FCER2

Fc epsilon receptor II, the group of Fc receptors|C-type lectin domain containing|CD molecules

Basic information

Region (hg38): 19:7688758-7702146

Previous symbols: [ "CD23A", "FCE2" ]

Links

ENSG00000104921 ∙ NCBI:2208 ∙ OMIM:151445 ∙ HGNC:3612 ∙ Uniprot:P06734 ∙ 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 FCER2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCER2 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			20	3		23
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	5	0

Variants in FCER2

This is a list of pathogenic ClinVar variants found in the FCER2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7689204-GA-G			Likely benign (Dec 31, 2019)
19-7689222-G-A		not specified	Uncertain significance (May 01, 2024)
19-7689243-G-A		not specified	Uncertain significance (Jun 24, 2022)
19-7689267-C-T		not specified	Uncertain significance (Jun 13, 2024)
19-7689335-C-T		not specified	Uncertain significance (Oct 04, 2022)
19-7689347-G-T		not specified	Uncertain significance (Apr 04, 2023)
19-7689359-C-G		not specified	Uncertain significance (Jun 05, 2023)
19-7689371-C-T		not specified	Likely benign (Apr 07, 2023)
19-7689423-C-A		not specified	Uncertain significance (Feb 28, 2024)
19-7690231-G-A		not specified	Uncertain significance (Dec 01, 2022)
19-7690235-C-T		not specified	Uncertain significance (Jun 05, 2024)
19-7690243-C-G		not specified	Uncertain significance (Mar 25, 2024)
19-7690411-C-T		not specified	Uncertain significance (Oct 25, 2022)
19-7690441-C-T		not specified	Uncertain significance (Aug 09, 2021)
19-7690507-A-T		not specified	Uncertain significance (Aug 12, 2021)
19-7696836-T-G		not specified	Uncertain significance (Jan 05, 2022)
19-7696870-G-A		not specified	Uncertain significance (Jun 04, 2024)
19-7697049-C-T		not specified	Likely benign (Aug 17, 2021)
19-7697247-A-G		not specified	Uncertain significance (Apr 12, 2023)
19-7697278-G-C		not specified	Uncertain significance (May 13, 2024)
19-7697290-T-C		not specified	Uncertain significance (Dec 20, 2021)
19-7697552-A-C			Likely benign (Jun 01, 2023)
19-7697572-T-C		not specified	Likely benign (Nov 06, 2023)
19-7698400-G-A		not specified	Uncertain significance (Jul 15, 2021)
19-7698767-C-T		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCER2	protein_coding	protein_coding	ENST00000346664	10	13389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.61e-12	0.0718	125615	1	132	125748	0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.592	221	198	1.12	0.0000117	2074
Missense in Polyphen		58	45.112	1.2857		517
Synonymous	-0.669	90	82.3	1.09	0.00000550	607
Loss of Function	0.317	18	19.5	0.923	9.52e-7	204

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000731	0.000730
Ashkenazi Jewish	0.00	0.00
East Asian	0.00461	0.00452
Finnish	0.00	0.00
European (Non-Finnish)	0.000257	0.000255
Middle Eastern	0.00461	0.00452
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Low-affinity receptor for immunoglobulin E (IgE) and CR2/CD21. Has essential roles in the regulation of IgE production and in the differentiation of B-cells (it is a B-cell-specific antigen).
• Pathway: Hematopoietic cell lineage - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Signaling by NOTCH2;Human Complement System;Interleukin-10 signaling;Interleukin-4 and 13 signaling;Signal Transduction;il 4 signaling pathway;NOTCH2 intracellular domain regulates transcription;Signaling by NOTCH2;Signaling by NOTCH;IL4-mediated signaling events (Consensus)

Intolerance Scores

• loftool: 0.935
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.66

Haploinsufficiency Scores

• pHI: 0.0703
• hipred: N
• hipred_score: 0.341
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.700

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fcer2a
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; immune system phenotype; digestive/alimentary phenotype; hematopoietic 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)

Gene ontology

• Biological process: positive regulation of humoral immune response mediated by circulating immunoglobulin;Notch signaling pathway;cytokine-mediated signaling pathway;positive regulation of nitric-oxide synthase activity;positive regulation of killing of cells of other organism;positive regulation of nitric-oxide synthase biosynthetic process
• Cellular component: plasma membrane;integral component of plasma membrane;external side of plasma membrane;extracellular exosome
• Molecular function: integrin binding;protein binding;IgE binding;carbohydrate binding;metal ion binding