ELF2

protein-coding

E74 like ETS transcription factor 2, the group of ETS transcription factor family

Gene summary

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

MANE transcript

NM_001331036.3

Inheritance

—

ClinVar variants

P:1U:74B:3

Top phenotype

Cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndrome

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr4:139,028,112-139,177,218

External References & Databases

Ensembl (ENSG00000109381)

Transcript & Mutation Effects

hg38 • Region Span ~149.1 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 ELF2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 70

not providedTotal: 4

Cerebellar ataxia with neuropathy and bilateral vestibular areflexia syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001331036.3. 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			3 clinvar	1 clinvar		4
missense		1 clinvar	70 clinvar	2 clinvar		73
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	1	74	3	0	78

Highest pathogenic variant AF is 0.000022576976

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001331036.3	RefSeq	NP_001317965.1	8	MANE Select
ENST00000686138.1	Ensembl	ENSP00000510098.1	8	MANE Select
NM_001276457.2	RefSeq	NP_001263386.1	6	Standard
NM_001276458.3	RefSeq	NP_001263387.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Beta-agonist/Beta-blocker Pathway, Pharmacodynamics
Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription
RUNX1 regulates transcription of genes involved in BCR signaling

Biological Process

regulation of transcription by RNA polymerase II
cell differentiation
positive regulation of transcription, DNA-templated
regulation of B cell receptor signaling pathway

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
protein binding
sequence-specific DNA binding

Cellular Component

nucleus
nucleoplasm
cytosol
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394235
Coding exons: 8
Length: 149107
Individuals with no LoFs: 125740
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125746
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.59	228	306	0.744	0.0000143	3739
Missense (PolyPhen)		67	119.25	0.56186		1495
Synonymous	0.771	98	108	0.906	0.00000526	1197
Loss of Function	4.20	2	24.4	0.0819	0.00000127	314

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Isoform 1 transcriptionally activates the LYN and BLK promoters and acts synergistically with RUNX1 to transactivate the BLK promoter.;

Recessive Scores

pRec: 0.141

Intolerance Scores

LoFtool: 0.0855
RVIS EVS: 0.53
RVIS percentile EVS: 80.82

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.985

Gene Damage Prediction

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