EHMT2
euchromatic histone lysine methyltransferase 2, the group of Lysine methyltransferases|Ankyrin repeat domain containing|SET domain containing
Basic information
Region (hg38): 6:31879759-31897698
Previous symbols: [ "C6orf30", "BAT8" ]
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (108 variants)
- not_provided (11 variants)
- Kleefstra-like_syndrome (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the EHMT2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006709.5. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 9 | |||||
| missense | 105 | 112 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 4 | 0 | 105 | 7 | 5 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EHMT2 | protein_coding | protein_coding | ENST00000375537 | 28 | 17929 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.000103 | 1.00 | 125708 | 0 | 40 | 125748 | 0.000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.71 | 483 | 773 | 0.624 | 0.0000505 | 7796 |
| Missense in Polyphen | 177 | 367.7 | 0.48138 | 3761 | ||
| Synonymous | 1.41 | 277 | 309 | 0.898 | 0.0000199 | 2462 |
| Loss of Function | 5.19 | 20 | 65.2 | 0.307 | 0.00000373 | 713 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000821 | 0.000767 |
| Ashkenazi Jewish | 0.000101 | 0.0000992 |
| East Asian | 0.0000551 | 0.0000544 |
| Finnish | 0.0000926 | 0.0000924 |
| European (Non-Finnish) | 0.000156 | 0.000149 |
| Middle Eastern | 0.0000551 | 0.0000544 |
| South Asian | 0.000213 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Histone methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting HP1 proteins to methylated histones. Also mediates monomethylation of 'Lys-56' of histone H3 (H3K56me1) in G1 phase, leading to promote interaction between histone H3 and PCNA and regulating DNA replication. Also weakly methylates 'Lys-27' of histone H3 (H3K27me). Also required for DNA methylation, the histone methyltransferase activity is not required for DNA methylation, suggesting that these 2 activities function independently. Probably targeted to histone H3 by different DNA-binding proteins like E2F6, MGA, MAX and/or DP1. May also methylate histone H1. In addition to the histone methyltransferase activity, also methylates non-histone proteins: mediates dimethylation of 'Lys- 373' of p53/TP53. Also methylates CDYL, WIZ, ACIN1, DNMT1, HDAC1, ERCC6, KLF12 and itself. {ECO:0000269|PubMed:11316813, ECO:0000269|PubMed:18438403, ECO:0000269|PubMed:20084102, ECO:0000269|PubMed:20118233, ECO:0000269|PubMed:22387026, ECO:0000269|PubMed:8457211}.;
- Pathway
- Lysine degradation - Homo sapiens (human);Longevity regulating pathway - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Histone Modifications;Ethanol effects on histone modifications;ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);Transcriptional Regulation by E2F6;Generic Transcription Pathway;Senescence-Associated Secretory Phenotype (SASP);Cellular Senescence;Cellular responses to stress;RNA Polymerase I Promoter Clearance;PKMTs methylate histone lysines;RNA Polymerase II Transcription;Chromatin modifying enzymes;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;Cellular responses to external stimuli;Lysine metabolism;Chromatin organization;Regulation of TP53 Activity through Methylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Regulation of Androgen receptor activity
(Consensus)
Recessive Scores
- pRec
- 0.120
Intolerance Scores
- loftool
- 0.626
- rvis_EVS
- -0.88
- rvis_percentile_EVS
- 10.5
Haploinsufficiency Scores
- pHI
- 0.299
- hipred
- Y
- hipred_score
- 0.520
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.990
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ehmt2
- Phenotype
- cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype;
Zebrafish Information Network
- Gene name
- ehmt2
- Affected structure
- retina
- Phenotype tag
- abnormal
- Phenotype quality
- increased occurrence
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of DNA replication;DNA methylation;cellular response to starvation;histone methylation;peptidyl-lysine dimethylation;histone lysine methylation;histone H3-K9 methylation;negative regulation of G0 to G1 transition;histone H3-K27 methylation
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;nuclear speck
- Molecular function
- p53 binding;protein binding;zinc ion binding;protein-lysine N-methyltransferase activity;histone-lysine N-methyltransferase activity;histone methyltransferase activity (H3-K9 specific);histone methyltransferase activity (H3-K27 specific);C2H2 zinc finger domain binding;promoter-specific chromatin binding