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
Links
Type Database ID Link
Gene MIM 146790 OMIM
HGNC 3616 HGNC
Ensembl ENSG00000143226 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv3527680 TogoVar
COSMIC
MONDO
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&lt;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&lt;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&gt;Arg, rs1801274), FCGR2B (FcγRIIB-18... BeFree 24586589 Detail
0.003 asthma Functional SNPs of FCGR2A (FcγRIIA-131His&gt;Arg, rs1801274), FCGR2B (FcγRIIB-18... BeFree 24586589 Detail
0.003 asthma Functional SNPs of FCGR2A (FcγRIIA-131His&gt;Arg, rs1801274), FCGR2B (FcγRIIB-18... BeFree 24586589 Detail
Annotation

Annotations

DescrptionSourceLinks
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&lt;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&lt;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&gt;Arg, rs1801274), FCGR2B (FcγRIIB-187Ile&gt;Thr, rs10505... DisGeNET Detail
Functional SNPs of FCGR2A (FcγRIIA-131His&gt;Arg, rs1801274), FCGR2B (FcγRIIB-187Ile&gt;Thr, rs10505... DisGeNET Detail
Functional SNPs of FCGR2A (FcγRIIA-131His&gt;Arg, rs1801274), FCGR2B (FcγRIIB-187Ile&gt;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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