FCGR2A
Basic information
Region (hg38): 1:161505430-161524013
Previous symbols: [ "FCG2", "FCGR2A1", "FCGR2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (50 variants)
- not_provided (9 variants)
- FCGR2A-related_disorder (2 variants)
- Malaria,_susceptibility_to (2 variants)
- Systemic_lupus_erythematosus (2 variants)
- Cystic_fibrosis (2 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. These statistics are base on transcript: NM_001136219.3. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 4 | |||||
missense | 45 | 55 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
Total | 0 | 0 | 47 | 13 | 1 |
GnomAD
Source:
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:
- 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