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Gene

KMT2C

lysine methyltransferase 2C

Summary

Cytogenetic location
7q36.1
Coordinates
Chromosome 7: 152,134,925–152,436,003 (GRCh38)
Exons
59 exons across 301.1 kb
Protein
4,911 amino acids
Also known as
KIAA1506, HALR
Previous symbols
MLL3
MANE Select transcript
ENST00000262189.11NM_170606.3
Locus type
gene with protein product

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.

      • 4 GenCC submitters rate it definitive or strong

    • One of 233 genes linked to it

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

How KMT2C is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 7, with a bracket where KMT2C sits. KMT2C and 5 genes near it on chromosome 7, from 151,785,464 to 152,785,463.Chromosome 77q36.1p22.3p22.2p22.1p21.3p21.2p21.1p15.3p15.2p15.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.21q11.22q11.23q21.11q21.12q21.13q21.2q21.3q22.1q22.2q22.3q31.1q31.2q31.31q31.32q31.33q32.1q32.2q32.3q33q34q35q36.1q36.2q36.3151.8 Mb152 Mb152.2 Mb152.4 Mb152.6 MbPRKAG2: 151,556,010–151,877,563, reverse strandPRKAG2GALNTL5: 151,956,379–152,019,929, forward strandGALNTL5GALNT11: 152,025,626–152,122,347, forward strandGALNT11KMT2C: 152,134,925–152,436,003, reverse strandKMT2CXRCC2: 152,644,771–152,676,201, reverse strandXRCC2ACTR3B: 152,759,731–152,855,378, forward strandACTR3BDiagram of KMT2C: 59 exons on the reverse strand of chromosome 7Exon 56: 2 known disease-causing sitesExon 54: 1 known disease-causing siteExon 53: 1 known disease-causing siteExon 52: 4 known disease-causing sitesExon 50: 1 known disease-causing siteExon 47: 1 known disease-causing siteExon 45: 1 known disease-causing siteExon 43: 7 known disease-causing sitesExon 40: 1 known disease-causing siteExon 38: 7 known disease-causing sitesExon 36: 8 known disease-causing sitesExon 35: 1 known disease-causing siteExon 33: 1 known disease-causing siteExon 31: 2 known disease-causing sitesExon 29: 1 known disease-causing siteExon 27: 1 known disease-causing siteExon 26: 1 known disease-causing siteExon 23: 2 known disease-causing sitesExon 22: 1 known disease-causing siteExon 20: 1 known disease-causing siteExon 18: 2 known disease-causing sitesExon 17: 2 known disease-causing sitesExon 14: 7 known disease-causing sitesExon 12: 1 known disease-causing siteExon 10: 2 known disease-causing sitesExon 9: 1 known disease-causing siteExon 6: 1 known disease-causing siteExon 4: 1 known disease-causing siteExon 1: 2 known disease-causing sitesExon 59: 152,134,925–152,136,924, 2,000 basesExon 58: 152,138,796–152,138,904, 109 basesExon 57: 152,139,186–152,139,259, 74 basesExon 56: 152,139,675–152,139,791, 117 basesExon 55: 152,144,713–152,144,881, 169 basesExon 54: 152,145,153–152,145,295, 143 basesExon 53: 152,146,599–152,146,735, 137 basesExon 52: 152,148,033–152,149,152, 1,120 basesExon 51: 152,150,900–152,151,007, 108 basesExon 50: 152,151,442–152,151,581, 140 basesExon 49: 152,152,705–152,152,954, 250 basesExon 48: 152,154,010–152,154,146, 137 basesExon 47: 152,154,267–152,154,445, 179 basesExon 46: 152,155,910–152,156,057, 148 basesExon 45: 152,156,205–152,156,346, 142 basesExon 44: 152,158,863–152,159,072, 210 basesExon 43: 152,162,117–152,163,826, 1,710 basesExon 42: 152,167,146–152,167,378, 233 basesExon 41: 152,169,186–152,169,249, 64 basesExon 40: 152,171,264–152,171,342, 79 basesExon 39: 152,174,131–152,174,242, 112 basesExon 38: 152,176,191–152,178,010, 1,820 basesExon 37: 152,179,834–152,180,126, 293 basesExon 36: 152,180,711–152,182,594, 1,884 basesExon 35: 152,182,974–152,183,156, 183 basesExon 34: 152,185,558–152,185,631, 74 basesExon 33: 152,187,262–152,187,476, 215 basesExon 32: 152,187,715–152,187,847, 133 basesExon 31: 152,194,009–152,194,128, 120 basesExon 30: 152,194,229–152,194,261, 33 basesExon 29: 152,194,440–152,194,568, 129 basesExon 28: 152,195,907–152,196,011, 105 basesExon 27: 152,199,279–152,199,459, 181 basesExon 26: 152,202,934–152,203,064, 131 basesExon 25: 152,205,106–152,205,225, 120 basesExon 24: 152,207,300–152,207,428, 129 basesExon 23: 152,220,523–152,220,735, 213 basesExon 22: 152,222,001–152,222,066, 66 basesExon 21: 152,222,573–152,222,682, 110 basesExon 20: 152,224,015–152,224,179, 165 basesExon 19: 152,224,435–152,224,616, 182 basesExon 18: 152,229,923–152,230,027, 105 basesExon 17: 152,230,220–152,230,321, 102 basesExon 16: 152,235,817–152,235,933, 117 basesExon 15: 152,238,707–152,238,826, 120 basesExon 14: 152,247,902–152,248,620, 719 basesExon 13: 152,249,876–152,249,953, 78 basesExon 12: 152,250,853–152,250,966, 114 basesExon 11: 152,251,939–152,252,090, 152 basesExon 10: 152,252,546–152,252,715, 170 basesExon 9: 152,263,016–152,263,130, 115 basesExon 8: 152,265,038–152,265,209, 172 basesExon 7: 152,273,705–152,273,867, 163 basesExon 6: 152,309,966–152,310,075, 110 basesExon 5: 152,311,798–152,311,946, 149 basesExon 4: 152,315,138–152,315,338, 201 basesExon 3: 152,330,601–152,330,739, 139 basesExon 2: 152,358,587–152,358,675, 89 basesExon 1: 152,435,626–152,436,003, 378 bases59504030201015′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 16.9 kb of the gene's 301.1 kb; 14,736 of those bases code for the protein.

How a genome test reads KMT2C

70

positions in KMT2C where ClinVar classes a change as pathogenic or likely pathogenic

24 of them (34%) fall in regions short reads find hard.

  • Low mappability (14 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.
  • Segmental duplications (24 sites)Copies of at least 1 kb sharing at least 90% identity with another part of the genome (paralogues, pseudogenes); reads may align to the wrong copy.

A whole genome covers all 301.1 kb of KMT2C, introns included, not only the 16.9 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.). KMT2C gene: lysine methyltransferase 2C. Retrieved 17 October 2026, from https://dantelabs.com/genes/kmt2c

Vancouver

Dante Labs. KMT2C gene: lysine methyltransferase 2C [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/kmt2c

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