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Gene

KMT2D

lysine methyltransferase 2D

Summary

Cytogenetic location
12q13.12
Coordinates
Chromosome 12: 49,018,978–49,060,794 (GRCh38)
Exons
55 exons across 41.8 kb
Protein
5,537 amino acids
Also known as
ALR, MLL4, CAGL114
Previous symbols
TNRC21, MLL2
MANE Select transcript
ENST00000301067.12NM_003482.4
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

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

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

How KMT2D is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 12, with a bracket where KMT2D sits. KMT2D and 30 genes near it on chromosome 12, from 48,539,886 to 49,539,885.Chromosome 1212q13.12p13.33p13.32p13.31p13.2p13.1p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11q12q13.11q13.12q13.13q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.11q24.12q24.13q24.21q24.22q24.23q24.31q24.32q24.3348.6 Mb48.8 Mb49 Mb49.2 Mb49.4 MbOR5BS1: 48,559,882–48,562,956, forward strandOR5BS1LALBA: 48,567,684–48,571,865, reverse strandLALBAKANSL2: 48,653,211–48,682,265, reverse strandKANSL2CCNT1: 48,687,601–48,716,998, reverse strandCCNT1SPMIP11: 48,727,435–48,765,790, forward strandSPMIP11ADCY6: 48,766,191–48,789,906, reverse strandADCY6CACNB3: 48,813,794–48,828,942, forward strandCACNB3DDX23: 48,829,756–48,852,842, reverse strandDDX23RND1: 48,857,134–48,865,870, reverse strandRND1ARF3: 48,903,141–48,957,531, reverse strandARF3: 48,903,503–48,957,365, reverse strandDRC2: 48,904,105–48,931,840, forward strandDRC2FKBP11: 48,921,518–48,927,909, reverse strandFKBP11WNT10B: 48,965,185–48,972,669, reverse strandWNT1: 48,978,322–48,982,620, forward strandWNT1DDN: 48,995,149–48,999,375, reverse strandDDNPRKAG1: 49,002,272–49,018,820, reverse strandPRKAG1: 49,002,274–49,024,075, reverse strandKMT2D: 49,018,978–49,060,794, reverse strandKMT2DRHEBL1: 49,064,675–49,070,127, reverse strandRHEBL1DHH: 49,086,656–49,094,807, reverse strandDHHLMBR1L: 49,096,550–49,110,900, reverse strandLMBR1LTUBA1B: 49,127,780–49,131,398, reverse strandTUBA1BTUBA1A: 49,184,146–49,189,324, reverse strandTUBA1ATUBA1C: 49,188,736–49,274,600, forward strandTUBA1CPRPH: 49,295,141–49,298,686, forward strandPRPHTROAP: 49,323,165–49,331,735, forward strandTROAPC1QL4: 49,332,409–49,337,227, reverse strandC1QL4DNAJC22: 49,345,607–49,357,546, forward strandDNAJC22SPATS2: 49,366,240–49,528,438, forward strandSPATS2KCNH3: 49,539,020–49,558,346, forward strandKCNH3Diagram of KMT2D: 55 exons on the reverse strand of chromosome 12Exon 55: 1 known disease-causing siteExon 54: 9 known disease-causing sitesExon 53: 4 known disease-causing sitesExon 52: 15 known disease-causing sitesExon 51: 5 known disease-causing sitesExon 50: 6 known disease-causing sitesExon 49: 62 known disease-causing sitesExon 48: 2 known disease-causing sitesExon 47: 2 known disease-causing sitesExon 46: 3 known disease-causing sitesExon 45: 6 known disease-causing sitesExon 44: 4 known disease-causing sitesExon 43: 5 known disease-causing sitesExon 42: 4 known disease-causing sitesExon 41: 6 known disease-causing sitesExon 40: 135 known disease-causing sitesExon 39: 16 known disease-causing sitesExon 38: 4 known disease-causing sitesExon 37: 2 known disease-causing sitesExon 36: 2 known disease-causing sitesExon 35: 50 known disease-causing sitesExon 34: 4 known disease-causing sitesExon 33: 6 known disease-causing sitesExon 32: 69 known disease-causing sitesExon 30: 7 known disease-causing sitesExon 29: 6 known disease-causing sitesExon 28: 1 known disease-causing siteExon 27: 3 known disease-causing sitesExon 26: 4 known disease-causing sitesExon 25: 3 known disease-causing sitesExon 24: 2 known disease-causing