EHMT1

Chr 9q34.3

euchromatic histone lysine methyltransferase 1

Aliases:: Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D
MANE:: ENST00000460843.6

OMIM: 607001 ↗NCBI: 79813 ↗Ensembl ↗

Annotations refreshed 9 hours ago.

Predicted protein structure

AlphaFold predicted structure

EHMT1 · Q9H9B1

v62025-08-01

Predicted Aligned Error matrix for EHMT1 — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

63.9/ 100

Low

1,298 residues

Confidence breakdown

Very high(≥ 90)35%
Confident(70–90)15%
Low(50–70)4%
Very low(< 50)46%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

DDG2P
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Early onset or syndromic epilepsy
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Fetal anomalies
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Intellectual disability
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Rare syndromic craniosynostosis or isolated multisuture synostosis
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Disease associations (Open Targets)

Kleefstra syndrome 1
0.75
Kleefstra syndrome
0.71
hereditary disease
0.55
Intellectual disability
0.51
Kleefstra syndrome due to 9q34 microdeletion
0.46
Global developmental delay
0.41
Kleefstra syndrome due to a point mutation
0.37
autism spectrum disorder
0.36
atopic eczema
0.34
Gait disturbance
0.34

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

Histone-lysine N-methyltransferase EHMT1

Histone methyltransferase that specifically mono-, di- and trimethylates 'Lys-9' of histone H3 (H3K9me1, H3K9me2 and H3K9me3, respectively) in euchromatin (PubMed:12004135). H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting HP1 proteins to methylated histones (PubMed:12004135). Also weakly methylates 'Lys-27' of histone H3 (H3K27me) (PubMed:12004135). Also required for DNA methylation, the histone methyltransferase activity is not required for DNA methylation, suggesting that these 2 activities function independently (By similarity). Probably targeted to histone H3 by different DNA-binding proteins like E2F6, MGA, MAX and/or DP1 (PubMed:12004135). During G0 phase, it probably contributes to silencing of MYC- and E2F-responsive genes, suggesting a role in G0/G1 transition in cell cycle (PubMed:12004135). Involved in the differentiation of myoblastic precursors into brown adipose cells: following recruitment to chromatin by PRDM16, mediates formation of H3K9me2 and H3K9me3, inhibiting the expression of white adipose-selective genes (By similarity). Also involved in the differentiation of beige adipocytes from white adipose cells following recruitment by PRDM16 (By similarity). EHMT1 also promotes protein stabilization of PRDM16, by preventing PRDM16 ubiquitination and degradation (By similarity). In addition to the histone methyltransferase activity, also methylates non-histone proteins: mediates dimethylation of 'Lys-373' of p53/TP53 (PubMed:20118233). Represses the expression of mitochondrial function-related genes, perhaps by occupying their promoter regions, working in concert with probable chromatin reader BAZ2B (By similarity)