FCER2

protein-coding

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

Gene summary

The protein encoded by this gene is a B-cell specific antigen, and a low-affinity receptor for IgE. It has essential roles in B cell growth and differentiation, and the regulation of IgE production. This protein also exists as a soluble secreted form, then functioning as a potent mitogenic growth factor. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Jul 2011]

Previous symbols:

CD23A
FCE2

MANE transcript

NM_001220500.2

Inheritance

—

ClinVar variants

U:53B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr19:7,688,758-7,702,146

External References & Databases

Ensembl (ENSG00000104921)

Transcript & Mutation Effects

hg38 • Region Span ~13.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FCER2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 54

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001220500.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			50 clinvar	5 clinvar		55
nonsense			1 clinvar			1
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	53	7	0	60

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001220500.2	RefSeq	NP_001207429.1	10	MANE Select
ENST00000597921.6	Ensembl	ENSP00000471974.1	10	MANE Select
NM_001207019.3	RefSeq	NP_001193948.2	10	Standard
NM_002002.5	RefSeq	NP_001993.2	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Hematopoietic cell lineage - Homo sapiens (human)
Epstein-Barr virus infection - Homo sapiens (human)
Signaling by NOTCH2
Human Complement System
Interleukin-10 signaling

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

Molecular Function

integrin binding
protein binding
IgE binding
carbohydrate binding
metal ion binding

Cellular Component

plasma membrane
integral component of plasma membrane
external side of plasma membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000346664
Coding exons: 10
Length: 13389
Individuals with no LoFs: 125615
Homozygous LoFs: 1
Heterozygous LoFs: 132
Defined: 125748
p: 0.000529

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.592	221	198	1.12	0.0000117	2074
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.00030	0.00029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0046	0.0045	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.00026	0.00025	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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).;

Intolerance Scores

LoFtool: 0.935
RVIS EVS: 0.31
RVIS percentile EVS: 72.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.700

Gene Damage Prediction

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