene

DDX3X

DEAD-box helicase 3 X-linked

Summary

Cytogenetic location
Xp11.4
Coordinates
Chromosome X: 41,334,162–41,350,274 (GRCh38)
Exons
17 exons across 16.1 kb
Protein
662 amino acids
Also known as
DBX, HLP2, DDX14, CAP-Rf
Previous symbols
DDX3
MANE Select transcript
ENST00000644876.2NM_001356.5
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

    • Intellectual Disability

      • One of 233 genes linked to it

        • ClinGen rates the link definitive
        • 6 GenCC submitters rate it definitive or strong

    How DDX3X is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome X, with a bracket where DDX3X sits. DDX3X and 6 genes near it on chromosome X, from 40,842,218 to 41,842,217.Chromosome XXp11.4p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2841 Mb41.2 Mb41.4 Mb41.6 Mb41.8 Mb: 40,834,445–40,934,085, forward strandUSP9X: 41,085,346–41,236,579, forward strandUSP9XDDX3X: 41,334,162–41,350,274, forward strandDDX3XNYX: 41,445,383–41,475,710, forward strandNYXCASK: 41,514,934–41,923,684, reverse strandCASKGPR34: 41,688,968–41,699,620, forward strandGPR34GPR82: 41,724,175–41,730,130, forward strandGPR82Diagram of DDX3X: 17 exons on the forward strand of chromosome XExon 1: 4 known disease-causing sitesExon 2: 3 known disease-causing sitesExon 3: 6 known disease-causing sitesExon 4: 8 known disease-causing sitesExon 5: 5 known disease-causing sitesExon 6: 5 known disease-causing sitesExon 7: 16 known disease-causing sitesExon 8: 3 known disease-causing sitesExon 9: 6 known disease-causing sitesExon 10: 14 known disease-causing sitesExon 11: 11 known disease-causing sitesExon 12: 18 known disease-causing sitesExon 13: 22 known disease-causing sitesExon 14: 13 known disease-causing sitesExon 15: 11 known disease-causing sitesExon 16: 3 known disease-causing sitesExon 1: 41,334,162–41,334,297, 136 basesExon 2: 41,337,408–41,337,465, 58 basesExon 3: 41,339,036–41,339,083, 48 basesExon 4: 41,341,484–41,341,616, 133 basesExon 5: 41,342,495–41,342,653, 159 basesExon 6: 41,342,737–41,342,836, 100 basesExon 7: 41,343,216–41,343,351, 136 basesExon 8: 41,343,737–41,343,822, 86 basesExon 9: 41,344,030–41,344,128, 99 basesExon 10: 41,344,239–41,344,399, 161 basesExon 11: 41,345,180–41,345,324, 145 basesExon 12: 41,345,404–41,345,548, 145 basesExon 13: 41,346,229–41,346,410, 182 basesExon 14: 41,346,505–41,346,622, 118 basesExon 15: 41,346,859–41,347,012, 154 basesExon 16: 41,347,312–41,347,451, 140 basesExon 17: 41,347,640–41,350,274, 2,635 bases1246810121416175′3′

    Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

    Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

    Nearby genes from Ensembl release 116, on GRCh38.

    Exons make up 4.6 kb of the gene's 16.1 kb; 1,989 of those bases code for the protein.

    How a genome test reads DDX3X

    165

    positions in DDX3X where ClinVar classes a change as pathogenic or likely pathogenic

    None of them falls in a region short reads find hard.

    A whole genome covers all 16.1 kb of DDX3X, introns included, not only the 4.6 kb of exons.

    Where this comes from

    • HGNC: the gene's symbol, name, other symbols and location.
    • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
    • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
    • The ACMG secondary findings list, SF v3.2.
    • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
    • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
    • Data release 2026.10.16-c6eea6bf.

    Cite this page

    APA

    Dante Labs. (n.d.). DDX3X gene: DEAD-box helicase 3 X-linked. Retrieved 16 October 2026, from https://dantelabs.com/genes/ddx3x

    Vancouver

    Dante Labs. DDX3X gene: DEAD-box helicase 3 X-linked [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/ddx3x

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