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): 17:42700275-42745049

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.

not_specified (36 variants)
not_provided (17 variants)
EZH1-neurodevelopmental_syndrome (5 variants)
EZH1-related_disorder (1 variants)

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. These statistics are base on transcript: NM_000001991.5. 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						0
missense		2 clinvar	48 clinvar			50
nonsense		1 clinvar				1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)		1 clinvar				1
Total	0	4	49	0	0

Loading clinvar variants...

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