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.

not_specified (28 variants)
not_provided (4 variants)

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. These statistics are base on transcript: NM_000018456.6. 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				1 clinvar	1 clinvar	2
missense			26 clinvar	3 clinvar		29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	26	4	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EAF2	protein_coding	protein_coding	ENST00000273668	6	51344

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.22e-7	0.280	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.248	129	137	0.940	0.00000630	1718
Missense in Polyphen		47	50.491	0.93086		623
Synonymous	0.680	40	45.9	0.872	0.00000203	470
Loss of Function	0.389	11	12.5	0.881	5.93e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000476	0.000475
Ashkenazi Jewish	0.000213	0.000198
East Asian	0.00134	0.00131
Finnish	0.00	0.00
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.00134	0.00131
South Asian	0.000201	0.000196
Other	0.000165	0.000163

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

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

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