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Gene

DNMT3A

DNA methyltransferase 3 alpha

Summary

Cytogenetic location
2p23.3
Coordinates
Chromosome 2: 25,227,874–25,341,925 (GRCh38)
Exons
23 exons across 114.1 kb
Protein
912 amino acids
Inheritance
Autosomal dominant
MANE Select transcript
ENST00000321117.10NM_022552.5
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

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 DNMT3A is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where DNMT3A sits. DNMT3A and 8 genes near it on chromosome 2, from 24,784,900 to 25,784,899.Chromosome 22p23.3p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.324.8 Mb25 Mb25.2 Mb25.4 Mb25.6 MbPTRHD1: 24,788,911–24,793,395, reverse strandPTRHD1CENPO: 24,793,100–24,822,376, forward strandCENPOADCY3: 24,819,169–24,920,299, reverse strandADCY3DNAJC27: 24,943,636–24,972,094, reverse strandDNAJC27EFR3B: 25,042,048–25,159,135, forward strandEFR3BPOMC: 25,160,361–25,168,952, reverse strandPOMCDNMT3A: 25,227,874–25,341,925, reverse strandDNMT3ADTNB: 25,377,028–25,673,717, reverse strandDTNBASXL2: 25,733,753–25,878,600, reverse strandASXL2Diagram of DNMT3A: 23 exons on the reverse strand of chromosome 2Exon 23: 6 known disease-causing sitesExon 22: 4 known disease-causing sitesExon 21: 1 known disease-causing siteExon 20: 4 known disease-causing sitesExon 19: 10 known disease-causing sitesExon 18: 3 known disease-causing sitesExon 17: 5 known disease-causing sitesExon 16: 5 known disease-causing sitesExon 15: 10 known disease-causing sitesExon 14: 4 known disease-causing sitesExon 13: 5 known disease-causing sitesExon 12: 1 known disease-causing siteExon 11: 4 known disease-causing sitesExon 10: 7 known disease-causing sitesExon 9: 7 known disease-causing sitesExon 8: 10 known disease-causing sitesExon 7: 7 known disease-causing sitesExon 6: 1 known disease-causing siteExon 5: 1 known disease-causing siteExon 4: 1 known disease-causing siteExon 3: 1 known disease-causing siteExon 2: 2 known disease-causing sitesExon 23: 25,227,874–25,234,420, 6,547 basesExon 22: 25,235,707–25,235,825, 119 basesExon 21: 25,236,936–25,237,005, 70 basesExon 20: 25,239,130–25,239,215, 86 basesExon 19: 25,240,302–25,240,450, 149 basesExon 18: 25,240,640–25,240,730, 91 basesExon 17: 25,241,562–25,241,707, 146 basesExon 16: 25,243,898–25,243,982, 85 basesExon 15: 25,244,155–25,244,338, 184 basesExon 14: 25,244,540–25,244,652, 113 basesExon 13: 25,245,253–25,245,332, 80 basesExon 12: 25,246,020–25,246,064, 45 basesExon 11: 25,246,160–25,246,309, 150 basesExon 10: 25,246,620–25,246,776, 157 basesExon 9: 25,247,051–25,247,158, 108 basesExon 8: 25,247,591–25,247,749, 159 basesExon 7: 25,248,037–25,248,252, 216 basesExon 6: 25,274,941–25,275,087, 147 basesExon 5: 25,275,500–25,275,543, 44 basesExon 4: 25,282,441–25,282,711, 271 basesExon 3: 25,300,139–25,300,243, 105 basesExon 2: 25,313,913–25,314,161, 249 basesExon 1: 25,341,826–25,341,925, 100 bases23201015′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 9.4 kb of the gene's 114.1 kb; 2,739 of those bases code for the protein.

How a genome test reads DNMT3A

116

positions in DNMT3A 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 114.1 kb of DNMT3A, introns included, not only the 9.4 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.). DNMT3A gene: DNA methyltransferase 3 alpha. Retrieved 17 October 2026, from https://dantelabs.com/genes/dnmt3a

Vancouver

Dante Labs. DNMT3A gene: DNA methyltransferase 3 alpha [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/dnmt3a

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