FCGR2A

protein-coding

Fc gamma receptor IIa, the group of Fc receptors|Immunoglobulin like domain containing|CD molecules

Gene summary

This gene encodes one member of a family of immunoglobulin Fc receptor genes found on the surface of many immune response cells. The protein encoded by this gene is a cell surface receptor found on phagocytic cells such as macrophages and neutrophils, and is involved in the process of phagocytosis and clearing of immune complexes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2008]

Previous symbols:

FCG2
FCGR2A1
FCGR2

MANE transcript

NM_001136219.3

Inheritance

—

ClinVar variants

U:56B:14

Top phenotype

FCGR2A-related disorder

gnomAD constraint

pLI —, LoF o/e 0.79

Max pathogenic AF

—

Genomic locus

chr1:161,505,430-161,524,013

External References & Databases

Ensembl (ENSG00000143226)

Transcript & Mutation Effects

hg38 • Region Span ~18.6 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 FCGR2A variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 58

not providedTotal: 10

FCGR2A-related disorderTotal: 2

Malaria, susceptibility toTotal: 2

Systemic lupus erythematosusTotal: 2

Cystic fibrosisTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001136219.3. 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				4 clinvar		4
missense			51 clinvar	9 clinvar	1 clinvar	61
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	56	13	1	70

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001136219.3	RefSeq	NP_001129691.1	7	MANE Select
ENST00000271450.12	Ensembl	ENSP00000271450.6	7	MANE Select
NM_001375296.1	RefSeq	NP_001362225.1	6	Standard
NM_001375297.1	RefSeq	NP_001362226.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Platelet activation - Homo sapiens (human)
Fc gamma R-mediated phagocytosis - Homo sapiens (human)
Systemic lupus erythematosus - Homo sapiens (human)
Phagosome - Homo sapiens (human)
Staphylococcus aureus infection - Homo sapiens (human)

Biological Process

Fc-gamma receptor signaling pathway involved in phagocytosis
neutrophil degranulation

Molecular Function

protein binding
IgG binding

Cellular Component

plasma membrane
integral component of membrane
secretory granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000271450
Coding exons: 7
Length: 18584
Individuals with no LoFs: 101421
Homozygous LoFs: 1800
Heterozygous LoFs: 22527
Defined: 125748
p: 0.102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.352	161	174	0.925	0.00000914	2085
Missense (PolyPhen)		46	66.333	0.69347		843
Synonymous	-1.16	81	68.8	1.18	0.00000402	610
Loss of Function	0.675	10	12.6	0.795	5.44e-7	140

Population LoF Frequency

Population	CAF	p-value	Status
African	0.025	0.025	notable
Latino/Admixed American	0.064	0.063	notable
Ashkenazi Jewish	0.26	0.26	notable
East Asian	0.00060	0.00060	rare
Finnish	0.12	0.12	notable
European (Non-Finnish)	0.13	0.13	notable
South Asian	0.089	0.088	notable
Other	0.13	0.13	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds to the Fc region of immunoglobulins gamma. Low affinity receptor. By binding to IgG it initiates cellular responses against pathogens and soluble antigens. Promotes phagocytosis of opsonized antigens. {ECO:0000269|PubMed:19011614}.;

Intolerance Scores

LoFtool: 0.871
RVIS EVS: 0.84
RVIS percentile EVS: 88.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00251

Gene Damage Prediction

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