SUV39H2
protein-codingSUV39H2 histone lysine methyltransferase, the group of Lysine methyltransferases|SET domain containing
Gene summary
Enables cation binding activity; histone H3K14ub reader activity; and histone H3K9 trimethyltransferase activity. Involved in epigenetic programming in the zygotic pronuclei and pericentric heterochromatin formation. Acts upstream of or within cellular response to hypoxia and negative regulation of transcription by RNA polymerase II. Located in chromatin. Is active in nucleus and pericentric heterochromatin. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~25.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SUV39H2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001193424.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 25 | 1 | 26 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 27 | 1 | 0 | 28 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001180353.1 | 6 | MANE Select | |
| Ensembl | ENSP00000346997.6 | 6 | MANE Select | |
| RefSeq | NP_001180354.1 | 4 | Standard | |
| RefSeq | NP_001180355.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Lysine degradation - Homo sapiens (human)
- Histone Modifications
- PKMTs methylate histone lysines
- Chromatin modifying enzymes
- Lysine metabolism
Biological Process
- negative regulation of transcription by RNA polymerase II
- chromatin assembly or disassembly
- chromatin remodeling
- cell cycle
- cell differentiation
Molecular Function
- transcription regulatory region sequence-specific DNA binding
- protein binding
- zinc ion binding
- histone-lysine N-methyltransferase activity
- histone methyltransferase activity (H3-K9 specific)
Cellular Component
- chromosome, centromeric region
- chromatin
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000354919
- Coding exons
- 6
- Length
- 25496
- Individuals with no LoFs
- 125729
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125732
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.28 | 76 | 210 | 0.362 | 0.0000102 | 2686 |
| Missense (PolyPhen) | 14 | 91.911 | 0.15232 | 1219 | ||
| Synonymous | 0.359 | 70 | 73.9 | 0.947 | 0.00000379 | 746 |
| Loss of Function | 3.72 | 3 | 21.7 | 0.138 | 0.00000133 | 253 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000026 | 0.000026 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Histone methyltransferase that specifically trimethylates 'Lys-9' of histone H3 using monomethylated H3 'Lys- 9' as substrate. H3 'Lys-9' trimethylation represents a specific tag for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3 and/or CBX5) proteins to methylated histones. Mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions. H3 'Lys-9' trimethylation is also required to direct DNA methylation at pericentric repeats. SUV39H1 is targeted to histone H3 via its interaction with RB1 and is involved in many processes, such as cell cycle regulation, transcriptional repression and regulation of telomere length. May participate in regulation of higher-order chromatin organization during spermatogenesis. Recruited by the large PER complex to the E-box elements of the circadian target genes such as PER2 itself or PER1, contributes to the conversion of local chromatin to a heterochromatin-like repressive state through H3 'Lys-9' trimethylation. {ECO:0000269|PubMed:14765126}.;
Recessive Scores
- pRec
- 0.0916
Intolerance Scores
- LoFtool
- 0.103
- RVIS EVS
- -0.3
- RVIS percentile EVS
- 32.62
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.998
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |