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Gene

KDM6A

lysine demethylase 6A

Summary

Cytogenetic location
Xp11.3
Coordinates
Chromosome X: 44,873,188–45,112,779 (GRCh38)
Exons
30 exons across 239.6 kb
Protein
1,453 amino acids
Previous symbols
UTX
MANE Select transcript
ENST00000611820.5NM_001291415.2
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

  • Kabuki Syndrome

    • A multi-system condition caused by KMT2D (type 1) or KDM6A (type 2) variants, with characteristic facial features, short stature and intellectual disability, and sometimes heart, kidney and immune problems or low blood sugar.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong
      What knowing changes

      Diagnosis guides screening for heart, kidney, hearing, immune and blood sugar problems.

How KDM6A 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 KDM6A sits. KDM6A and 3 genes near it on chromosome X, from 44,492,984 to 45,492,983.Chromosome XXp11.3p22.33p22.32p22.31p22.2p22.13p22.12p22.11p21.3p21.2p21.1p11.4p11.3p11.23p11.22p11.21p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.31q21.32q21.33q22.1q22.2q22.3q23q24q25q26.1q26.2q26.3q27.1q27.2q27.3q2844.6 Mb44.8 Mb45 Mb45.2 Mb45.4 MbFUNDC1: 44,522,431–44,543,013, reverse strandFUNDC1DUSP21: 44,844,021–44,844,888, forward strandDUSP21KDM6A: 44,873,188–45,112,779, forward strandKDM6ADIPK2B: 45,148,373–45,200,965, reverse strandDIPK2BDiagram of KDM6A: 30 exons on the forward strand of chromosome XExon 1: 4 known disease-causing sitesExon 4: 2 known disease-causing sitesExon 5: 1 known disease-causing siteExon 6: 4 known disease-causing sitesExon 7: 2 known disease-causing sitesExon 8: 1 known disease-causing siteExon 9: 1 known disease-causing siteExon 10: 2 known disease-causing sitesExon 11: 2 known disease-causing sitesExon 12: 3 known disease-causing sitesExon 15: 3 known disease-causing sitesExon 17: 5 known disease-causing sitesExon 18: 15 known disease-causing sitesExon 19: 1 known disease-causing siteExon 21: 4 known disease-causing sitesExon 22: 1 known disease-causing siteExon 23: 3 known disease-causing sitesExon 24: 4 known disease-causing sitesExon 25: 3 known disease-causing sitesExon 26: 8 known disease-causing sitesExon 27: 5 known disease-causing sitesExon 28: 1 known disease-causing siteExon 29: 4 known disease-causing sitesExon 1: 44,873,188–44,873,712, 525 basesExon 2: 44,873,924–44,873,987, 64 basesExon 3: 44,961,284–44,961,392, 109 basesExon 4: 44,974,666–44,974,715, 50 basesExon 5: 45,010,961–45,011,019, 59 basesExon 6: 45,020,610–45,020,730, 121 basesExon 7: 45,034,931–45,034,985, 55 basesExon 8: 45,037,655–45,037,689, 35 basesExon 9: 45,051,709–45,051,802, 94 basesExon 10: 45,053,829–45,053,955, 127 basesExon 11: 45,059,006–45,059,104, 99 basesExon 12: 45,059,247–45,059,466, 220 basesExon 13: 45,060,022–45,060,156, 135 basesExon 14: 45,060,609–45,060,764, 156 basesExon 15: 45,061,324–45,061,419, 96 basesExon 16: 45,062,647–45,062,748, 102 basesExon 17: 45,063,422–45,063,817, 396 basesExon 18: 45,069,579–45,070,357, 779 basesExon 19: 45,076,697–45,076,826, 130 basesExon 20: 45,078,400–45,078,505, 106 basesExon 21: 45,079,146–45,079,351, 206 basesExon 22: 45,082,576–45,082,640, 65 basesExon 23: 45,082,715–45,082,789, 75 basesExon 24: 45,083,460–45,083,608, 149 basesExon 25: 45,085,865–45,085,979, 115 basesExon 26: 45,089,743–45,089,930, 188 basesExon 27: 45,090,723–45,090,864, 142 basesExon 28: 45,107,410–45,107,536, 127 basesExon 29: 45,110,079–45,110,249, 171 basesExon 30: 45,111,382–45,112,779, 1,398 bases1510152025305′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 6.1 kb of the gene's 239.6 kb; 4,362 of those bases code for the protein.

How a genome test reads KDM6A

99

positions in KDM6A 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 239.6 kb of KDM6A, introns included, not only the 6.1 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.). KDM6A gene: lysine demethylase 6A. Retrieved 17 October 2026, from https://dantelabs.com/genes/kdm6a

Vancouver

Dante Labs. KDM6A gene: lysine demethylase 6A [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/kdm6a

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