rs10490924
| age related macular degeneration |
| Orientation | plus |
| Stabilized | plus |
| Geno | Mag | Summary |
|---|---|---|
| (G;G) | 0 | normal |
| (G;T) | 2.5 | 2.7x risk for age related macular degeneration |
| (T;T) | 3.5 | 8.2x risk for age related macular degeneration |
| Reference | GRCh38 38.1/141 |
| Chromosome | 10 |
| Position | 122454932 |
| Gene | ARMS2, LOC105378525 |
| is a | snp |
| is | mentioned by |
| dbSNP | rs10490924 |
| dbSNP (classic) | rs10490924 |
| ClinGen | rs10490924 |
| ebi | rs10490924 |
| HLI | rs10490924 |
| Exac | rs10490924 |
| Gnomad | rs10490924 |
| Varsome | rs10490924 |
| LitVar | rs10490924 |
| Map | rs10490924 |
| PheGenI | rs10490924 |
| Biobank | rs10490924 |
| 1000 genomes | rs10490924 |
| hgdp | rs10490924 |
| ensembl | rs10490924 |
| geneview | rs10490924 |
| scholar | rs10490924 |
| rs10490924 | |
| pharmgkb | rs10490924 |
| gwascentral | rs10490924 |
| openSNP | rs10490924 |
| 23andMe | rs10490924 |
| SNPshot | rs10490924 |
| SNPdbe | rs10490924 |
| MSV3d | rs10490924 |
| GWAS Ctlg | rs10490924 |
| GMAF | 0.2736 |
| Max Magnitude | 3.5 |
| ? | (G;G) (G;T) (T;T) | 28 |
|---|---|---|
|
| ||
| This SNP has been recognized by the Coriell Personalized Medicine Collaborative ICOB.
|
rs10490924, also known as c.205G>T, p.Ala69Ser and A69S, was identified as a risk factor from chromosome 10 related to age related macular degeneration. The risk allele is (T). Odds ratios for heterozygotes and homozygotes are, respectively, 2.69 (CI: 2.22-3.27) and 8.21 (CI: 5.79-11.65).[PMID 16174643]
Disease risk in combination with the rs1061170 SNP in the CFH gene is dramatically increased. Homozygotes for both the rare/risk alleles at both loci are estimated to be at 57 fold higher risk for age related macular degeneration than individuals homozygous for the common alleles at both loci. [PMID 16174643]
A subsequent study indicated that the risk based on solely the ARMS2 SNP rs10490924 is significantly higher in smokers than in non-smokers. [PMID 16642439
]
Based on a study of ~750 patients, rs10490924 is significantly higher in participants with choroidal neovascularization than in those with geographic atrophy (odds ratio 1.37, CI: 1.21-1.54, p = 4.2 × 10(-7)).[PMID 21122828]
Note that this SNP is completely predictive (ie is in perfect linkage disequilibrium) with rs11200638, thus the status of one predicts the status of the other.
[PMID 17884985] A likely biological mechanism is that the A69S change in the LOC387715/ARMS2 protein affects its presumptive function in mitochondria.
[PMID 18164066] rs10490924 and rs11200638 defined 2 significant haplotypes associated with increased risk of neovascular AMD.
[PMID 18400199] In comparison with wild-type homozygosity (G;G), homozygosity for the at-risk allele genotype (T;T) increased the likelihood for polypoidal choroidal vasculopathy (PCV) 8.4-fold (CI: 3.6-19.5) and heterozygosity for the at-risk allele genotype (G;T) increased the risk for PCV 4x (CI: 1.9-8.4), based on a study of ~100 Japanese patients.
[PMID 18682806] An analysis of the joint effects of rs1061170, rs11200638 and rs10490924 on AMD
[PMID 19268887] ARMS2 (LOC387715) Variants in Japanese Patients with Exudative Age-related Macular Degeneration and Polypoidal Choroidal Vasculopathy.
[PMID 19259132] Multilocus analysis of age-related macular degeneration.
[PMID 19255159] Age-Related Macular Degeneration Associated ARMS2 is not a Mitochondrial but Cytosolic Protein.
