EGR3

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

Basic information

Region (hg38): 8:22687659-22693480

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.

not_specified (23 variants)
not_provided (7 variants)
EGR3-related_disorder (2 variants)
Neurodevelopmental_delay (1 variants)

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. These statistics are base on transcript: NM_000004430.3. 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	3 clinvar	6
missense			25 clinvar			25
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	26	3	3

Loading clinvar variants...

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

loftool
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