EAF2

protein-coding

ELL associated factor 2

Gene summary

Enables transcription elongation factor activity. Involved in positive regulation of transcription by RNA polymerase II and regulation of transcription elongation by RNA polymerase II. Part of transcription elongation factor complex. Biomarker of prostate cancer. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_018456.6

Inheritance

—

ClinVar variants

U:27B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr3:121,835,183-121,886,526

External References & Databases

Ensembl (ENSG00000145088)

Transcript & Mutation Effects

hg38 • Region Span ~51.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EAF2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 29

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018456.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			27 clinvar	3 clinvar		30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	4	1	32

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018456.6	RefSeq	NP_060926.2	6	MANE Select
ENST00000273668.7	Ensembl	ENSP00000273668.2	6	MANE Select
NM_001320041.2	RefSeq	NP_001306970.1	3	Standard
ENST00000451944.2	Ensembl	ENSP00000410708.2	6	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
eaf2	Danio rerio	Structure: neuroectoderm Quality: decreased size abnormal

Gene / Model

Organism

Observed Phenotype

eaf2

Danio rerio

Structure: neuroectoderm

Quality: decreased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

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

Molecular Function

RNA polymerase II regulatory region sequence-specific DNA binding
DNA-binding transcription activator activity, RNA polymerase II-specific
protein binding

Cellular Component

nucleoplasm
transcription elongation factor complex
nuclear speck
ELL-EAF complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000273668
Coding exons: 6
Length: 51344
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125748
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.248	129	137	0.940	0.00000630	1718
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00023	0.00020	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0.0013	0.0013	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.00011	rare
South Asian	0.00020	0.00020	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.117

Intolerance Scores

LoFtool: 0.434
RVIS EVS: 0.13
RVIS percentile EVS: 63.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0997

Gene Damage Prediction

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