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rs2230199

From SNPedia

Orientationminus
Stabilizedminus
Geno Mag Summary
(C;C) 0 common
(C;G) 2 1.6x+ risk of ARMD
(G;G) 2 2.5x+ risk of ARMD
ReferenceGRCh38 38.1/141
Chromosome19
Position6718376
GeneC3
is asnp
is mentioned by
dbSNPrs2230199
ebirs2230199
HLIrs2230199
Exacrs2230199
Varsomers2230199
Maprs2230199
PheGenIrs2230199
hapmaprs2230199
1000 genomesrs2230199
hgdprs2230199
ensemblrs2230199
gopubmedrs2230199
geneviewrs2230199
scholarrs2230199
googlers2230199
pharmgkbrs2230199
gwascentralrs2230199
openSNPrs2230199
23andMers2230199
23andMe allrs2230199
SNP Nexus

SNPshotrs2230199
SNPdbers2230199
MSV3drs2230199
GWAS Ctlgrs2230199
GMAF0.0978
Max Magnitude2
? (C;C) (C;G) (G;G) 28
rs2230199, a SNP in the complement component C3 gene, has been reported by several investigators to be associated with ARMD. The common allele at this SNP is known as Arg102; the variant and risk allele is known as Gly102. The risk allele, in orientation to the dbSNP entry for this rs#, is (G).

In one of the largest case-control studies, the odds ratio associated with heterozygotes is 1.61, and for homozygotes, 3.26 (p = 4.5 x 10e-12). 10.1038/ng2131

NEJM reports significant associate with ARMD.

blog post

OMIM120700
DescC3S/C3F POLYMORPHISM
Variant0001
Relatedalso
Neighborrs1047286
Distance5125


Venter snp
Source plos
Gene C3
allele C
frequency
sift TOLERATED
HuRef 1103691081610
Disease Association Defects in C3 are the cause of C3 deficiency (MIM:120700). It can result in susceptibility to pyogenic infection.



[PMID 19399715] Impact of interacting functional variants in COMT on regional gray matter volume in human brain

OMIM611378
DescMACULAR DEGENERATION, AGE-RELATED, 9; ARMD9
Variant
Relatedalso

[PMID 19234341] Complement component 3 (C3) haplotypes and risk of advanced age-related macular degeneration

[PMID 19797206] Susceptibility genes and progression in age-related maculopathy - a study of single eyes. The prospective Muenster Ageing and Retina Study (MARS)

[PMID 19850835] The noncoding variant in complement factor H gene increases risk of exudative age-related macular degeneration in a Chinese population


[PMID 19899988] Association of c3 gene polymorphisms with neovascular age-related macular degeneration in a chinese population


[PMID 20157618OA-icon.png] Complement Component 3: an assessment of association with AMD and analysis of gene-gene and gene-environment interactions in a Northern Irish cohort

GWAS snp
PMID [PMID 20385819OA-icon.png]
Trait Age-related macular degeneration
Title Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration
Risk Allele C
P-val 1E-10
Odds Ratio 1.74 [1.47-2.06]
GWAS snp
PMID [PMID 20385826OA-icon.png]
Trait Age-related macular degeneration
Title Genome-wide association study of advanced age-related macular degeneration identifies a role of the hepatic lipase gene (LIPC)
Risk Allele
P-val 2E-8
Odds Ratio None None
GWAS snp
PMID [PMID 20861866OA-icon.png]
Trait
Title Genome-wide association identifies SKIV2L and MYRIP as protective factors for age-related macular degeneration
Risk Allele C
P-val 1E-8
Odds Ratio 1.44 [NR]
GWAS snp
PMID [PMID 21665990OA-icon.png]
Trait
Title Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration.
Risk Allele C
P-val 5E-29
Odds Ratio 1.5300 [NR]


[PMID 21871809] Complement Factor H Y402H polymorphism is associated with an increased risk of mortality after intracerebral hemorrhage


[PMID 22174912OA-icon.png] A Common Complement C3 Variant Is Associated with Protection against Wet Age-Related Macular Degeneration in a Japanese Population


[PMID 22699975OA-icon.png] Genetic analysis of simultaneous geographic atrophy and choroidal neovascularization


[PMID 22718507] The investigation of allele and genotype frequencies of human C3 (rs2230199) in south Iranian population


ClinVar
Risk rs2230199(G;G)
Alt rs2230199(G;G)
Reference rs2230199(C;C)
Significance Other
Disease MACULAR DEGENERATION C3S/C3F POLYMORPHISM
Variation info
Gene C3
CLNDBN MACULAR DEGENERATION, AGE-RELATED, 9, SUSCEPTIBILITY TO C3S/C3F POLYMORPHISM
Reversed 1
HGVS NC_000019.9:g.6718387G>C
CLNSRC OMIM Allelic Variant
CLNACC RCV000018584.5, RCV000018585.5,



[PMID 15726497OA-icon.png] Gene-environment interaction effects on the development of immune responses in the 1st year of life.


[PMID 19043567OA-icon.png] Evaluation of clustering and genotype distribution for replication in genome wide association studies: the age-related eye disease study.


