chr1:161479745:A>G Detail (hg19) (FCGR2A)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr1:161,479,745-161,479,745 |
| hg38 | chr1:161,509,955-161,509,955 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001136219.1:c.500A>G | NP_001129691.1:p.His167Arg |
| NM_021642.3:c.500A>G | NP_067674.2:p.His167Arg | |
| Ensemble | ENST00000699278.1:c.242A>G | ENST00000699278.1:p.His81Arg |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.217 |
| ToMMo:0.193 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.327 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
risk factor
|
2010-07-01 | no assertion criteria provided | Lupus nephritis, susceptibility to |
germline
|
Detail |
|
risk factor
|
2010-07-01 | no assertion criteria provided | Pseudomonas aeruginosa, susceptibility to chronic infection by, in cystic fibrosis |
germline
|
Detail |
|
risk factor
|
2010-07-01 | no assertion criteria provided | Malaria, severe, susceptibility to |
germline
|
Detail |
|
Benign
|
2016-03-28 | criteria provided, single submitter | not specified |
germline
|
Detail |
CIViC
| Disease | Drug | EL | ET | ED | CS | VO | TR | Pubmed | Links |
|---|---|---|---|---|---|---|---|---|---|
| breast cancer | B |
Prognostic
|
Does Not Support
|
N/A | Common Germline | 3 | 22906996 | Detail | |
| breast cancer | B |
Prognostic
|
Does Not Support
|
N/A | Common Germline | 4 | 24989892 | Detail |
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | stomach carcinoma | E-selectin rs5361 and FCGR2A rs1801274 variants were associated with increased r... | BeFree | 21780194 | Detail |
| 0.248 | ulcerative colitis | A genome-wide association study identifies three new susceptibility loci for ulc... | GWASCAT | 19915573 | Detail |
| 0.006 | Immune thrombocytopenic purpura | FCGR2A rs1801274 polymorphism is associated with risk of childhood-onset idiopat... | BeFree | 25457587 | Detail |
| <0.001 | stomach carcinoma | Interleukin-4 receptor (IL-4R) variant rs2107356 presented negative correlations... | BeFree | 21780194 | Detail |
| 0.247 | Mucocutaneous Lymph Node Syndrome | Genome-wide association study identifies FCGR2A as a susceptibility locus for Ka... | GWASCAT | 22081228 | Detail |
| 0.003 | Malignant neoplasm of stomach | Interleukin-4 receptor (IL-4R) variant rs2107356 presented negative correlations... | BeFree | 21780194 | Detail |
| 0.248 | ulcerative colitis | Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing ... | GWASCAT | 21297633 | Detail |
| <0.001 | Clinical infection | A single-nucleotide polymorphism in FcγRIIa (rs1801274) results in altered affin... | BeFree | 26240159 | Detail |
| 0.247 | Mucocutaneous Lymph Node Syndrome | A genetic variant rs1801274 in FCGR2A as a potential risk marker for Kawasaki di... | BeFree | 25093412 | Detail |
| 0.120 | Malaria, severe, susceptibility to | NA | CLINVAR | Detail | |
| 0.247 | Mucocutaneous Lymph Node Syndrome | [Genome-wide association study identifies FCGR2A as a susceptibility locus for K... | GAD | 22081228 | Detail |
| <0.001 | pneumonia | Four risk single-nucleotide polymorphisms were significantly (p<0.0001) assoc... | BeFree | 21737555 | Detail |
| 0.247 | Mucocutaneous Lymph Node Syndrome | Absence of association of FCGR2A gene polymorphism rs1801274 with Kawasaki disea... | BeFree | 24775607 | Detail |
| 0.004 | Autoimmune Diseases | rs1801274 is a nonsynonymous SNP of FCGR2A that is reported to have a critical e... | BeFree | 19915573 | Detail |
| 0.003 | Heparin-induced thrombocytopenia | [Development of a real-time PCR detection method for a FCGR2A polymorphism in th... | GAD | 19664613 | Detail |
| 0.008 | Lupus Erythematosus, Systemic | The Fc Gamma Receptor IIa (FcGRIIa) molecule is involved in the clearance of aut... | BeFree | 20148910 | Detail |
| 0.120 | Inflammatory Bowel Diseases | Host-microbe interactions have shaped the genetic architecture of inflammatory b... | GWASCAT | 23128233 | Detail |
| <0.001 | Lymphoma, Non-Hodgkin | A functional nonsynonymous SNP in the innate immune gene Fc gamma receptor 2A (F... | BeFree | 17018637 | Detail |
| <0.001 | Diabetes Mellitus, Insulin-Dependent | The Fc Gamma Receptor IIa (FcGRIIa) molecule is involved in the clearance of aut... | BeFree | 20148910 | Detail |
| 0.248 | ulcerative colitis | [A genome-wide association study identifies three new susceptibility loci for ul... | GAD | 19915573 | Detail |
