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Gene

DNMT1

DNA methyltransferase 1

Summary

Cytogenetic location
19p13.2
Coordinates
Chromosome 19: 10,133,346–10,194,953 (GRCh38)
Exons
41 exons across 61.6 kb
Protein
1,632 amino acids
Inheritance
Autosomal dominant
Also known as
MCMT, CXXC9
Previous symbols
DNMT
MANE Select transcript
ENST00000359526.9NM_001130823.3
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

  • Autosomal Dominant Cerebellar Ataxias (SCAs and DRPLA)

    • Autosomal Dominant Cerebellar AtaxiaAutosomal dominant

      A group of dominantly inherited ataxias, including SCA1, SCA2, SCA3 (Machado-Joseph disease), SCA6, SCA7, SCA17, SCA27B and DRPLA, caused by repeat expansions or point variants in genes such as ATXN1, ATXN2, ATXN3, CACNA1A, ATXN7, TBP, ATN1 and FGF14.

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

      Genetic counselling and presymptomatic testing for relatives, physiotherapy and symptom management; some forms, such as SCA27B, may respond to specific medication.

  • DNMT1-Related Ataxia, Deafness and Narcolepsy (ADCA-DN)

    • Autosomal Dominant Cerebellar Ataxia, Deafness and NarcolepsyAutosomal dominant

      An adult-onset disorder caused by DNMT1 variants, with cerebellar ataxia, sensorineural hearing loss, narcolepsy with cataplexy and later dementia.

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

      Sleep, hearing and neurological assessment, with symptom treatment for narcolepsy and hearing loss, and genetic counselling for relatives.

  • Hereditary Sensory and Autonomic Neuropathies (incl. Familial Dysautonomia)

    • Hereditary Sensory and Autonomic Neuropathy

      A group of neuropathies, including familial dysautonomia (ELP1), HSAN1 (SPTLC1/SPTLC2), HSAN2 (WNK1, RETREG1) and congenital insensitivity to pain (NTRK1, SCN9A, PRDM12), most of which are recessive while HSAN1 is dominant.

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

      Protection against unnoticed injuries, burns and infections, management of autonomic symptoms, and carrier testing for relatives (familial dysautonomia is included in Ashkenazi Jewish carrier screening).

