EGR4

early growth response 4, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 2:73290929-73293701

Links

ENSG00000135625 ∙ NCBI:1961 ∙ OMIM:128992 ∙ HGNC:3241 ∙ Uniprot:Q05215 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EGR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EGR4 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	3	5
missense			40	3		43
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	5	3

Variants in EGR4

This is a list of pathogenic ClinVar variants found in the EGR4 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-73291486-A-T		not specified	Uncertain significance (Jun 29, 2022)
2-73291489-A-T		not specified	Uncertain significance (Dec 30, 2023)
2-73291519-C-A		not specified	Uncertain significance (Dec 14, 2021)
2-73291584-C-T		not specified	Uncertain significance (Dec 20, 2021)
2-73291607-A-G			Benign (Sep 24, 2018)
2-73291658-G-A			Likely benign (Jun 23, 2018)
2-73291737-G-A		not specified	Uncertain significance (Nov 21, 2023)
2-73291744-C-G		not specified	Uncertain significance (Nov 08, 2022)
2-73291770-G-C		not specified	Uncertain significance (May 30, 2023)
2-73291846-G-A		not specified	Uncertain significance (Mar 08, 2024)
2-73291851-G-C		not specified	Uncertain significance (Apr 28, 2023)
2-73291851-G-T		not specified	Uncertain significance (Jan 22, 2024)
2-73291865-G-C		not specified	Uncertain significance (Nov 09, 2022)
2-73291899-G-A		not specified	Uncertain significance (Dec 16, 2023)
2-73291944-G-A		not specified	Uncertain significance (Nov 12, 2021)
2-73291997-C-T			Benign (Mar 29, 2018)
2-73292008-G-A			Benign (May 15, 2018)
2-73292044-C-G		not specified	Uncertain significance (May 31, 2023)
2-73292049-G-A			Likely benign (Sep 12, 2018)
2-73292117-G-T		not specified	Uncertain significance (Dec 01, 2022)
2-73292154-A-C		not specified	Likely benign (Oct 02, 2023)
2-73292155-C-G		not specified	Uncertain significance (Jan 03, 2022)
2-73292198-A-C		not specified	Uncertain significance (Jun 24, 2022)
2-73292223-C-G		not specified	Uncertain significance (Mar 15, 2024)
2-73292224-G-A		not specified	Uncertain significance (Mar 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EGR4	protein_coding	protein_coding	ENST00000545030	2	2776

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00635	0.918	124753	0	3	124756	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.136	291	285	1.02	0.0000131	3638
Missense in Polyphen		111	125.74	0.88276		1591
Synonymous	-3.90	181	125	1.44	0.00000612	1298
Loss of Function	1.53	5	10.3	0.486	4.45e-7	148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000547	0.0000486
European (Non-Finnish)	0.00000989	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator. Recognizes and binds to the DNA sequence 5'-GCGGGGGCG-3' (GSG). Activates the transcription of target genes whose products are required for mitogenesis and differentiation (By similarity). {ECO:0000250}.
• Pathway: Downstream signaling in naïve CD8+ T cells;Calcineurin-regulated NFAT-dependent transcription in lymphocytes (Consensus)

Recessive Scores

• pRec: 0.151

Haploinsufficiency Scores

• pHI: 0.498
• hipred: N
• hipred_score: 0.275
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.484

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Egr4
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;positive regulation of cell population proliferation;positive regulation of transcription by RNA polymerase II;cellular response to growth factor stimulus
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region 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;sequence-specific DNA binding;metal ion binding