HomeAboutRankingsData Sources
Β© 2026 GeneE
🧬
GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
EHMT1
euchromatic histone lysine methyltransferase 1
Chromosome 9 Β· 9q34.3
NCBI Gene: 79813Ensembl: ENSG00000181090.21HGNC: HGNC:24650UniProt: A0A1B0GUD1
163PubMed Papers
21Diseases
0Drugs
267Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
peptidyl-lysine dimethylationmethyltransferase activitynuclear bodychromatin organizationKleefstra syndrome 1Kleefstra syndromegenetic disorderIntellectual disability
✦AI Summary

EHMT1 (euchromatic histone lysine methyltransferase 1) is a histone methyltransferase that catalyzes mono-, di-, and trimethylation of histone H3 lysine 9 (H3K9me1/2/3) in euchromatin, establishing an epigenetic mark for transcriptional repression through HP1 protein recruitment 1. Beyond histone modification, EHMT1 methylates non-histone proteins including p53 2 and contributes to DNA methylation through mechanisms independent of its methyltransferase activity. EHMT1 regulates cell cycle progression by silencing MYC- and E2F-responsive genes during G0/G1 transition and participates in brown adipocyte differentiation through PRDM16-mediated chr9 recruitment 1. EHMT1 haploinsufficiency causes Kleefstra syndrome 1, characterized by neurodevelopmental delay, intellectual disability, hypotonia, and seizures 3. The disorder exhibits broad phenotypic spectrum with genotype-phenotype associations dependent on which functional domains are disrupted: reader function disruption causes typical disease with characteristic DNA methylation signatures, while SET domain disruption alone produces milder phenotypes 3. EHMT1 controls the pace of human neuronal maturation by establishing an epigenetic barrier in progenitor cells that gradually releases transcriptional programs 4. EHMT1 also represses mitochondrial function genes in concert with BAZ2B, and elevated EHMT1 expression correlates with Alzheimer's disease progression 5. In cancer, EHMT1 contributes to epithelial-mesenchymal transition, cancer stemness, and drug resistance 6, with EHMT1/2 inhibition showing therapeutic potential in PARPi-resistant ovarian cancer 7.

Sources cited
1
EHMT1 catalyzes H3K9 mono-, di-, and trimethylation in euchromatin for transcriptional repression via HP1 recruitment; regulates cell cycle and adipocyte differentiation
PMID: 12004135
2
EHMT1 mediates dimethylation of p53/TP53 at lysine 373
PMID: 20118233
3
EHMT1 haploinsufficiency causes Kleefstra syndrome; reader domain disruption produces typical phenotype with DNA methylation signature while SET domain disruption does not
PMID: 39013458
4
EHMT1 inhibition in progenitor stage enables precocious neuronal maturation; establishes epigenetic barrier controlling pace of human cortical neuron maturation
PMID: 38297124
5
EHMT1 orthologue represses mitochondrial function genes with BAZ2B; elevated EHMT1 expression correlates with Alzheimer's disease progression
PMID: 32103178
6
EHMT1/EHMT2 are aberrantly expressed in cancers and associated with epithelial-mesenchymal transition, cancer stemness, and therapy resistance
PMID: 34954891
7
EHMT1/2 inhibition resensitizes PARPi-resistant ovarian cancer cells and reduces tumor burden in a CD8 T-cell-dependent manner
PMID: 39136655
Disease Associationsβ“˜21
Kleefstra syndrome 1Open Targets
0.77Strong
Kleefstra syndromeOpen Targets
0.71Strong
genetic disorderOpen Targets
0.54Moderate
Intellectual disabilityOpen Targets
0.51Moderate
Kleefstra syndrome due to 9q34 microdeletionOpen Targets
0.46Moderate
Global developmental delayOpen Targets
0.41Moderate
Kleefstra syndrome due to a point mutationOpen Targets
0.37Weak
atopic eczemaOpen Targets
0.37Weak
autism spectrum disorderOpen Targets
0.36Weak
neurodegenerative diseaseOpen Targets
0.34Weak
Abnormal facial shapeOpen Targets
0.34Weak
Gait disturbanceOpen Targets
0.34Weak
polymicrogyriaOpen Targets
0.34Weak
marfanoid habitus and intellectual disabilityOpen Targets
0.33Weak
hidradenitisOpen Targets
0.32Weak
obesityOpen Targets
0.32Weak
esophageal diseaseOpen Targets
0.30Weak
vascular diseaseOpen Targets
0.28Weak
cholelithiasisOpen Targets
0.28Weak
