ELF1

protein-coding

E74 like ETS transcription factor 1, the group of ETS transcription factor family

Gene summary

This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2009]

MANE transcript

NM_172373.4

Inheritance

—

ClinVar variants

U:86B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr13:40,931,919-41,061,440

External References & Databases

Ensembl (ENSG00000120690)

Transcript & Mutation Effects

hg38 • Region Span ~129.5 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 ELF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 81

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_172373.4. 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			2 clinvar		2 clinvar	4
missense			82 clinvar	1 clinvar		83
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	86	1	2	89

Loading ClinVar variants...

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_172373.4	RefSeq	NP_758961.1	8	MANE Select
ENST00000239882.7	Ensembl	ENSP00000239882.3	8	MANE Select
NM_001145353.1	RefSeq	NP_001138825.1	8	Standard
NM_001370329.1	RefSeq	NP_001357258.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription
RUNX1 regulates transcription of genes involved in BCR signaling
Angiopoietin receptor Tie2-mediated signaling

Biological Process

regulation of cytokine production
regulation of cytokine-mediated signaling pathway
regulation of transcription by RNA polymerase II
cell differentiation
positive regulation of transcription, DNA-templated

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
protein binding

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000239882
Coding exons: 8
Length: 129521
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125748
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.914	279	325	0.857	0.0000165	4008
Missense (PolyPhen)		65	107.06	0.60713		1404
Synonymous	0.466	114	121	0.946	0.00000674	1245
Loss of Function	3.12	8	24.7	0.324	0.00000123	305

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.000095	0.000092	rare
European (Non-Finnish)	0.000097	0.000097	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcription factor that activates the LYN and BLK promoters. Appears to be required for the T-cell-receptor-mediated trans activation of HIV-2 gene expression. Binds specifically to two purine-rich motifs in the HIV-2 enhancer. {ECO:0000269|PubMed:8756667}.;

Recessive Scores

pRec: 0.115

Intolerance Scores

LoFtool: 0.501
RVIS EVS: 0.31
RVIS percentile EVS: 72.71

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High