sitesExon 23: 6 known disease-causing sitesExon 22: 7 known disease-causing sitesExon 21: 4 known disease-causing sitesExon 20: 6 known disease-causing sitesExon 19: 2 known disease-causing sitesExon 18: 2 known disease-causing sitesExon 17: 7 known disease-causing sitesExon 16: 11 known disease-causing sitesExon 15: 8 known disease-causing sitesExon 14: 2 known disease-causing sitesExon 13: 3 known disease-causing sitesExon 12: 30 known disease-causing sitesExon 11: 39 known disease-causing sitesExon 10: 5 known disease-causing sitesExon 9: 2 known disease-causing sitesExon 8: 4 known disease-causing sitesExon 7: 8 known disease-causing sitesExon 6: 5 known disease-causing sitesExon 5: 5 known disease-causing sitesExon 4: 6 known disease-causing sitesExon 3: 3 known disease-causing sitesExon 55: 49,018,978–49,021,872, 2,895 basesExon 54: 49,022,043–49,022,151, 109 basesExon 53: 49,022,280–49,022,353, 74 basesExon 52: 49,022,590–49,022,875, 286 basesExon 51: 49,024,578–49,024,708, 131 basesExon 50: 49,024,810–49,024,946, 137 basesExon 49: 49,026,182–49,027,322, 1,141 basesExon 48: 49,027,803–49,027,930, 128 basesExon 47: 49,028,009–49,028,141, 133 basesExon 46: 49,028,828–49,028,958, 131 basesExon 45: 49,029,061–49,029,236, 176 basesExon 44: 49,029,401–49,029,476, 76 basesExon 43: 49,030,280–49,030,439, 160 basesExon 42: 49,030,601–49,030,768, 168 basesExon 41: 49,030,893–49,031,033, 141 basesExon 40: 49,031,175–49,033,964, 2,790 basesExon 39: 49,034,067–49,034,299, 233 basesExon 38: 49,034,410–49,034,476, 67 basesExon 37: 49,034,582–49,034,666, 85 basesExon 36: 49,034,812–49,034,935, 124 basesExon 35: 49,037,125–49,038,989, 1,865 basesExon 34: 49,039,222–49,039,358, 137 basesExon 33: 49,039,435–49,039,617, 183 basesExon 32: 49,039,724–49,041,535, 1,812 basesExon 31: 49,041,655–49,041,705, 51 basesExon 30: 49,041,917–49,041,990, 74 basesExon 29: 49,042,089–49,042,330, 242 basesExon 28: 49,042,561–49,042,645, 85 basesExon 27: 49,042,741–49,042,878, 138 basesExon 26: 49,043,076–49,043,186, 111 basesExon 25: 49,043,363–49,043,428, 66 basesExon 24: 49,043,635–49,043,782, 148 basesExon 23: 49,043,868–49,043,998, 131 basesExon 22: 49,044,200–49,044,304, 105 basesExon 21: 49,044,403–49,044,522, 120 basesExon 20: 49,044,744–49,044,965, 222 basesExon 19: 49,045,920–49,045,967, 48 basesExon 18: 49,046,065–49,046,174, 110 basesExon 17: 49,046,260–49,046,424, 165 basesExon 16: 49,046,609–49,046,790, 182 basesExon 15: 49,047,965–49,048,069, 105 basesExon 14: 49,048,659–49,048,769, 111 basesExon 13: 49,049,105–49,049,218, 114 basesExon 12: 49,049,682–49,050,790, 1,109 basesExon 11: 49,050,886–49,052,424, 1,539 basesExon 10: 49,052,564–49,052,709, 146 basesExon 9: 49,052,915–49,053,072, 158 basesExon 8: 49,053,207–49,053,321, 115 basesExon 7: 49,053,476–49,053,641, 166 basesExon 6: 49,053,978–49,054,140, 163 basesExon 5: 49,054,307–49,054,416, 110 basesExon 4: 49,054,528–49,054,751, 224 basesExon 3: 49,054,900–49,055,026, 127 basesExon 2: 49,055,276–49,055,361, 86 basesExon 1: 49,059,613–49,060,794, 1,182 bases55504540353025201510515′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 20.6 kb of the gene's 41.8 kb; 16,614 of those bases code for the protein.

How a genome test reads KMT2D

679

positions in KMT2D 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 41.8 kb of KMT2D, introns included, not only the 20.6 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.). KMT2D gene: lysine methyltransferase 2D. Retrieved 16 October 2026, from https://dantelabs.com/genes/kmt2d

Vancouver

Dante Labs. KMT2D gene: lysine methyltransferase 2D [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/kmt2d

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