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Gene

EHMT1

euchromatic histone lysine methyltransferase 1

Summary

Cytogenetic location
9q34.3
Coordinates
Chromosome 9: 137,619,005–137,836,127 (GRCh38)
Exons
27 exons across 217.1 kb
Protein
1,298 amino acids
Also known as
Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D, FLJ40292, GLP
Previous symbols
EHMT1-IT1
MANE Select transcript
ENST00000460843.6NM_024757.5
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

    • Kleefstra syndrome

      A condition caused by variants or deletions affecting EHMT1 (or KMT2C) that causes intellectual disability, low muscle tone and autistic features.

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

    • One of 233 genes linked to it

      • 4 GenCC submitters rate it definitive or strong

How EHMT1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 9, with a bracket where EHMT1 sits. EHMT1 and 18 genes near it on chromosome 9, from 137,227,566 to 138,227,565.Chromosome 99q34.3p24.3p24.2p24.1p23p22.3p22.2p22.1p21.3p21.2p21.1p13.3p13.2p13.1p12p11.2p11.1q11q12q13q21.11q21.12q21.13q21.2q21.31q21.32q21.33q22.1q22.2q22.31q22.32q22.33q31.1q31.2q31.3q32q33.1q33.2q33.3q34.11q34.12q34.13q34.2q34.3137.4 Mb137.6 Mb137.8 Mb138 Mb138.2 MbRNF224: 137,226,908–137,229,640, forward strandSLC34A3: 137,230,757–137,236,555, forward strandTUBB4B: 137,241,278–137,243,713, forward strandCIMIP2A: 137,243,584–137,247,770, reverse strandSTPG3: 137,250,608–137,253,483, forward strandSTPG3NELFB: 137,255,210–137,273,542, forward strandNELFBTOR4A: 137,274,854–137,282,641, forward strandTOR4ANRARP: 137,299,631–137,302,271, reverse strandNRARPEXD3: 137,306,894–137,423,911, reverse strandEXD3NOXA1: 137,422,752–137,434,451, forward strandNOXA1ENTPD8: 137,434,362–137,441,881, reverse strandENTPD8NSMF: 137,447,570–137,459,576, reverse strandNSMFPNPLA7: 137,459,952–137,550,560, reverse strandPNPLA7MRPL41: 137,550,424–137,552,555, forward strandMRPL41DPH7: 137,554,436–137,578,936, reverse strandDPH7ZMYND19: 137,582,066–137,590,520, reverse strandZMYND19ARRDC1: 137,605,619–137,617,859, forward strandARRDC1EHMT1: 137,619,005–137,836,127, forward strandEHMT1CACNA1B: 137,877,782–138,124,624, forward strandCACNA1BDiagram of EHMT1: 27 exons on the forward strand of chromosome 9Exon 1: 2 known disease-causing sitesExon 2: 4 known disease-causing sitesExon 3: 16 known disease-causing sitesExon 4: 8 known disease-causing sitesExon 5: 2 known disease-causing sitesExon 6: 5 known disease-causing sitesExon 7: 1 known disease-causing siteExon 8: 3 known disease-causing sitesExon 9: 5 known disease-causing sitesExon 10: 3 known disease-causing sitesExon 11: 4 known disease-causing sitesExon 12: 9 known disease-causing sitesExon 13: 8 known disease-causing sitesExon 14: 5 known disease-causing sitesExon 15: 3 known disease-causing sitesExon 16: 5 known disease-causing sitesExon 17: 6 known disease-causing sitesExon 18: 7 known disease-causing sitesExon 19: 11 known disease-causing sitesExon 20: 9 known disease-causing sitesExon 21: 3 known disease-causing sitesExon 22: 6 known disease-causing sitesExon 23: 9 known disease-causing sitesExon 24: 6 known disease-causing sitesExon 25: 3 known disease-causing sitesExon 26: 10 known disease-causing sitesExon 1: 137,619,005–137,619,049, 45 basesExon 2: 137,710,967–137,711,030, 64 basesExon 3: 137,716,626–137,717,182, 557 basesExon 4: 137,728,349–137,728,529, 181 basesExon 5: 137,743,371–137,743,528, 158 basesExon 6: 137,743,902–137,744,090, 189 basesExon 7: 137,752,331–137,752,408, 78 basesExon 8: 137,754,171–137,754,291, 121 basesExon 9: 137,757,880–137,758,011, 132 basesExon 10: 137,762,675–137,762,820, 146 basesExon 11: 137,775,109–137,775,252, 144 basesExon 12: 137,776,618–137,776,844, 227 basesExon 13: 137,777,882–137,778,055, 174 basesExon 14: 137,779,635–137,779,717, 83 basesExon 15: 137,782,291–137,782,397, 107 basesExon 16: 137,790,848–137,790,970, 123 basesExon 17: 137,798,813–137,798,914, 102 basesExon 18: 137,800,880–137,800,984, 105 basesExon 19: 137,811,461–137,811,615, 155 basesExon 20: 137,813,006–137,813,173, 168 basesExon 21: 137,813,386–137,813,530, 145 basesExon 22: 137,814,431–137,814,508, 78 basesExon 23: 137,815,947–137,816,062, 116 basesExon 24: 137,817,439–137,817,525, 87 basesExon 25: 137,818,060–137,818,138, 79 basesExon 26: 137,834,349–137,834,524, 176 basesExon 27: 137,834,773–137,836,127, 1,355 bases1510152025275′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 5.1 kb of the gene's 217.1 kb; 3,897 of those bases code for the protein.

How a genome test reads EHMT1

182

positions in EHMT1 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 217.1 kb of EHMT1, introns included, not only the 5.1 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.). EHMT1 gene: euchromatic histone lysine methyltransferase 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/ehmt1

Vancouver

Dante Labs. EHMT1 gene: euchromatic histone lysine methyltransferase 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/ehmt1

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