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Gene

ATRX

ATRX chromatin remodeler

Summary

Cytogenetic location
Xq21.1
Coordinates
Chromosome X: 77,504,880–77,786,216 (GRCh38)
Exons
35 exons across 281.3 kb
Protein
2,492 amino acids
Also known as
XH2, XNP
Previous symbols
RAD54, JMS, MRX52
MANE Select transcript
ENST00000373344.11NM_000489.6
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 reports relevant to this gene

  • 46,XY Differences of Sex Development and Gonadal Dysgenesis

    • 46,XY differences of sex development

      Conditions in people with XY chromosomes in which gonadal or genital development is atypical, caused by variants in genes such as SRD5A2, HSD17B3, NR5A1, MAP3K1, DHH, WT1, CYP11A1 and LHCGR.

      • 4 GenCC submitters rate it definitive or strong
      What knowing changes

      Diagnosis informs hormone treatment, fertility counselling and, where dysgenetic gonads carry Y material, assessment of gonadal tumour risk.

Broader groupings

  • Intellectual Disability

    • One of 233 genes linked to it

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

How ATRX 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 ATRX sits. ATRX and 7 genes near it on chromosome X, from 77,145,548 to 78,145,547.Chromosome XXq21.1p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2877.2 Mb77.4 Mb77.6 Mb77.8 Mb78 MbFGF16: 77,447,388–77,457,278, forward strandFGF16ATRX: 77,504,880–77,786,216, reverse strandATRXMAGT1: 77,825,747–77,899,271, reverse strandMAGT1COX7B: 77,895,727–77,907,555, forward strandCOX7BATP7A: 77,910,688–78,050,395, forward strandATP7APGK1: 77,910,739–78,132,378, forward strandPGK1PGAM4: 77,967,949–77,969,638, reverse strandPGAM4TAF9B: 78,126,646–78,139,705, reverse strandTAF9BDiagram of ATRX: 35 exons on the reverse strand of chromosome XExon 35: 2 known disease-causing sitesExon 34: 4 known disease-causing sitesExon 31: 3 known disease-causing sitesExon 30: 2 known disease-causing sitesExon 29: 2 known disease-causing sitesExon 28: 2 known disease-causing sitesExon 27: 2 known disease-causing sitesExon 26: 1 known disease-causing siteExon 23: 1 known disease-causing siteExon 22: 1 known disease-causing siteExon 21: 5 known disease-causing sitesExon 19: 4 known disease-causing sitesExon 18: 3 known disease-causing sitesExon 17: 1 known disease-causing siteExon 15: 2 known disease-causing sitesExon 14: 1 known disease-causing siteExon 13: 1 known disease-causing siteExon 12: 2 known disease-causing sitesExon 10: 1 known disease-causing siteExon 9: 25 known disease-causing sitesExon 8: 1 known disease-causing siteExon 7: 5 known disease-causing sitesExon 6: 1 known disease-causing siteExon 3: 2 known disease-causing sitesExon 2: 2 known disease-causing sitesExon 35: 77,504,880–77,508,629, 3,750 basesExon 34: 77,520,788–77,520,916, 129 basesExon 33: 77,521,403–77,521,498, 96 basesExon 32: 77,522,263–77,522,388, 126 basesExon 31: 77,523,252–77,523,401, 150 basesExon 30: 77,557,451–77,557,645, 195 basesExon 29: 77,558,669–77,558,846, 178 basesExon 28: 77,574,250–77,574,358, 109 basesExon 27: 77,589,834–77,589,940, 107 basesExon 26: 77,593,696–77,593,849, 154 basesExon 25: 77,599,411–77,599,580, 170 basesExon 24: 77,599,732–77,599,820, 89 basesExon 23: 77,600,434–77,600,564, 131 basesExon 22: 77,616,613–77,616,730, 118 basesExon 21: 77,618,806–77,618,981, 176 basesExon 20: 77,620,395–77,620,532, 138 basesExon 19: 77,633,207–77,633,384, 178 basesExon 18: 77,633,566–77,633,712, 147 basesExon 17: 77,634,594–77,634,703, 110 basesExon 16: 77,635,915–77,636,056, 142 basesExon 15: 77,652,114–77,652,353, 240 basesExon 14: 77,654,098–77,654,200, 103 basesExon 13: 77,656,560–77,656,653, 94 basesExon 12: 77,663,382–77,663,558, 177 basesExon 11: 77,664,645–77,664,778, 134 basesExon 10: 77,676,226–77,676,298, 73 basesExon 9: 77,681,520–77,684,593, 3,074 basesExon 8: 77,684,939–77,685,006, 68 basesExon 7: 77,688,818–77,688,927, 110 basesExon 6: 77,693,824–77,693,937, 114 basesExon 5: 77,696,577–77,696,704, 128 basesExon 4: 77,697,583–77,697,635, 53 basesExon 3: 77,698,574–77,698,629, 56 basesExon 2: 77,717,131–77,717,243, 113 basesExon 1: 77,785,982–77,786,216, 235 bases353025201510515′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 11.2 kb of the gene's 281.3 kb; 7,479 of those bases code for the protein.

How a genome test reads ATRX

85

positions in ATRX 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 281.3 kb of ATRX, introns included, not only the 11.2 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.). ATRX gene: ATRX chromatin remodeler. Retrieved 17 October 2026, from https://dantelabs.com/genes/atrx

Vancouver

Dante Labs. ATRX gene: ATRX chromatin remodeler [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/atrx

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