EBI3

Epstein-Barr virus induced 3, the group of Fibronectin type III domain containing|Minor histocompatibility antigens

Basic information

Region (hg38): 19:4229523-4237528

Links

ENSG00000105246 ∙ NCBI:10148 ∙ OMIM:605816 ∙ HGNC:3129 ∙ Uniprot:Q14213 ∙ 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 EBI3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EBI3 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	1
missense			18	3		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	18	3	1

Variants in EBI3

This is a list of pathogenic ClinVar variants found in the EBI3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4229587-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-4229590-A-G		not specified	Likely benign (Sep 01, 2021)
19-4231218-G-A		not specified	Uncertain significance (Jan 27, 2022)
19-4231265-T-C		not specified	Uncertain significance (Nov 27, 2023)
19-4231286-A-G		not specified	Uncertain significance (May 24, 2023)
19-4231301-G-A		not specified	Uncertain significance (Mar 30, 2024)
19-4231304-T-G		not specified	Uncertain significance (Jan 11, 2023)
19-4231326-C-T			Benign (Jun 29, 2018)
19-4233146-G-A		not specified	Likely benign (Mar 01, 2023)
19-4233159-G-T		not specified	Uncertain significance (Feb 05, 2024)
19-4233163-T-C		not specified	Uncertain significance (Dec 21, 2023)
19-4233181-A-G		not specified	Likely benign (Aug 11, 2022)
19-4234672-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-4234675-G-A		not specified	Uncertain significance (Sep 27, 2022)
19-4234690-G-T		not specified	Uncertain significance (Apr 01, 2024)
19-4234693-C-T		not specified	Uncertain significance (Mar 31, 2024)
19-4234694-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-4234696-C-T			Benign (Jun 30, 2017)
19-4234715-G-A		not specified	Uncertain significance (Dec 28, 2023)
19-4234729-C-G		not specified	Uncertain significance (Feb 15, 2023)
19-4234785-G-T		not specified	Uncertain significance (May 06, 2022)
19-4236937-T-G		not specified	Uncertain significance (Dec 16, 2023)
19-4236955-C-T		not specified	Uncertain significance (Apr 23, 2024)
19-4236958-C-T		not specified	Uncertain significance (Apr 22, 2024)
19-4237011-G-T		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EBI3	protein_coding	protein_coding	ENST00000221847	5	8034

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.108	0.865	125718	0	20	125738	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.276	152	143	1.06	0.00000931	1454
Missense in Polyphen		43	38.906	1.1052		401
Synonymous	-0.348	61	57.6	1.06	0.00000383	479
Loss of Function	1.90	3	9.22	0.326	4.72e-7	90

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000426	0.000419
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000555	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000565	0.0000527
Middle Eastern	0.0000555	0.0000544
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with IL27 to form the IL-27 interleukin, a heterodimeric cytokine which functions in innate immunity. IL-27 has pro- and anti-inflammatory properties, that can regulate T- helper cell development, suppress T-cell proliferation, stimulate cytotoxic T-cell activity, induce isotype switching in B-cells, and that has diverse effects on innate immune cells. Among its target cells are CD4 T-helper cells which can differentiate in type 1 effector cells (TH1), type 2 effector cells (TH2) and IL17 producing helper T-cells (TH17). It drives rapid clonal expansion of naive but not memory CD4 T-cells. It also strongly synergizes with IL-12 to trigger interferon-gamma/IFN-gamma production of naive CD4 T-cells, binds to the cytokine receptor WSX-1/TCCR. Another important role of IL-27 is its antitumor activity as well as its antiangiogenic activity with activation of production of antiangiogenic chemokines. {ECO:0000269|PubMed:12121660}.
• Pathway: Interleukin-12 family signaling;Signaling by Interleukins;Cytokine Signaling in Immune system;Immune System;Interleukin-27 signaling;IL27-mediated signaling events (Consensus)

Recessive Scores

• pRec: 0.186

Intolerance Scores

• loftool: 0.584
• rvis_EVS: -0.49
• rvis_percentile_EVS: 22.36

Haploinsufficiency Scores

• pHI: 0.0842
• hipred: N
• hipred_score: 0.182
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.741

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ebi3
• 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); hematopoietic system phenotype; 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); digestive/alimentary phenotype; immune system phenotype; renal/urinary system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: humoral immune response;regulation of signaling receptor activity;T-helper 1 type immune response;T cell proliferation;positive regulation of interferon-gamma biosynthetic process;positive regulation of alpha-beta T cell proliferation;interleukin-27-mediated signaling pathway;ciliary neurotrophic factor-mediated signaling pathway;interleukin-35-mediated signaling pathway
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;plasma membrane;external side of plasma membrane;receptor complex;ciliary neurotrophic factor receptor complex;CNTFR-CLCF1 complex
• Molecular function: cytokine receptor activity;ciliary neurotrophic factor receptor activity;cytokine activity;protein binding;cytokine binding;interleukin-27 receptor binding