ELF3

protein-coding

E74 like ETS transcription factor 3, the group of ETS transcription factor family

Gene summary

Enables DNA-binding transcription activator activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Involved in inflammatory response; negative regulation of DNA-templated transcription; and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

MANE transcript

NM_004433.5

Inheritance

—

ClinVar variants

U:25B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr1:202,007,945-202,017,183

External References & Databases

Ensembl (ENSG00000163435)

Transcript & Mutation Effects

hg38 • Region Span ~9.2 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 ELF3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 20

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004433.5. 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	1 clinvar	4
missense			21 clinvar	1 clinvar		22
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	25	3	1	29

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004433.5	RefSeq	NP_004424.3	8	MANE Select
ENST00000367284.10	Ensembl	ENSP00000356253.5	8	MANE Select
NM_001114309.2	RefSeq	NP_001107781.1	8	Standard
ENST00000359651.7	Ensembl	ENSP00000352673.3	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
Pre-NOTCH Transcription and Translation
Pre-NOTCH Expression and Processing
Signaling by NOTCH
EGFR1

Biological Process

blastocyst development
regulation of transcription by RNA polymerase II
transcription by RNA polymerase II
inflammatory response
multicellular organism development

Molecular Function

RNA polymerase II proximal promoter sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription activator activity, RNA polymerase II-specific
DNA-binding transcription factor activity
transcription coactivator activity

Cellular Component

nucleus
nucleoplasm
Golgi apparatus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359651
Coding exons: 8
Length: 9244
Individuals with no LoFs: 125744
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125748
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.88	152	233	0.653	0.0000147	2435
Missense (PolyPhen)		41	85.858	0.47753		927
Synonymous	0.597	87	94.4	0.922	0.00000620	707
Loss of Function	3.87	2	21.3	0.0941	0.00000136	203

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcriptional activator that binds and transactivates ETS sequences containing the consensus nucleotide core sequence GGA[AT]. Acts synergistically with POU2F3 to transactivate the SPRR2A promoter and with RUNX1 to transactivate the ANGPT1 promoter. Also transactivates collagenase, CCL20, CLND7, FLG, KRT8, NOS2, PTGS2, SPRR2B, TGFBR2 and TGM3 promoters. Represses KRT4 promoter activity. Involved in mediating vascular inflammation. May play an important role in epithelial cell differentiation and tumorigenesis. May be a critical downstream effector of the ERBB2 signaling pathway. May be associated with mammary gland development and involution. Plays an important role in the regulation of transcription with TATA-less promoters in preimplantation embryos, which is essential in preimplantation development (By similarity). {ECO:0000250, ECO:0000269|PubMed:10391676, ECO:0000269|PubMed:10644990, ECO:0000269|PubMed:10773884, ECO:0000269|PubMed:11036073, ECO:0000269|PubMed:11313868, ECO:0000269|PubMed:12414801, ECO:0000269|PubMed:12624109, ECO:0000269|PubMed:12682075, ECO:0000269|PubMed:12713734, ECO:0000269|PubMed:14715662, ECO:0000269|PubMed:14767472, ECO:0000269|PubMed:15075319, ECO:0000269|PubMed:15169914, ECO:0000269|PubMed:15794755, ECO:0000269|PubMed:16307850, ECO:0000269|PubMed:17060315, ECO:0000269|PubMed:9129154, ECO:0000269|PubMed:9234700, ECO:0000269|PubMed:9336459, ECO:0000269|PubMed:9395241, ECO:0000269|PubMed:9417054}.;

Recessive Scores

pRec: 0.314

Intolerance Scores

LoFtool: 0.0980
RVIS EVS: 0.04
RVIS percentile EVS: 57.31

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.884

Gene Damage Prediction

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