FCGR2A

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

Basic information

Region (hg38): 1:161505429-161524013

Previous symbols: [ "FCG2", "FCGR2A1", "FCGR2" ]

Links

ENSG00000143226 ∙ NCBI:2212 ∙ OMIM:146790 ∙ HGNC:3616 ∙ Uniprot:P12318 ∙ 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 FCGR2A gene.

• Inborn genetic diseases (13 variants)
• not specified (6 variants)
• not provided (4 variants)
• Systemic lupus erythematosus;Malaria, susceptibility to;Cystic fibrosis (2 variants)
• Lupus nephritis, susceptibility to (1 variants)
• Malaria, severe, susceptibility to (1 variants)
• Pseudomonas aeruginosa, susceptibility to chronic infection by, in cystic fibrosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCGR2A 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	2	3
missense			11	5	3	19
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding					1	1
Total	0	0	12	6	7

Variants in FCGR2A

This is a list of pathogenic ClinVar variants found in the FCGR2A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-161506371-G-A		FCGR2A-related disorder	Likely benign (May 28, 2019)
1-161506380-C-T		FCGR2A-related disorder	Likely benign (Apr 12, 2019)
1-161506414-C-T		not specified • FCGR2A-related disorder	Benign (Jan 10, 2020)
1-161506415-A-G		not specified • FCGR2A-related disorder	Benign (Oct 21, 2019)
1-161506437-C-T			Benign/Likely benign (Apr 01, 2024)
1-161506448-A-C		not specified	Uncertain significance (May 18, 2022)
1-161506484-C-T		not specified	Uncertain significance (Jan 19, 2024)
1-161506508-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-161506535-C-T		not specified	Uncertain significance (Feb 21, 2024)
1-161506568-C-T		not specified	Uncertain significance (Oct 10, 2023)
1-161506590-C-T			Likely benign (-)
1-161509809-G-A		not specified	Benign (Mar 28, 2016)
1-161509873-A-G			Likely benign (-)
1-161509904-C-G		not specified	Uncertain significance (Feb 06, 2023)
1-161509952-C-T		Systemic lupus erythematosus;Malaria, susceptibility to;Cystic fibrosis	Uncertain significance (Jul 14, 2021)
1-161509955-A-G		Lupus nephritis, susceptibility to • Pseudomonas aeruginosa, susceptibility to chronic infection by, in cystic fibrosis • Malaria, severe, susceptibility to • not specified	Benign (Mar 28, 2016)
1-161509969-T-C		not specified	Uncertain significance (Nov 07, 2022)
1-161510069-T-C		not specified	Uncertain significance (Nov 09, 2021)
1-161510840-G-C		not specified	Uncertain significance (May 30, 2023)
1-161510849-G-A		not specified	Uncertain significance (Jun 16, 2023)
1-161510859-A-G		not specified	Benign (Mar 28, 2016)
1-161510862-G-A			Likely benign (Jan 01, 2023)
1-161510885-T-C		not specified	Likely benign (Nov 15, 2021)
1-161510888-C-G		not specified	Likely benign (Nov 15, 2021)
1-161510891-C-T		not specified	Likely benign (Nov 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCGR2A	protein_coding	protein_coding	ENST00000271450	7	18584

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000201	0.470	101421	1800	22527	125748	0.102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.352	161	174	0.925	0.00000914	2085
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0891	0.0892
Ashkenazi Jewish	0.256	0.255
East Asian	0.000599	0.000598
Finnish	0.120	0.120
European (Non-Finnish)	0.130	0.130
Middle Eastern	0.000599	0.000598
South Asian	0.0890	0.0875
Other	0.132	0.131

dbNSFP

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}.
• Pathway: 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);Tuberculosis - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Spinal Cord Injury;Neutrophil degranulation;FCGR activation;Role of phospholipids in phagocytosis;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System;Regulation of actin dynamics for phagocytic cup formation;Signaling events mediated by PTP1B;Beta2 integrin cell surface interactions (Consensus)

Intolerance Scores

• loftool: 0.871
• rvis_EVS: 0.84
• rvis_percentile_EVS: 88.36

Haploinsufficiency Scores

• pHI: 0.157
• hipred: N
• hipred_score: 0.304
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00251

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fcgr3
• Phenotype: immune system phenotype; skeleton phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: Fc-gamma receptor signaling pathway involved in phagocytosis;neutrophil degranulation
• Cellular component: plasma membrane;integral component of membrane;secretory granule membrane
• Molecular function: protein binding;IgG binding