[PMID 19048105OA-icon.png] Multifactor effects and evidence of potential interaction between complement factor H Y402H and LOC387715 A69S in age-related macular degeneration.


[PMID 19131662OA-icon.png] A meta-analysis of candidate gene polymorphisms and ischemic stroke in 6 study populations: association of lymphotoxin-alpha in nonhypertensive patients.


[PMID 19169411OA-icon.png] Common variation in the SERPING1 gene is not associated with age-related macular degeneration in two independent groups of subjects.


[PMID 19202148OA-icon.png] Assessing susceptibility to age-related macular degeneration with proteomic and genomic biomarkers.


[PMID 19259132OA-icon.png] Multilocus analysis of age-related macular degeneration.


[PMID 19263529OA-icon.png] Genetic risk factors in recurrent venous thromboembolism: A multilocus, population-based, prospective approach.


[PMID 19330901OA-icon.png] Association of 77 polymorphisms in 52 candidate genes with blood pressure progression and incident hypertension: the Women's Genome Health Study.


[PMID 19381347OA-icon.png] Single nucleotide polymorphisms of the tenomodulin gene (TNMD) in age-related macular degeneration.


[PMID 19559392OA-icon.png] A candidate gene association study of 77 polymorphisms in migraine.


[PMID 19661236OA-icon.png] Plasma complement components and activation fragments: associations with age-related macular degeneration genotypes and phenotypes.


[PMID 19823576OA-icon.png] CFH, C3 and ARMS2 are significant risk loci for susceptibility but not for disease progression of geographic atrophy due to AMD.


[PMID 19828715] Complement component 3 polymorphisms interact with polyunsaturated fatty acids to modulate risk of metabolic syndrome.


[PMID 20157352OA-icon.png] Genetic analysis of typical wet-type age-related macular degeneration and polypoidal choroidal vasculopathy in Japanese population.


[PMID 20664795OA-icon.png] R102G polymorphism of the C3 gene associated with exudative age-related macular degeneration in a French population.


[PMID 21402993OA-icon.png] Assessing susceptibility to age-related macular degeneration with genetic markers and environmental factors.


[PMID 21455292OA-icon.png] Using genetic variation and environmental risk factor data to identify individuals at high risk for age-related macular degeneration.


[PMID 22273503] Association of polymorphisms in C2, CFB and C3 with exudative age-related macular degeneration in a Korean population.


[PMID 22361228] Complement C3 gene polymorphism in renal transplantation (an Iranian experience).

GWAS snp
PMID [PMID 22705344OA-icon.png]
Trait
Title Heritability and Genome-Wide Association Study to Assess Genetic Differences between Advanced Age-Related Macular Degeneration Subtypes.
Risk Allele C
P-val 5E-13
Odds Ratio 1.8300 None


GET Evidence
C3-R102G
aa_change Arg102Gly
aa_change_short R102G
impact pathogenic
qualified_impact Moderate clinical importance, Likely pathogenic
overall_frequency 0.152073
summary This variant (also called C3F) is common in Europeans (10.2% allele frequency), and is associated with age-related macular degeneration. In the US, 1.5% of adults over 40 have the disease, but the incidence increases strongly with age (>15% in women over 80). Assuming an average lifetime risk of ~10%, heterozygous individuals have a ~13% risk and homozygous have ~20%.



[PMID 23337555OA-icon.png] Pharmacogenetics for Genes Associated with Age-Related Macular Degeneration in the Comparison of AMD Treatments Trials (CATT)


[PMID 23582991] Genetic Influences on the Outcome of Anti-Vascular Endothelial Growth Factor Treatment in Neovascular Age-related Macular Degeneration

GWAS snp
PMID [PMID 23455636OA-icon.png]
Trait Age-related macular degeneration
Title Seven new loci associated with age-related macular degeneration.
Risk Allele C
P-val 1E-41
Odds Ratio 1.42 [1.37-1.47]


[PMID 23919682OA-icon.png] Complement alternative pathway genetic variation and Dengue infection in the Thai population


[PMID 23068452] Common polymorphisms in the complement system and susceptiblity to bacterial meningitis.


[PMID 23233260OA-icon.png] Association between polymorphisms of complement pathway genes and age-related macular degeneration in a Chinese population.


[PMID 25688879] Nonsynonymous single nucleotide polymorphisms in the complement component 3 gene are associated with risk of age-related macular degeneration: a meta-analysis


[PMID 24675670OA-icon.png] Impact of the common genetic associations of age-related macular degeneration upon systemic complement component C3d levels


[PMID 26154559] The genetic variant rs4073 A→T of the Interleukin-8 promoter region is associated with the earlier onset of exudative age-related macular degeneration


[PMID 26505407] Association between a functional genetic polymorphism (rs2230199) and age-related macular degeneration risk: a meta-analysis


[PMID 27099955] Single-Nucleotide Polymorphisms Associated With Age-Related Macular Degeneration and Lesion Phenotypes in the Comparison of Age-Related Macular Degeneration Treatments Trials.


[PMID 27116510] Effect of Risk Alleles in CFH, C3, and VEGFA on the Response to Intravitreal Bevacizumab in Tunisian Patients with Neovascular Age-related Macular Degeneration.