GeneBe

EAF2

ELL associated factor 2

Basic information

Region (hg38): 3:121835183-121886526

Links

ENSG00000145088 ∙ NCBI:55840 ∙ OMIM:607659 ∙ HGNC:23115 ∙ Uniprot:Q96CJ1 ∙ 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 EAF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EAF2 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
1
clinvar
1
clinvar
 2
missense
7
clinvar
1
clinvar
 8
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
 1
non coding
0
Total 0 0 7 2 1

Variants in EAF2

This is a list of pathogenic ClinVar variants found in the EAF2 region.

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

Position Type Phenotype Significance ClinVar
3-121835350-G-A not specified Uncertain significance (May 14, 2024)3274326
3-121835377-T-G not specified Uncertain significance (Jan 23, 2024)3086806
3-121854688-G-T not specified Uncertain significance (Jan 22, 2024)3086805
3-121854827-T-A Uncertain significance (Jun 01, 2023)2654073
3-121857063-A-C not specified Uncertain significance (Jun 29, 2023)2603661
3-121857106-C-A not specified Uncertain significance (Jul 09, 2021)2387016
3-121857126-C-T not specified Uncertain significance (Jun 09, 2022)2294405
3-121857150-G-A not specified Uncertain significance (Jun 23, 2023)2588236
3-121872621-G-C not specified Uncertain significance (Apr 30, 2024)3274325
3-121872655-T-C Likely benign (Jul 31, 2018)761634
3-121872683-A-T not specified Uncertain significance (Aug 16, 2022)2214083
3-121872748-T-C Benign (Jul 17, 2018)752374
3-121886356-C-G not specified Uncertain significance (May 24, 2024)3274327
3-121886372-G-A Likely benign (Jun 09, 2018)728765

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EAF2protein_codingprotein_codingENST00000273668 651344
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
2.22e-70.2801256910571257480.000227
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2481291370.9400.000006301718
Missense in Polyphen4750.4910.93086623
Synonymous0.6804045.90.8720.00000203470
Loss of Function0.3891112.50.8815.93e-7163

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004760.000475
Ashkenazi Jewish0.0002130.000198
East Asian0.001340.00131
Finnish0.000.00
European (Non-Finnish)0.0001170.000114
Middle Eastern0.001340.00131
South Asian0.0002010.000196
Other0.0001650.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Acts as a transcriptional transactivator of TCEA1 elongation activity (By similarity). Acts as a transcriptional transactivator of ELL and ELL2 elongation activities. Potent inducer of apoptosis in prostatic and non-prostatic cell lines. Inhibits prostate tumor growth in vivo. {ECO:0000250, ECO:0000269|PubMed:12446457, ECO:0000269|PubMed:12907652, ECO:0000269|PubMed:16006523}.;
Pathway
Gene expression (Transcription);RNA Polymerase II Pre-transcription Events;Formation of RNA Pol II elongation complex ;RNA Polymerase II Transcription;RNA Polymerase II Transcription Elongation (Consensus)

Recessive Scores

pRec
0.117

Intolerance Scores

loftool
0.434
rvis_EVS
0.13
rvis_percentile_EVS
63.2

Haploinsufficiency Scores

pHI
0.129
hipred
Y
hipred_score
0.517
ghis
0.535

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.0997

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Eaf2
Phenotype
endocrine/exocrine gland 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); neoplasm; 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan);

Zebrafish Information Network

Gene name
eaf2
Affected structure
neuroectoderm
Phenotype tag
abnormal
Phenotype quality
decreased size

Gene ontology

Biological process
transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;apoptotic process;negative regulation of cell growth;positive regulation of transcription by RNA polymerase II;negative regulation of epithelial cell proliferation involved in prostate gland development
Cellular component
nucleoplasm;transcription elongation factor complex;nuclear speck;ELL-EAF complex
Molecular function
RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding