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

ENSG00000204371 ∙ NCBI:10919 ∙ OMIM:604599 ∙ HGNC:14129 ∙ Uniprot:Q96KQ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EHMT2 gene.

• Kleefstra-like syndrome (1 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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	5	9
missense	1		40		1	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					1	1
Total	1	0	40	4	7

Variants in EHMT2

This is a list of pathogenic ClinVar variants found in the EHMT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-31880157-C-T		not specified	Uncertain significance (Jun 04, 2024)
6-31880779-C-T		not specified	Uncertain significance (Sep 20, 2023)
6-31881061-C-A		Kleefstra-like syndrome	Pathogenic (-)
6-31882754-T-A		not specified	Uncertain significance (Nov 19, 2022)
6-31883395-G-A			Likely benign (Mar 01, 2022)
6-31883816-G-C		not specified	Uncertain significance (May 13, 2024)
6-31883825-C-A		not specified	Uncertain significance (Feb 17, 2024)
6-31883845-C-T			Benign (Aug 03, 2017)
6-31884428-C-T		not specified	Uncertain significance (Jul 07, 2022)
6-31884444-G-T		not specified	Uncertain significance (Oct 04, 2022)
6-31884482-C-T		not specified	Uncertain significance (Mar 04, 2024)
6-31884714-T-C		not specified	Uncertain significance (Sep 22, 2023)
6-31884729-G-A		not specified	Uncertain significance (Jul 31, 2023)
6-31884796-C-T		not specified	Uncertain significance (Sep 01, 2021)
6-31884941-G-A		not specified	Uncertain significance (Jun 06, 2023)
6-31886807-T-C		not specified	Uncertain significance (Feb 26, 2024)
6-31886809-T-C		not specified	Uncertain significance (Feb 01, 2023)
6-31886815-G-A		not specified	Uncertain significance (May 04, 2022)
6-31886857-G-A		not specified	Uncertain significance (Jul 13, 2022)
6-31887095-T-C		not specified	Uncertain significance (Mar 23, 2022)
6-31887640-G-A		not specified	Uncertain significance (Jan 16, 2024)
6-31887829-C-A			Benign (Dec 31, 2019)
6-31887860-C-A		not specified	Uncertain significance (Feb 05, 2024)
6-31887929-C-T		not specified	Uncertain significance (Feb 23, 2023)
6-31887944-T-A		not specified	Uncertain significance (Oct 13, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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