FCER1A

Fc epsilon receptor Ia, the group of Fc receptors|Immunoglobulin like domain containing

Basic information

Region (hg38): 1:159289713-159308224

Previous symbols: [ "FCE1A" ]

Links

ENSG00000179639 ∙ NCBI:2205 ∙ OMIM:147140 ∙ HGNC:3609 ∙ Uniprot:P12319 ∙ 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 FCER1A gene.

• Inborn genetic diseases (13 variants)
• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCER1A 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			12	1	5	18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	6

Variants in FCER1A

This is a list of pathogenic ClinVar variants found in the FCER1A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-159304035-A-G		not specified	Uncertain significance (Oct 26, 2022)
1-159304051-A-G		not specified	Uncertain significance (Mar 06, 2023)
1-159304057-G-A		not specified	Uncertain significance (Nov 09, 2022)
1-159304102-A-G			Benign (Jul 04, 2018)
1-159304153-G-A			Benign (Jul 04, 2018)
1-159304175-C-T			Benign (Dec 31, 2019)
1-159306017-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-159306030-G-T		not specified	Uncertain significance (Nov 22, 2022)
1-159306041-T-A		not specified	Uncertain significance (Jun 28, 2022)
1-159306062-A-G		not specified	Uncertain significance (Dec 13, 2023)
1-159306071-G-A		not specified	Likely benign (Oct 05, 2021)
1-159306074-G-A		not specified	Uncertain significance (Apr 18, 2023)
1-159306130-C-A		not specified	Uncertain significance (May 30, 2023)
1-159306159-T-C		not specified	Uncertain significance (Nov 21, 2023)
1-159306186-C-T			Benign (Jun 13, 2018)
1-159306222-C-T		not specified	Uncertain significance (Jul 12, 2023)
1-159307882-G-T		not specified	Uncertain significance (Sep 14, 2021)
1-159307883-G-C		not specified	Uncertain significance (Jan 19, 2022)
1-159307892-T-A		not specified	Uncertain significance (Mar 06, 2023)
1-159307892-T-G		not specified	Uncertain significance (Mar 11, 2022)
1-159307899-C-A			Benign (May 10, 2018)
1-159307919-C-T			Benign (Jun 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCER1A	protein_coding	protein_coding	ENST00000368115	5	18511

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000308	0.578	125721	0	5	125726	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.416	144	131	1.10	0.00000598	1692
Missense in Polyphen		43	36.211	1.1875		501
Synonymous	-0.568	55	49.9	1.10	0.00000233	469
Loss of Function	0.720	8	10.5	0.760	4.45e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the Fc region of immunoglobulins epsilon. High affinity receptor. Responsible for initiating the allergic response. Binding of allergen to receptor-bound IgE leads to cell activation and the release of mediators (such as histamine) responsible for the manifestations of allergy. The same receptor also induces the secretion of important lymphokines.
• Pathway: Fc epsilon RI signaling pathway - Homo sapiens (human);Asthma - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Phospholipase D signaling pathway - Homo sapiens (human);Fc Epsilon Receptor I Signaling in Mast Cells;IL1 and megakaryocytes in obesity;fc epsilon receptor i signaling in mast cells;Fc-epsilon receptor I signaling in mast cells (Consensus)

Recessive Scores

• pRec: 0.731

Intolerance Scores

• loftool: 0.784
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63

Haploinsufficiency Scores

• pHI: 0.0272
• hipred: N
• hipred_score: 0.112
• ghis: 0.428

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.593

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fcer1a
• Phenotype: immune 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); hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: Fc-epsilon receptor signaling pathway
• Cellular component: plasma membrane;integral component of plasma membrane;cell surface
• Molecular function: IgE binding