EGR1

early growth response 1, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 5:138465478-138469303

Links

ENSG00000120738 ∙ NCBI:1958 ∙ OMIM:128990 ∙ HGNC:3238 ∙ Uniprot:P18146 ∙ 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 EGR1 gene.

• Inborn genetic diseases (8 variants)
• not provided (4 variants)
• Squamous cell carcinoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EGR1 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				1	2	3
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	9	2	2

Variants in EGR1

This is a list of pathogenic ClinVar variants found in the EGR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-138465557-G-A		Squamous cell carcinoma	Uncertain significance (Jun 06, 2022)
5-138465903-T-C		not specified	Uncertain significance (Jan 18, 2022)
5-138465910-G-A		not specified	Uncertain significance (May 27, 2022)
5-138465943-ACAG-A			Likely benign (Dec 31, 2019)
5-138466962-G-C			Benign (Aug 18, 2018)
5-138466963-T-G		not specified	Uncertain significance (Jan 26, 2023)
5-138467080-A-C		not specified	Uncertain significance (Aug 02, 2021)
5-138467231-A-G		not specified	Uncertain significance (Mar 01, 2024)
5-138467466-T-G			Benign (Jun 05, 2018)
5-138467505-C-T			Likely benign (May 01, 2022)
5-138467521-C-T		not specified	Uncertain significance (Jun 17, 2022)
5-138467894-A-G		not specified	Uncertain significance (Dec 12, 2023)
5-138467927-C-G		not specified	Uncertain significance (Apr 25, 2023)
5-138467984-G-T		not specified	Uncertain significance (Mar 28, 2023)
5-138468019-G-A		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EGR1	protein_coding	protein_coding	ENST00000239938	2	3826

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.351	0.647	125741	0	4	125745	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.90	232	329	0.705	0.0000211	3509
Missense in Polyphen		15	26.19	0.57274		277
Synonymous	0.543	140	148	0.943	0.0000107	1169
Loss of Function	2.59	3	13.1	0.228	6.22e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional regulator (PubMed:20121949). Recognizes and binds to the DNA sequence 5'-GCG(T/G)GGGCG-3'(EGR-site) in the promoter region of target genes (By similarity). Binds double- stranded target DNA, irrespective of the cytosine methylation status (PubMed:25258363, PubMed:25999311). Regulates the transcription of numerous target genes, and thereby plays an important role in regulating the response to growth factors, DNA damage, and ischemia. Plays a role in the regulation of cell survival, proliferation and cell death. Activates expression of p53/TP53 and TGFB1, and thereby helps prevent tumor formation. Required for normal progress through mitosis and normal proliferation of hepatocytes after partial hepatectomy. Mediates responses to ischemia and hypoxia; regulates the expression of proteins such as IL1B and CXCL2 that are involved in inflammatory processes and development of tissue damage after ischemia. Regulates biosynthesis of luteinizing hormone (LHB) in the pituitary (By similarity). {ECO:0000250|UniProtKB:P08046, ECO:0000269|PubMed:20121949, ECO:0000269|PubMed:25258363, ECO:0000269|PubMed:25999311}.
• Pathway: Prion diseases - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Apelin signaling pathway - Homo sapiens (human);Human Thyroid Stimulating Hormone (TSH) signaling pathway;Oncostatin M Signaling Pathway;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;Spinal Cord Injury;Nuclear Receptors Meta-Pathway;NRF2 pathway;let-7 inhibition of ES cell reprogramming;Ovarian Infertility Genes;Preimplantation Embryo;VEGFA-VEGFR2 Signaling Pathway;Insulin Signaling;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Serotonin Receptor 4-6-7 and NR3C Signaling;Signal Transduction;phosphorylation of mek1 by cdk5/p35 down regulates the map kinase pathway;Cytokine Signaling in Immune system;TCR;Oncostatin_M;Immune System;Glucocorticoid receptor regulatory network;ErbB1 downstream signaling;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Interferon alpha/beta signaling;Intracellular signaling by second messengers;Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met);Downstream signaling in naïve CD8+ T cells;Calcineurin-regulated NFAT-dependent transcription in lymphocytes;Interferon Signaling;AP-1 transcription factor network;Regulation of Androgen receptor activity;Trk receptor signaling mediated by PI3K and PLC-gamma;Trk receptor signaling mediated by the MAPK pathway;Signaling events mediated by PRL (Consensus)

Recessive Scores

• pRec: 0.887

Intolerance Scores

• loftool: 0.299
• rvis_EVS: -0.85
• rvis_percentile_EVS: 11.06

Haploinsufficiency Scores

• pHI: 0.989
• hipred: Y
• hipred_score: 0.825
• ghis: 0.490

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Egr1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: egr1
• Affected structure: retinal bipolar neuron
• Phenotype tag: abnormal
• Phenotype quality: poorly differentiated

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;response to hypoxia;response to ischemia;regulation of transcription by RNA polymerase II;transcription by RNA polymerase II;response to glucose;positive regulation of gene expression;T cell differentiation;BMP signaling pathway;response to insulin;circadian regulation of gene expression;regulation of protein sumoylation;skeletal muscle cell differentiation;regulation of apoptotic process;estrous cycle;positive regulation of chemokine biosynthetic process;locomotor rhythm;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of hormone biosynthetic process;positive regulation of interleukin-1 beta biosynthetic process;circadian temperature homeostasis;type I interferon signaling pathway;regulation of transcription from RNA polymerase II promoter in response to hypoxia;interleukin-1-mediated signaling pathway;cellular response to gamma radiation;cellular response to heparin;cellular response to mycophenolic acid;glomerular mesangial cell proliferation;positive regulation of glomerular metanephric mesangial cell proliferation;negative regulation of canonical Wnt signaling pathway;cellular response to interleukin-8;positive regulation of neuron death;positive regulation of tau-protein kinase activity;regulation of progesterone biosynthetic process
• Cellular component: nucleus;nucleoplasm;cytoplasm
• Molecular function: transcription regulatory region sequence-specific DNA binding;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;DNA-binding transcription factor activity;protein binding;zinc ion binding;double-stranded methylated DNA binding;histone acetyltransferase binding;sequence-specific DNA binding;hemi-methylated DNA-binding;promoter-specific chromatin binding