| 0.248 | ulcerative colitis | [Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing... | GAD | 21297633 | Detail |
| 0.003 | Malignant neoplasm of stomach | E-selectin rs5361 and FCGR2A rs1801274 variants were associated with increased r... | BeFree | 21780194 | Detail |
| 0.004 | rheumatoid arthritis | We conducted a meta-analysis on the association between FCGR2A H131R (rs1801274)... | BeFree | 26314337 | Detail |
| 0.010 | Lymphoma, Non-Hodgkin | A functional nonsynonymous SNP in the innate immune gene Fc gamma receptor 2A (F... | BeFree | 17018637 | Detail |
| 0.002 | stomach carcinoma | E-selectin rs5361 and FCGR2A rs1801274 variants were associated with increased r... | BeFree | 21780194 | Detail |
| 0.201 | Lupus Erythematosus, Systemic | [The genetic contribution towards predicting early-onset disease in patients wit... | GAD | 20881011 | Detail |
| 0.008 | celiac disease | We studied the FcgammaRIIa*A519G (rs1801274) and FcgammaRIIIa*A559C (rs396991) s... | BeFree | 19140833 | Detail |
| 0.005 | Autoimmune Diseases | The Fc Gamma Receptor IIa (FcGRIIa) molecule is involved in the clearance of aut... | BeFree | 20148910 | Detail |
| <0.001 | pneumonia | Four risk single-nucleotide polymorphisms were significantly (p<0.0001) assoc... | BeFree | 21737555 | Detail |
| 0.247 | Mucocutaneous Lymph Node Syndrome | We also replicated the association of a functional SNP of FCGR2A (rs1801274, P =... | BeFree | 22446962 | Detail |
| 0.002 | Malignant neoplasm of stomach | E-selectin rs5361 and FCGR2A rs1801274 variants were associated with increased r... | BeFree | 21780194 | Detail |
| <0.001 | Severe Dengue | Two single nucleotide polymorphisms (SNPs), rs1801274 of FcγRIIa and rs4804803 o... | BeFree | 24911936 | Detail |
| <0.001 | periodontitis | Associations between FCGR2A rs1801274, FCGR3A rs396991, FCGR3B NA1/NA2 polymorph... | BeFree | 23649770 | Detail |
| <0.001 | asthma | Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-18... | BeFree | 24586589 | Detail |
| 0.003 | asthma | Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-18... | BeFree | 24586589 | Detail |
| 0.003 | asthma | Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-18... | BeFree | 24586589 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| A total of 57 women with HER2-positive metastatic breast cancer were analyzed after taxane plus tras... | CIViC Evidence | Detail |
| 1325 HER2-positive breast cancer patients treated with trastuzumab and chemotherapy from the N9831 c... | CIViC Evidence | Detail |
| NM_001136219.3(FCGR2A):c.500A>G (p.His167Arg) AND Lupus nephritis, susceptibility to | ClinVar | Detail |
| NM_001136219.3(FCGR2A):c.500A>G (p.His167Arg) AND Pseudomonas aeruginosa, susceptibility to chronic ... | ClinVar | Detail |
| NM_001136219.3(FCGR2A):c.500A>G (p.His167Arg) AND Malaria, severe, susceptibility to | ClinVar | Detail |
| NM_001136219.3(FCGR2A):c.500A>G (p.His167Arg) AND not specified | ClinVar | Detail |
| E-selectin rs5361 and FCGR2A rs1801274 variants were associated with increased risk of gastric cance... | DisGeNET | Detail |
| A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in t... | DisGeNET | Detail |
| FCGR2A rs1801274 polymorphism is associated with risk of childhood-onset idiopathic (immune) thrombo... | DisGeNET | Detail |
| Interleukin-4 receptor (IL-4R) variant rs2107356 presented negative correlations to E-selectin varia... | DisGeNET | Detail |
| Genome-wide association study identifies FCGR2A as a susceptibility locus for Kawasaki disease. | DisGeNET | Detail |
| Interleukin-4 receptor (IL-4R) variant rs2107356 presented negative correlations to E-selectin varia... | DisGeNET | Detail |
| Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confir... | DisGeNET | Detail |
| A single-nucleotide polymorphism in FcγRIIa (rs1801274) results in altered affinity of the receptor ... | DisGeNET | Detail |
| A genetic variant rs1801274 in FCGR2A as a potential risk marker for Kawasaki disease: a case-contro... | DisGeNET | Detail |
| NA | DisGeNET | Detail |
| [Genome-wide association study identifies FCGR2A as a susceptibility locus for Kawasaki disease.] | DisGeNET | Detail |
| Four risk single-nucleotide polymorphisms were significantly (p<0.0001) associated with severe pn... | DisGeNET | Detail |
| Absence of association of FCGR2A gene polymorphism rs1801274 with Kawasaki disease in Greek patients... | DisGeNET | Detail |
