EZH1

enhancer of zeste 1 polycomb repressive complex 2 subunit, the group of Lysine methyltransferases|MicroRNA protein coding host genes|SET domain containing|Myb/SANT domain containing|Polycomb repressive complex 2

Basic information

Region (hg38): 17:42700274-42745049

Links

ENSG00000108799 ∙ NCBI:2145 ∙ OMIM:601674 ∙ HGNC:3526 ∙ Uniprot:Q92800 ∙ 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 EZH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EZH1 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						0
missense		2	18			20
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region						0
non coding						0
Total	0	4	18	0	0

Variants in EZH1

This is a list of pathogenic ClinVar variants found in the EZH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42702573-G-A		EZH1-neurodevelopmental syndrome	Uncertain significance (Jan 13, 2022)
17-42702585-G-C		EZH1-neurodevelopmental syndrome	Likely pathogenic (-)
17-42703805-G-C		EZH1-related disorder • EZH1-neurodevelopmental syndrome	Likely pathogenic (-)
17-42708030-G-A		not specified	Uncertain significance (May 26, 2024)
17-42709886-C-A		EZH1-neurodevelopmental syndrome	Likely pathogenic (Mar 26, 2024)
17-42712405-A-G		not specified	Uncertain significance (Dec 28, 2022)
17-42712473-C-T			Uncertain significance (Aug 08, 2019)
17-42713286-G-A		not specified	Uncertain significance (Jun 02, 2024)
17-42713308-T-C		not specified	Uncertain significance (Mar 07, 2024)
17-42718068-C-T		EZH1-neurodevelopmental syndrome	Likely pathogenic (-)
17-42718486-C-T			Uncertain significance (May 10, 2023)
17-42718582-G-C		not specified	Uncertain significance (Jan 17, 2024)
17-42719183-T-G		not specified	Uncertain significance (Mar 28, 2024)
17-42719189-T-C		not specified	Uncertain significance (Nov 17, 2023)
17-42720287-C-T		not specified	Uncertain significance (Jan 22, 2024)
17-42720353-T-C		not specified	Uncertain significance (Jul 27, 2022)
17-42720396-C-T		not specified	Uncertain significance (May 03, 2023)
17-42720445-C-T		not specified	Uncertain significance (Mar 11, 2024)
17-42722827-T-C		not specified	Uncertain significance (Dec 12, 2023)
17-42722902-G-A		not specified	Uncertain significance (Apr 21, 2022)
17-42724402-G-A		not specified	Uncertain significance (Mar 29, 2023)
17-42727670-T-A		not specified	Uncertain significance (Mar 04, 2024)
17-42727670-T-C		not specified	Uncertain significance (Jan 19, 2022)
17-42727760-A-C		not specified	Uncertain significance (Dec 21, 2023)
17-42728916-G-A		not specified	Uncertain significance (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EZH1	protein_coding	protein_coding	ENST00000428826	19	44779

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0425	0.958	125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.20	179	422	0.425	0.0000228	4980
Missense in Polyphen		68	213.99	0.31778		2565
Synonymous	1.95	116	146	0.795	0.00000769	1345
Loss of Function	4.66	12	46.1	0.260	0.00000264	506

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000873	0.0000873
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000621	0.0000527
Middle Eastern	0.000272	0.000272
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Polycomb group (PcG) protein. Catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. Able to mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. Required for embryonic stem cell derivation and self-renewal, suggesting that it is involved in safeguarding embryonic stem cell identity. Compared to EZH2-containing complexes, it is less abundant in embryonic stem cells, has weak methyltransferase activity and plays a less critical role in forming H3K27me3, which is required for embryonic stem cell identity and proper differentiation. {ECO:0000269|PubMed:19026781}.
• Pathway: Lysine degradation - Homo sapiens (human);Histone Modifications;Interactome of polycomb repressive complex 2 (PRC2) (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.330
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24.19

Haploinsufficiency Scores

• pHI: 0.560
• hipred: Y
• hipred_score: 0.674
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.995

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ezh1
• Phenotype: cellular phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system 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); hematopoietic system phenotype; reproductive system phenotype; normal 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)

Gene ontology

• Biological process: anatomical structure morphogenesis;hippocampus development;positive regulation of transcription by RNA polymerase II;histone H3-K27 methylation
• Cellular component: nucleoplasm;ESC/E(Z) complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;histone-lysine N-methyltransferase activity