SUV39H1 (Suppressor of Variegation 3-9 Homolog 1)
A histone methyltransferase regulating heterochromatin and genomic stability
Gene Information Card
| Symbol | SUV39H1 |
|---|---|
| Full Name | Suppressor of Variegation 3-9 Homolog 1 |
| Gene Type | Protein coding |
| Chromosomal Location | Xp11.23 |
| NCBI Gene ID | 6851 ncbi.nlm.nih.gov/gene/6851 |
| Ensembl ID | ENSG00000101945 |
| UniProt ID | O43463 |
| OMIM ID | 300254 |
| HGNC ID | 11479 |
| Aliases | SUV39H, H3-K9-HMTase 1, KMT1A |
Description
SUV39H1 encodes a histone methyltransferase that specifically trimethylates histone H3 at lysine 9 (H3K9me3), a key epigenetic mark for heterochromatin formation and transcriptional silencing. It plays a critical role in maintaining genomic stability, regulating telomere length, and suppressing repetitive elements. Mutations in SUV39H1 are associated with immunodeficiency and certain cancers.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Immunodeficiency 95 (IMD95) | Loss-of-function mutations impair H3K9me3 deposition, leading to defective T-cell differentiation and immune response | ClinVar, OMIM |
| Acute myeloid leukemia (AML) | SUV39H1 downregulation or mutation disrupts heterochromatin, promoting genomic instability and leukemogenesis | COSMIC, PubMed |
| Breast cancer | Reduced SUV39H1 expression correlates with poor prognosis and increased metastasis | PubMed |
| Colorectal cancer | Epigenetic silencing of SUV39H1 contributes to tumor progression | PubMed |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 12.5 | Medium |
| Bone marrow | 8.2 | Low |
| Lymph node | 7.9 | Low |
| Brain | 6.1 | Low |
| Liver | 4.3 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| K562 (leukemia) | 10.1 | Myelogenous leukemia line |
| HeLa (cervical) | 7.8 | Cervical adenocarcinoma |
| HEK293 (embryonic kidney) | 6.5 | Transformed embryonic kidney |
| MCF7 (breast) | 5.2 | Breast adenocarcinoma |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1054C>T (p.Arg352*) | Nonsense | Rare | Loss of function; truncation of catalytic SET domain |
| c.1286G>A (p.Arg429Gln) | Missense | Rare | Impaired methyltransferase activity |
| c.1462_1463del (p.Leu488fs) | Frameshift | Rare | Loss of function; associated with IMD95 |
Mutation functional classification
Loss of Function (LOF)
Nonsense, frameshift, and missense mutations that reduce or abolish H3K9 methyltransferase activity, leading to heterochromatin defects and immune dysfunction.
Gain of Function (GOF)
Not reported in literature.
Dominant Negative (DN)
Not reported; SUV39H1 mutations are typically recessive or haploinsufficient.
View complete mutation data：
Gene Ontology (GO)
| • Histone H3-K9 methyltransferase activity | • Chromatin binding |
| • Regulation of heterochromatin formation | • Negative regulation of transcription by RNA polymerase II |
| • Telomere maintenance | • Cell cycle arrest |
Pathways
• Chromatin modifying enzymes (Reactome R-HSA-3244850)
• Epigenetic regulation of gene expression (Reactome R-HSA-212165)
• Telomere maintenance (Reactome R-HSA-157579)
Protein Summary
SUV39H1 is a 412-amino-acid protein containing a chromodomain and a SET domain. It catalyzes the trimethylation of histone H3 lysine 9, a mark essential for heterochromatin assembly and silencing of repetitive DNA. The protein localizes to pericentromeric heterochromatin and telomeres, and its activity is regulated by phosphorylation and interaction with HP1 proteins.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| SUV39H1 Knockout HEK293 Cell Line | EDJ-KQ5870 | Human | 6839 | Details Get a Quote |
| SUV39H1 Knockout A-549 Cell Line | EDJ-KQ29363 | Human | 6839 | Details Get a Quote |
| SUV39H1 Knockout HCT 116 Cell Line | EDJ-KQ29364 | Human | 6839 | Details Get a Quote |
| SUV39H1 Knockout HeLa Cell Line | EDJ-KQ29365 | Human | 6839 | Details Get a Quote |
