FCGR1A
Basic information
Region (hg38): 1:149782671-149791675
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCGR1A 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 | 2 | |||||
missense | 13 | 15 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 13 | 4 | 1 |
Variants in FCGR1A
This is a list of pathogenic ClinVar variants found in the FCGR1A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-149782764-G-A | Likely benign (May 18, 2018) | |||
1-149784064-C-T | Likely benign (May 17, 2018) | |||
1-149784140-C-G | not specified | Uncertain significance (Mar 02, 2023) | ||
1-149784224-C-T | IGG receptor I, phagocytic, familial deficiency of | Uncertain significance (Dec 18, 2024) | ||
1-149788393-G-C | not specified | Uncertain significance (Jul 14, 2024) | ||
1-149788410-G-A | not specified | Uncertain significance (Aug 28, 2024) | ||
1-149788567-G-A | not specified | Uncertain significance (Sep 30, 2024) | ||
1-149788581-C-T | not specified | Uncertain significance (Feb 02, 2024) | ||
1-149790164-C-A | not specified | Uncertain significance (Jan 19, 2022) | ||
1-149790210-G-A | not specified | Uncertain significance (Nov 14, 2024) | ||
1-149790230-C-T | Peritoneal Gliomatosis | Uncertain significance (Aug 01, 2019) | ||
1-149790308-C-T | not specified | Uncertain significance (Oct 20, 2023) | ||
1-149790323-G-C | not specified | Uncertain significance (May 24, 2023) | ||
1-149790325-G-C | not specified | Uncertain significance (Nov 03, 2023) | ||
1-149790332-G-T | not specified | Uncertain significance (Jul 25, 2024) | ||
1-149791297-T-C | not specified | Uncertain significance (Sep 09, 2024) | ||
1-149791298-G-A | not specified | Likely benign (Mar 23, 2022) | ||
1-149791327-C-A | not specified | Uncertain significance (Mar 21, 2023) | ||
1-149791332-C-T | not specified | Uncertain significance (Sep 01, 2021) | ||
1-149791405-T-C | not specified | Likely benign (Mar 01, 2024) | ||
1-149791413-C-T | not specified | Uncertain significance (Oct 12, 2022) | ||
1-149791459-A-G | not specified | Uncertain significance (Jul 07, 2024) | ||
1-149791461-AAAG-A | Benign (Feb 01, 2018) | |||
1-149791483-G-T | not specified | Uncertain significance (Apr 17, 2023) | ||
1-149791485-G-T | not specified | Uncertain significance (Mar 31, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
FCGR1A | protein_coding | protein_coding | ENST00000369168 | 6 | 9848 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000131 | 0.860 | 123711 | 6 | 1042 | 124759 | 0.00421 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.579 | 150 | 171 | 0.875 | 0.00000860 | 2410 |
Missense in Polyphen | 26 | 46.8 | 0.55555 | 721 | ||
Synonymous | 0.372 | 63 | 66.9 | 0.942 | 0.00000327 | 739 |
Loss of Function | 1.35 | 8 | 13.3 | 0.600 | 7.18e-7 | 160 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00448 | 0.00424 |
Ashkenazi Jewish | 0.000303 | 0.000299 |
East Asian | 0.000167 | 0.000163 |
Finnish | 0.000515 | 0.000509 |
European (Non-Finnish) | 0.00639 | 0.00628 |
Middle Eastern | 0.000167 | 0.000163 |
South Asian | 0.00589 | 0.00573 |
Other | 0.00456 | 0.00444 |
dbNSFP
Source:
- Function
- FUNCTION: High affinity receptor for the Fc region of immunoglobulins gamma. Functions in both innate and adaptive immune responses. {ECO:0000269|PubMed:10397749, ECO:0000269|PubMed:10514529, ECO:0000269|PubMed:21965667, ECO:0000269|PubMed:8611682, ECO:0000269|PubMed:9881690}.;
- Pathway
- Fc gamma R-mediated phagocytosis - Homo sapiens (human);Systemic lupus erythematosus - Homo sapiens (human);Acute myeloid leukemia - Homo sapiens (human);Phagosome - Homo sapiens (human);Staphylococcus aureus infection - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Microglia Pathogen Phagocytosis Pathway;Cytokine Signaling in Immune system;FCGR activation;Role of phospholipids in phagocytosis;Fcgamma receptor (FCGR) dependent phagocytosis;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Regulation of actin dynamics for phagocytic cup formation;Interferon gamma signaling;Cross-presentation of soluble exogenous antigens (endosomes);Interferon Signaling
(Consensus)
Recessive Scores
- pRec
- 0.265
Haploinsufficiency Scores
- pHI
- 0.101
- hipred
- N
- hipred_score
- 0.380
- ghis
- 0.500
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.308
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fcgr1
- Phenotype
- cellular phenotype; immune system phenotype; skeleton phenotype; normal phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;receptor-mediated endocytosis;phagocytosis, engulfment;immune response;signal transduction;Fc-gamma receptor signaling pathway involved in phagocytosis;regulation of immune response;interferon-gamma-mediated signaling pathway
- Cellular component
- plasma membrane;integral component of membrane;clathrin-coated endocytic vesicle membrane;early endosome membrane
- Molecular function
- protein binding;IgG binding