EED
embryonic ectoderm development, the group of Polycomb repressive complex 2|WD repeat domain containing|MicroRNA protein coding host genes
Basic information
Region (hg38): 11:86201212-86279807
Links
Phenotypes
GenCC
Source:
- Cohen-Gibson syndrome (Moderate), mode of inheritance: AD
- Cohen-Gibson syndrome (Strong), mode of inheritance: AD
- Weaver syndrome (Supportive), mode of inheritance: AD
- Cohen-Gibson syndrome (Moderate), mode of inheritance: AD
- Cohen-Gibson syndrome (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Cohen-Gibson syndrome | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Musculoskeletal; Neurologic | 25787343; 27193220; 27868325; 28229514 |
ClinVar
This is a list of variants' phenotypes submitted to
- Cohen-Gibson_syndrome (62 variants)
- not_provided (29 variants)
- Inborn_genetic_diseases (28 variants)
- EED-related_disorder (11 variants)
- not_specified (3 variants)
- Hereditary_breast_ovarian_cancer_syndrome (1 variants)
- Autism_spectrum_disorder (1 variants)
- Neurodevelopmental_delay (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the EED gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003797.5. 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 | 19 | 23 | ||||
| missense | 59 | 74 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 5 | 7 | 62 | 21 | 4 |
Highest pathogenic variant AF is 0.00000136983
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| EED | protein_coding | protein_coding | ENST00000263360 | 12 | 34270 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000708 | 125154 | 0 | 3 | 125157 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.73 | 118 | 236 | 0.499 | 0.0000115 | 2963 |
| Missense in Polyphen | 8 | 71.005 | 0.11267 | 916 | ||
| Synonymous | -0.121 | 79 | 77.6 | 1.02 | 0.00000392 | 763 |
| Loss of Function | 4.48 | 1 | 25.4 | 0.0394 | 0.00000132 | 304 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000280 | 0.0000265 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Polycomb group (PcG) protein. Component of the PRC2/EED- EZH2 complex, which methylates 'Lys-9' and 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. Also recognizes 'Lys-26' trimethylated histone H1 with the effect of inhibiting PRC2 complex methyltransferase activity on nucleosomal histone H3 'Lys-27', whereas H3 'Lys-27' recognition has the opposite effect, enabling the propagation of this repressive mark. The PRC2/EED-EZH2 complex may also serve as a recruiting platform for DNA methyltransferases, thereby linking two epigenetic repression systems. Genes repressed by the PRC2/EED-EZH2 complex include HOXC8, HOXA9, MYT1 and CDKN2A. {ECO:0000269|PubMed:10581039, ECO:0000269|PubMed:14532106, ECO:0000269|PubMed:15225548, ECO:0000269|PubMed:15231737, ECO:0000269|PubMed:15385962, ECO:0000269|PubMed:16357870, ECO:0000269|PubMed:18285464, ECO:0000269|PubMed:20974918, ECO:0000269|PubMed:28229514, ECO:0000269|PubMed:9584199}.;
- Disease
- DISEASE: Cohen-Gibson syndrome (COGIS) [MIM:617561]: An autosomal dominant overgrowth disorder characterized by accelerated osseous maturation, advanced bone age, skeletal abnormalities including flaring of the metaphyses of the long bones, large hands with long fingers and camptodactyly, scoliosis, cervical spine anomalies, dysmorphic facial features, and variable intellectual disability. {ECO:0000269|PubMed:25787343, ECO:0000269|PubMed:27193220, ECO:0000269|PubMed:27868325, ECO:0000269|PubMed:28229514, ECO:0000269|PubMed:28475857}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Histone Modifications;Interactome of polycomb repressive complex 2 (PRC2);Oxidative Stress Induced Senescence;Tumor suppressor activity of SMARCB1;EMT transition in Colorectal Cancer;Signal Transduction;Epigenetic regulation of gene expression;Gene expression (Transcription);the prc2 complex sets long-term gene silencing through modification of histone tails;Transcriptional Regulation by E2F6;Generic Transcription Pathway;Oxidative Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;PKMTs methylate histone lysines;RNA Polymerase II Transcription;Chromatin modifying enzymes;Cellular responses to external stimuli;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Chromatin organization;TNFalpha;Intracellular signaling by second messengers;PRC2 methylates histones and DNA
(Consensus)
Recessive Scores
- pRec
- 0.149
Intolerance Scores
- loftool
- rvis_EVS
- -0.43
- rvis_percentile_EVS
- 25.15
Haploinsufficiency Scores
- pHI
- 0.922
- hipred
- Y
- hipred_score
- 0.777
- ghis
- 0.717
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.972
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Eed
- Phenotype
- hematopoietic system phenotype; pigmentation 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);
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;chromatin silencing;regulation of gene expression by genetic imprinting;spinal cord development;negative regulation of gene expression, epigenetic;negative regulation of transcription, DNA-templated;positive regulation of histone H3-K27 methylation;negative regulation of G0 to G1 transition;histone H3-K27 methylation;cellular response to leukemia inhibitory factor;regulation of adaxial/abaxial pattern formation
- Cellular component
- sex chromatin;nucleus;nucleoplasm;cytosol;ESC/E(Z) complex;pronucleus
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;protein binding;nucleosome binding;histone methyltransferase activity;identical protein binding;histone methyltransferase activity (H3-K27 specific)