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Gene

USP9X

ubiquitin specific peptidase 9 X-linked

Summary

Cytogenetic location
Xp11.4
Coordinates
Chromosome X: 41,085,445–41,236,579 (GRCh38)
Exons
45 exons across 151.1 kb
Protein
2,554 amino acids
Also known as
DFFRX, FAF, FAF-X, MRX99
MANE Select transcript
ENST00000378308.7NM_001039591.3
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
        • 5 GenCC submitters rate it definitive or strong

    How USP9X 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 USP9X sits. USP9X and 5 genes near it on chromosome X, from 40,661,012 to 41,661,011.Chromosome XXp11.4p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2840.8 Mb41 Mb41.2 Mb41.4 Mb41.6 MbMED14: 40,648,305–40,735,924, reverse strandMED14: 40,834,445–40,934,085, forward strandUSP9X: 41,085,445–41,236,579, forward strandUSP9XDDX3X: 41,333,348–41,364,472, forward strandDDX3XNYX: 41,445,383–41,475,710, forward strandNYXCASK: 41,514,934–41,923,684, reverse strandCASKDiagram of USP9X: 45 exons on the forward strand of chromosome XExon 2: 2 known disease-causing sitesExon 3: 1 known disease-causing siteExon 4: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 7: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 11: 1 known disease-causing siteExon 12: 3 known disease-causing sitesExon 13: 2 known disease-causing sitesExon 14: 2 known disease-causing sitesExon 16: 1 known disease-causing siteExon 17: 1 known disease-causing siteExon 18: 1 known disease-causing siteExon 19: 2 known disease-causing sitesExon 20: 1 known disease-causing siteExon 26: 1 known disease-causing siteExon 28: 1 known disease-causing siteExon 29: 1 known disease-causing siteExon 31: 1 known disease-causing siteExon 32: 1 known disease-causing siteExon 33: 3 known disease-causing sitesExon 34: 2 known disease-causing sitesExon 35: 7 known disease-causing sitesExon 37: 2 known disease-causing sitesExon 38: 1 known disease-causing siteExon 40: 1 known disease-causing siteExon 41: 1 known disease-causing siteExon 42: 2 known disease-causing sitesExon 43: 1 known disease-causing siteExon 1: 41,085,445–41,086,109, 665 basesExon 2: 41,123,471–41,123,724, 254 basesExon 3: 41,129,000–41,129,145, 146 basesExon 4: 41,131,457–41,131,536, 80 basesExon 5: 41,134,725–41,134,837, 113 basesExon 6: 41,136,804–41,137,022, 219 basesExon 7: 41,140,656–41,140,771, 116 basesExon 8: 41,140,966–41,141,217, 252 basesExon 9: 41,141,293–41,141,431, 139 basesExon 10: 41,143,291–41,143,443, 153 basesExon 11: 41,144,522–41,144,626, 105 basesExon 12: 41,148,369–41,148,575, 207 basesExon 13: 41,150,921–41,151,057, 137 basesExon 14: 41,152,948–41,153,081, 134 basesExon 15: 41,162,790–41,162,877, 88 basesExon 16: 41,165,872–41,166,214, 343 basesExon 17: 41,167,482–41,167,577, 96 basesExon 18: 41,168,007–41,168,218, 212 basesExon 19: 41,169,995–41,170,235, 241 basesExon 20: 41,170,470–41,170,619, 150 basesExon 21: 41,171,838–41,171,958, 121 basesExon 22: 41,183,998–41,184,128, 131 basesExon 23: 41,184,397–41,184,675, 279 basesExon 24: 41,186,517–41,186,642, 126 basesExon 25: 41,187,992–41,188,117, 126 basesExon 26: 41,189,309–41,189,475, 167 basesExon 27: 41,196,251–41,196,359, 109 basesExon 28: 41,196,592–41,196,738, 147 basesExon 29: 41,197,364–41,197,510, 147 basesExon 30: 41,198,528–41,198,750, 223 basesExon 31: 41,201,060–41,201,280, 221 basesExon 32: 41,205,303–41,205,493, 191 basesExon 33: 41,210,509–41,210,682, 174 basesExon 34: 41,214,568–41,214,709, 142 basesExon 35: 41,215,899–41,216,652, 754 basesExon 36: 41,217,220–41,217,343, 124 basesExon 37: 41,218,372–41,218,597, 226 basesExon 38: 41,219,102–41,219,231, 130 basesExon 39: 41,223,217–41,223,402, 186 basesExon 40: 41,224,742–41,224,962, 221 basesExon 41: 41,225,049–41,225,137, 89 basesExon 42: 41,229,253–41,229,409, 157 basesExon 43: 41,229,567–41,229,779, 213 basesExon 44: 41,230,501–41,230,596, 96 basesExon 45: 41,232,387–41,236,579, 4,193 bases1510152025303540455′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 12.5 kb of the gene's 151.1 kb; 7,665 of those bases code for the protein.

    How a genome test reads USP9X

    50

    positions in USP9X 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 151.1 kb of USP9X, introns included, not only the 12.5 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.). USP9X gene: ubiquitin specific peptidase 9 X-linked. Retrieved 16 October 2026, from https://dantelabs.com/genes/usp9x

    Vancouver

    Dante Labs. USP9X gene: ubiquitin specific peptidase 9 X-linked [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/usp9x

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