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How DNMT1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 19, with a bracket where DNMT1 sits. DNMT1 and 36 genes near it on chromosome 19, from 9,664,150 to 10,664,149.Chromosome 1919p13.2p13.3p13.2p13.13p13.12p13.11p12p11q11q12q13.11q13.12q13.13q13.2q13.31q13.32q13.33q13.41q13.42q13.439.8 Mb10 Mb10.2 Mb10.4 Mb10.6 MbZNF562: 9,641,807–9,675,106, reverse strandZNF562ZNF846: 9,749,546–9,793,180, reverse strandZNF846FBXL12: 9,810,267–9,827,816, reverse strandFBXL12UBL5: 9,827,887–9,830,369, forward strandUBL5PIN1: 9,835,257–9,849,690, forward strandPIN1OLFM2: 9,853,717–9,936,559, reverse strandOLFM2COL5A3: 9,959,561–10,010,511, reverse strandCOL5A3RDH8: 10,013,249–10,022,279, forward strandRDH8SHFL: 10,086,017–10,093,252, forward strandANGPTL6: 10,092,335–10,106,612, reverse strandPPAN-P2RY11: 10,106,223–10,114,780, forward strandPPAN-P2RY11PPAN: 10,106,300–10,112,813, forward strandP2RY11: 10,111,689–10,118,085, forward strandP2RY11EIF3G: 10,115,010–10,119,951, reverse strandEIF3GDNMT1: 10,133,346–10,194,953, reverse strandDNMT1S1PR2: 10,221,433–10,231,331, reverse strandS1PR2MRPL4: 10,251,901–10,260,060, forward strandMRPL4ICAM1: 10,271,093–10,286,617, forward strandICAM1ICAM4: 10,286,946–10,288,522, forward strandICAM4ICAM5: 10,289,940–10,296,778, forward strandICAM5ZGLP1: 10,304,803–10,309,880, reverse strandFDX2-ZGLP1: 10,305,427–10,316,009, reverse strandFDX2: 10,309,898–10,316,026, reverse strand: 10,315,471–10,320,678, reverse strandRAVER1: 10,316,212–10,333,548, reverse strandICAM3: 10,333,776–10,339,847, reverse strandTYK2: 10,350,528–10,380,608, reverse strandTYK2CDC37: 10,391,090–10,420,224, reverse strandCDC37PDE4A: 10,416,773–10,469,816, forward strandPDE4AKEAP1: 10,484,512–10,503,558, reverse strandKEAP1S1PR5: 10,512,742–10,517,981, reverse strandS1PR5ATG4D: 10,543,533–10,553,556, forward strandATG4DKRI1: 10,553,085–10,566,031, reverse strandKRI1CDKN2D: 10,566,460–10,569,059, reverse strandCDKN2DAP1M2: 10,569,431–10,587,317, reverse strandAP1M2SLC44A2: 10,602,457–10,644,559, forward strandSLC44A2ILF3: 10,654,261–10,692,415, forward strandILF3Diagram of DNMT1: 41 exons on the reverse strand of chromosome 19Exon 38: 1 known disease-causing siteExon 37: 1 known disease-causing siteExon 25: 1 known disease-causing siteExon 21: 3 known disease-causing sitesExon 20: 3 known disease-causing sitesExon 41: 10,133,346–10,133,701, 356 basesExon 40: 10,134,217–10,134,307, 91 basesExon 39: 10,135,736–10,135,852, 117 basesExon 38: 10,136,121–10,136,287, 167 basesExon 37: 10,137,085–10,137,280, 196 basesExon 36: 10,137,832–10,138,009, 178 basesExon 35: 10,138,439–10,138,605, 167 basesExon 34: 10,139,676–10,139,817, 142 basesExon 33: 10,140,046–10,140,328, 283 basesExon 32: 10,140,781–10,140,909, 129 basesExon 31: 10,141,105–10,141,189, 85 basesExon 30: 10,142,028–10,142,220, 193 basesExon 29: 10,143,766–10,143,987, 222 basesExon 28: 10,146,351–10,146,524, 174 basesExon 27: 10,148,884–10,149,017, 134 basesExon 26: 10,149,453–10,149,657, 205 basesExon 25: 10,149,853–10,149,968, 116 basesExon 24: 10,151,398–10,151,545, 148 basesExon 23: 10,151,750–10,151,847, 98 basesExon 22: 10,154,293–10,154,479, 187 basesExon 21: 10,154,586–10,154,773, 188 basesExon 20: 10,154,905–10,155,056, 152 basesExon 19: 10,155,853–10,155,945, 93 basesExon 18: 10,156,391–10,156,509, 119 basesExon 17: 10,159,658–10,159,767, 110 basesExon 16: 10,159,842–10,159,922, 81 basesExon 15: 10,160,018–10,160,063, 46 basesExon 14: 10,160,384–10,160,418, 35 basesExon 13: 10,162,667–10,162,748, 82 basesExon 12: 10,163,326–10,163,360, 35 basesExon 11: 10,166,598–10,166,685, 88 basesExon 10: 10,168,330–10,168,364, 35 basesExon 9: 10,173,090–10,173,174, 85 basesExon 8: 10,173,871–10,173,905, 35 basesExon 7: 10,175,540–10,175,618, 79 basesExon 6: 10,177,292–10,177,367, 76 basesExon 5: 10,180,187–10,180,234, 48 basesExon 4: 10,180,350–10,180,569, 220 basesExon 3: 10,180,778–10,180,885, 108 basesExon 2: 10,182,041–10,182,077, 37 basesExon 1: 10,194,820–10,194,953, 134 bases412515′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 5.3 kb of the gene's 61.6 kb; 4,899 of those bases code for the protein.

How a genome test reads DNMT1

10

positions in DNMT1 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 61.6 kb of DNMT1, introns included, not only the 5.3 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.). DNMT1 gene: DNA methyltransferase 1. Retrieved 16 October 2026, from https://dantelabs.com/genes/dnmt1

Vancouver

Dante Labs. DNMT1 gene: DNA methyltransferase 1 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/dnmt1

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