schizophreniaOpen Targets
0.27Weak
Kleefstra syndrome 1UniProt
Pathogenic Variants267
NM_024757.5(EHMT1):c.40dup (p.Glu14fs)Pathogenic
Kleefstra syndrome 1|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 14
NM_024757.5(EHMT1):c.736C>T (p.Arg246Ter)Pathogenic
Kleefstra syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 246
NM_024757.5(EHMT1):c.3126_3127del (p.Gln1043fs)Pathogenic
not provided|Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 1043
NM_024757.5(EHMT1):c.2712+1G>APathogenic
Abnormal facial shape;Polymicrogyria;Difficulty walking;Global developmental delay|not provided|Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2025
NM_024757.5(EHMT1):c.2426C>T (p.Pro809Leu)Pathogenic
not provided|Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 809
NM_024757.5(EHMT1):c.673C>T (p.Arg225Ter)Pathogenic
Kleefstra syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 225
NM_024757.5(EHMT1):c.2525G>A (p.Cys842Tyr)Likely pathogenic
Kleefstra syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 842
NM_024757.5(EHMT1):c.2995del (p.Ala999fs)Pathogenic
Kleefstra syndrome 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 999
NM_024757.5(EHMT1):c.346C>T (p.Gln116Ter)Pathogenic
Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 116
NM_024757.5(EHMT1):c.871C>T (p.Arg291Ter)Pathogenic
Kleefstra syndrome 1|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 291
NM_024757.5(EHMT1):c.1370-1G>CLikely pathogenic
Kleefstra syndrome 1|not provided
β˜…β˜…β˜†β˜†2025
NM_024757.5(EHMT1):c.2333A>C (p.His778Pro)Pathogenic
Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2025β†’ Residue 778
NM_024757.5(EHMT1):c.2276-2A>GPathogenic
Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2024
NM_024757.5(EHMT1):c.3000del (p.Asp1001fs)Pathogenic
Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2024β†’ Residue 1001
NM_024757.5(EHMT1):c.3520del (p.Leu1174fs)Pathogenic
not provided|Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2024β†’ Residue 1174
NM_024757.5(EHMT1):c.3589C>T (p.Arg1197Trp)Pathogenic
Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2024β†’ Residue 1197
NM_024757.5(EHMT1):c.3310G>A (p.Glu1104Lys)Pathogenic
Kleefstra syndrome 1|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 1104
NM_024757.5(EHMT1):c.3036-1G>APathogenic
Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2024
NM_024757.5(EHMT1):c.1468C>T (p.Arg490Ter)Pathogenic
Marfanoid habitus and intellectual disability|not provided|Inborn genetic diseases|Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2024β†’ Residue 490
NM_024757.5(EHMT1):c.3072_3073del (p.Val1026fs)Pathogenic
not provided|Kleefstra syndrome 1
β˜…β˜…β˜†β˜†2024β†’ Residue 1026
View on ClinVar β†—
Related Genes
H3-5Protein interaction100%H3-4Protein interaction100%H3-3BProtein interaction100%H3C12Protein interaction100%H3C13Protein interaction100%PCGF6Protein interaction100%
Tissue Expression6 tissues
Ovary
100%
Lung
86%
Liver
83%
Brain
71%
Bone Marrow
67%
Heart
54%
Gene Interaction Network
Click a node to explore
EHMT1H3-5H3-4H3-3BH3C12H3C13PCGF6
PROTEIN STRUCTURE
Preparing viewer…
PDB3HNA Β· 1.50 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.16Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.10 [0.07–0.16]
RankingsWhere EHMT1 stands among ~20K protein-coding genes
  • #2,749of 20,598
    Most Researched163 Β· top quartile
  • #236of 5,498
    Most Pathogenic Variants267 Β· top 5%
  • #250of 17,882
    Most Constrained (LOEUF)0.16 Β· top 5%
Genes detectedEHMT1
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
An epigenetic barrier sets the timing of human neuronal maturation.
PMID: 38297124
Nature Β· 2024
1.00
2
Pathogenic variants in KMT2C result in a neurodevelopmental disorder distinct from Kleefstra and Kabuki syndromes.
PMID: 39013459
Am J Hum Genet Β· 2024
0.90
3
Comprehensive EHMT1 variants analysis broadens genotype-phenotype associations and molecular mechanisms in Kleefstra syndrome.
PMID: 39013458
Am J Hum Genet Β· 2024
0.80
4
PMID: 20945554
0.70
5
Clinical characteristics and genetic analysis of four pediatric patients with Kleefstra syndrome.
PMID: 39696517
BMC Med Genomics Β· 2024
0.64