EGR3

early growth response 3, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 8:22687658-22693480

Links

ENSG00000179388 ∙ NCBI:1960 ∙ OMIM:602419 ∙ HGNC:3240 ∙ Uniprot:Q06889 ∙ 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 EGR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EGR3 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				3	4	7
missense			7			7
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	9	3	4

Variants in EGR3

This is a list of pathogenic ClinVar variants found in the EGR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-22690509-G-A			Likely benign (Oct 02, 2018)
8-22690515-C-G			Likely benign (Jun 08, 2018)
8-22690538-C-T		not specified	Uncertain significance (Aug 16, 2022)
8-22690557-C-T			Benign (Dec 31, 2019)
8-22690598-C-T		EGR3-related disorder	Uncertain significance (Dec 29, 2023)
8-22690623-G-A			Benign (Dec 31, 2019)
8-22690776-G-C		not specified	Uncertain significance (Mar 30, 2024)
8-22691039-G-T		not specified	Uncertain significance (Nov 15, 2021)
8-22691046-G-T		Neurodevelopmental delay	Uncertain significance (Jul 13, 2017)
8-22691271-C-A			Likely benign (May 14, 2018)
8-22691277-G-T			Benign (Sep 14, 2018)
8-22691361-G-C		not specified	Uncertain significance (Dec 22, 2023)
8-22691393-T-G		not specified	Uncertain significance (Jun 13, 2024)
8-22691401-C-A		not specified	Uncertain significance (Apr 23, 2024)
8-22691403-G-A			Benign (Dec 31, 2019)
8-22691428-T-A		not specified	Uncertain significance (May 06, 2022)
8-22691435-G-C			Uncertain significance (Sep 24, 2018)
8-22692301-C-A		EGR3-related disorder	Uncertain significance (May 22, 2023)
8-22692822-G-C		not specified	Uncertain significance (May 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EGR3	protein_coding	protein_coding	ENST00000317216	2	5644

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.953	0.0470	123420	0	1	123421	0.00000405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.38	107	260	0.411	0.0000153	2554
Missense in Polyphen		28	112.5	0.24889		1062
Synonymous	1.31	97	115	0.844	0.00000730	787
Loss of Function	2.87	0	9.60	0.00	4.08e-7	114

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	0.00	0.00
European (Non-Finnish)	0.00000907	0.00000907
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable transcription factor involved in muscle spindle development.
• Pathway: C-type lectin receptor signaling pathway - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Hepatitis B - Homo sapiens (human);VEGFA-VEGFR2 Signaling Pathway;Calcineurin-regulated NFAT-dependent transcription in lymphocytes (Consensus)

Intolerance Scores

• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.15

Haploinsufficiency Scores

• pHI: 0.954
• hipred: Y
• hipred_score: 0.625
• ghis: 0.555

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.431

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Egr3
• Phenotype: homeostasis/metabolism phenotype; muscle phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton 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); vision/eye 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)

Gene ontology

• Biological process: positive regulation of endothelial cell proliferation;cell migration involved in sprouting angiogenesis;regulation of transcription by RNA polymerase II;neuromuscular synaptic transmission;peripheral nervous system development;muscle organ development;circadian rhythm;positive regulation of T cell differentiation in thymus;endothelial cell chemotaxis;cellular response to vascular endothelial growth factor stimulus;negative regulation of apoptotic process;cellular response to fibroblast growth factor stimulus;regulation of gamma-delta T cell differentiation;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 factor activity;metal ion binding