| rs1801274 is a nonsynonymous SNP of FCGR2A that is reported to have a critical effect on receptor bi... | DisGeNET | Detail |
| [Development of a real-time PCR detection method for a FCGR2A polymorphism in the LightCycler and ap... | DisGeNET | Detail |
| The Fc Gamma Receptor IIa (FcGRIIa) molecule is involved in the clearance of autoantibodies and a fu... | DisGeNET | Detail |
| Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. | DisGeNET | Detail |
| A functional nonsynonymous SNP in the innate immune gene Fc gamma receptor 2A (FCGR2A; rs1801274) wa... | DisGeNET | Detail |
| The Fc Gamma Receptor IIa (FcGRIIa) molecule is involved in the clearance of autoantibodies and a fu... | DisGeNET | Detail |
| [A genome-wide association study identifies three new susceptibility loci for ulcerative colitis in ... | DisGeNET | Detail |
| [Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confi... | DisGeNET | Detail |
| E-selectin rs5361 and FCGR2A rs1801274 variants were associated with increased risk of gastric cance... | DisGeNET | Detail |
| We conducted a meta-analysis on the association between FCGR2A H131R (rs1801274), FCGR3A F158V (rs39... | DisGeNET | Detail |
| A functional nonsynonymous SNP in the innate immune gene Fc gamma receptor 2A (FCGR2A; rs1801274) wa... | DisGeNET | Detail |
| E-selectin rs5361 and FCGR2A rs1801274 variants were associated with increased risk of gastric cance... | DisGeNET | Detail |
| [The genetic contribution towards predicting early-onset disease in patients with SLE is quantified ... | DisGeNET | Detail |
| We studied the FcgammaRIIa*A519G (rs1801274) and FcgammaRIIIa*A559C (rs396991) single nucleotide pol... | DisGeNET | Detail |
| The Fc Gamma Receptor IIa (FcGRIIa) molecule is involved in the clearance of autoantibodies and a fu... | DisGeNET | Detail |
| Four risk single-nucleotide polymorphisms were significantly (p<0.0001) associated with severe pn... | DisGeNET | Detail |
| We also replicated the association of a functional SNP of FCGR2A (rs1801274, P = 1.6 × 10(-6)) ident... | DisGeNET | Detail |
| E-selectin rs5361 and FCGR2A rs1801274 variants were associated with increased risk of gastric cance... | DisGeNET | Detail |
| Two single nucleotide polymorphisms (SNPs), rs1801274 of FcγRIIa and rs4804803 of DC-SIGN, have been... | DisGeNET | Detail |
| Associations between FCGR2A rs1801274, FCGR3A rs396991, FCGR3B NA1/NA2 polymorphisms and periodontit... | DisGeNET | Detail |
| Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-187Ile>Thr, rs10505... | DisGeNET | Detail |
| Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-187Ile>Thr, rs10505... | DisGeNET | Detail |
| Functional SNPs of FCGR2A (FcγRIIA-131His>Arg, rs1801274), FCGR2B (FcγRIIB-187Ile>Thr, rs10505... | DisGeNET | Detail |
Overlapped Transcript Coordinates
| Gene | Transcript ID | Exon Number | Chromosome | Start | Stop | Type | Amino Mutation | Transcript Position | Links |
|---|
Overlapped Transcript
| Gene | Transcript ID | Chromosome | Start | Stop | Links |
|---|
- Gene
- -
- dbSNP
- rs1801274 dbSNP
- Genome
- hg19
- Position
- chr1:161,479,745-161,479,745
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 797
- Mean of sample read depth (HGVD)
- 19.72
- Standard deviation of sample read depth (HGVD)
- 34.37
- Number of reference allele (HGVD)
- 1247
- Number of alternative allele (HGVD)
- 346
- Allele Frequency (HGVD)
- 0.21720025109855617
- Gene Symbol (HGVD)
- FCGR2A
- ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- PASS
- Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- rs1801274
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.1935
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 3243
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8634
- East Asian Allele Counts (ExAC)
- 2827
- East Asian Heterozygous Counts (ExAC)
- 1945
- East Asian Homozygous Counts (ExAC)
- 441
- East Asian Allele Frequency (ExAC)
- 0.32742645355571
- Chromosome Counts in All Race (ExAC)
- 121362
- Allele Counts in All Race (ExAC)
- 58144
- Heterozygous Counts in All Race (ExAC)
- 29622
- Homozygous Counts in All Race (ExAC)
- 14261
- Allele Frequency in All Race (ExAC)
- 0.4790955982927111
- Variant (CIViC) (CIViC Variant)
- H167R
- Transcript 1 (CIViC Variant)
- ENST00000271450.6
- Variant URL (CIViC Variant)
- https://civic.genome.wustl.edu/links/variants/456
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