EAF1

protein-coding

ELL associated factor 1

Gene summary

Enables transcription elongation factor activity. Involved in regulation of transcription elongation by RNA polymerase II. Located in nuclear body. Part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_033083.7

Inheritance

—

ClinVar variants

U:36B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr3:15,427,598-15,450,635

External References & Databases

Ensembl (ENSG00000144597)

Transcript & Mutation Effects

hg38 • Region Span ~23.0 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 EAF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 33

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033083.7. 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		2 clinvar	3
missense			33 clinvar	1 clinvar		34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	36	1	2	39

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033083.7	RefSeq	NP_149074.3	6	MANE Select
ENST00000396842.7	Ensembl	ENSP00000380054.2	6	MANE Select
ENST00000449565.1	Ensembl	ENSP00000399636.1	3	Standard
ENST00001024010.1	Ensembl	ENSP00000693827.1	5	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
eaf1	Danio rerio	Structure: neuroectoderm Quality: decreased size abnormal

Gene / Model

Organism

Observed Phenotype

eaf1

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

regulation of transcription, DNA-templated
transcription by RNA polymerase II
transcription elongation from RNA polymerase II promoter

Molecular Function

protein binding

Cellular Component

nucleoplasm
transcription elongation factor complex
Cajal body
nuclear body
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396842
Coding exons: 6
Length: 15259
Individuals with no LoFs: 125728
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125746
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.01	114	149	0.766	0.00000740	1767
Missense (PolyPhen)		22	32.632	0.67418		458
Synonymous	-0.0427	54	53.6	1.01	0.00000275	506
Loss of Function	2.13	4	11.9	0.335	5.90e-7	143

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a transcriptional transactivator of ELL and ELL2 elongation activities. {ECO:0000269|PubMed:11418481, ECO:0000269|PubMed:16006523}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.242
RVIS EVS: 0.62
RVIS percentile EVS: 83.14

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.830

Gene Damage Prediction

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