ELF4

E74 like ETS transcription factor 4, the group of ETS transcription factor family

Basic information

Region (hg38): X:130063955-130110716

Links

ENSG00000102034

∙ NCBI:2000 ∙ OMIM:300775 ∙ HGNC:3319 ∙ Uniprot:Q99607 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

short stature due to isolated growth hormone deficiency with X-linked hypogammaglobulinemia (Supportive), mode of inheritance: XL
autoinflammatory syndrome, familial, X-linked, Behcet-like 2 (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Autoinflammatory syndrome, familial, X-linked, Behcet-like 2	XL	Allergy/Immunology/Infectious	The condition involves autoinflammatory manifestations, and medical management (eg, with steroids, TNFA blockade) have been described as beneficial; The condition may involve frequent infections, and prophylactic measures and prompt and aggressive management of infections may be beneficial	Allergy/Immunology/Infectious	34326534; 35266071

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ELF4 gene.

not_specified (49 variants)
not_provided (14 variants)
Autoinflammatory_syndrome,_familial,_X-linked,_Behcet-like_2 (7 variants)
ELF4-related_disorder (3 variants)
See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ELF4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001421.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar	2 clinvar	5
missense	3 clinvar		52 clinvar	4 clinvar	2 clinvar	61
nonsense		1 clinvar	1 clinvar			2
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	4	1	53	7	4

Highest pathogenic variant AF is 0.000107412896

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ELF4	protein_coding	protein_coding	ENST00000308167	8	45843

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0614	0.936	125740	1	6	125747	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	212	265	0.799	0.0000206	4274
Missense in Polyphen		55	92.085	0.59727		1625
Synonymous	0.629	111	120	0.927	0.0000104	1457
Loss of Function	2.60	5	16.3	0.306	0.00000126	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000113	0.0000980
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Transcriptional activator that binds to DNA sequences containing the consensus 5'-WGGA-3'. Transactivates promoters of the hematopoietic growth factor genes CSF2, IL3, IL8, and of the bovine lysozyme gene. Acts synergistically with RUNX1 to transactivate the IL3 promoter (By similarity). Also transactivates the PRF1 promoter in natural killer (NK) cells. Plays a role in the development and function of NK and NK T-cells and in innate immunity. Controls the proliferation and homing of CD8+ T-cells via the Kruppel-like factors KLF4 and KLF2 (By similarity). Controls cell senescence in a p53-dependent manner. Can also promote cellular transformation through inhibition of the p16 pathway. {ECO:0000250, ECO:0000269|PubMed:10207087, ECO:0000269|PubMed:14625302, ECO:0000269|PubMed:14976184, ECO:0000269|PubMed:19380490, ECO:0000269|PubMed:8895518, ECO:0000269|PubMed:9524226}.;
Disease: DISEASE: Note=A chromosomal aberration involving ELF4 has been found in a case of acute myeloid leukemia (AML). Translocation t(X;21)(q25-26;q22) with ERG. {ECO:0000269|PubMed:16303180}.;
Pathway: TYROBP Causal Network (Consensus)

Recessive Scores

pRec: 0.0870

Intolerance Scores

loftool: 0.359
rvis_EVS: -0.11
rvis_percentile_EVS: 45.26

Haploinsufficiency Scores

pHI: 0.495
hipred: Y
hipred_score: 0.701
ghis: 0.531

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.632

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Elf4
Phenotype: immune system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process: natural killer cell proliferation;NK T cell proliferation;regulation of transcription by RNA polymerase II;cell differentiation;innate immune response;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
Cellular component: nucleus;nucleoplasm;nuclear body;PML body
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;protein binding