[PMID 19680273] ARMS2/HTRA1 and CFH polymorphisms are not associated with choroidal neovascularization in highly myopic eyes of the elderly Japanese population
[PMID 19797206] Susceptibility genes and progression in age-related maculopathy - a study of single eyes. The prospective Muenster Ageing and Retina Study (MARS)
[PMID 19796758] Comprehensive Analysis of Complement Factor H and LOC387715/ARMS2/HTRA1 Variants with Respect to Phenotype in Advanced Age-related Macular Degeneration
[PMID 19491722] Analyses of single nucleotide polymorphisms and haplotype linkage of LOC387715 and the HTRA1 gene in exudative age-related macular degeneration in a Chinese cohort
[PMID 19898184] Angiographic lesion size associated with loc387715 a69s genotype in subfoveal polypoidal choroidal vasculopathy
[PMID 19933195] Analysis of six genetic risk factors highly associated with AMD in the region surrounding ARMS2 and HTRA1 on chromosome 10q26
[PMID 20157352] Genetic analysis of typical wet-type age-related macular degeneration and polypoidal choroidal vasculopathy in Japanese population
[PMID 20182747] Analysis of the indel at the ARMS2 3'UTR in age-related macular degeneration
[PMID 20381870] Progression of Geographic Atrophy and Genotype in Age-Related Macular Degeneration
| GWAS snp | |
|---|---|
| PMID | [PMID 20385826]
|
| 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 | 5E-119 |
| Odds Ratio | None None |
[PMID 20664795] R102G polymorphism of the C3 gene associated with exudative age-related macular degeneration in a French population
[PMID 20688737] Joint Effect of Cigarette Smoking, CFH and LOC387715/HTRA1 Polymorphisms on Polypoidal Choroidal Vasculopathy
| GWAS snp | |
|---|---|
| PMID | [PMID 20861866]
|
| Trait | |
| Title | Genome-wide association identifies SKIV2L and MYRIP as protective factors for age-related macular degeneration |
| Risk Allele | T |
| P-val | 1E-60 |
| Odds Ratio | 2.75 [NR] |
[PMID 21067572] Association Analysis of Nine Candidate Gene Polymorphisms in Indian Patients with Type 2 Diabetic Retinopathy
[PMID 21621535] No association between the T280M polymorphism of the CX3CR1 gene and exudative AMD
| GWAS snp | |
|---|---|
| PMID | [PMID 21665990]
|
| Trait | |
| Title | Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration. |
| Risk Allele | T |
| P-val | 0 |
| Odds Ratio | 2.9400 [NR] |
[PMID 21825189] Complement Factor H 402H Variant and Reticular Macular Disease
[PMID 21878851] ASSOCIATION BETWEEN HIGH-RISK DISEASE LOCI AND RESPONSE TO ANTI-VASCULAR ENDOTHELIAL GROWTH FACTOR TREATMENT FOR WET AGE-RELATED MACULAR DEGENERATION
[PMID 21882634] [Influence of genetic mutations on clinical presentation of subretinal neovascularization. Report 2: The impact of HTRA and VEGF genes polymorphism]
[PMID 22049084] HTRA1 regulates angiogenesis through TGF-? family member GDF6
[PMID 22509112] Genetic associations in polypoidal choroidal vasculopathy: A systematic review and meta-analysis
[PMID 22552255] Retinal function and CFH-ARMS2 polymorphisms analysis: a pilot study in Italian AMD patients
[PMID 21959923] Association of ARMS2/HTRA1 variants with polypoidal choroidal vasculopathy phenotype in a Korean population
[PMID 22594510] Association of genetic polymorphisms with response to bevacizumab for neovascular age-related macular degeneration in the Chinese population
[PMID 22699975] Genetic analysis of simultaneous geographic atrophy and choroidal neovascularization
| ClinVar | |
|---|---|
| Risk | Rs10490924(T;T) |
| Alt | Rs10490924(T;T) |
| Reference | Rs10490924(G;G) |
| Significance | Other |
| Disease | Age-related macular degeneration 8 not provided Macular degeneration |
| Variation | info |
| Gene | ARMS2 |
| CLNDBN | Age-related macular degeneration 8 not provided Macular degeneration |
| Reversed | 0 |
| HGVS | NC_000010.10:g.124214448G>T |
| CLNSRC | OMIM Allelic Variant UniProtKB (protein) |
| CLNACC | RCV000001030.3, RCV000190307.1, RCV000371544.1, |
[PMID 16080115] Susceptibility genes for age-related maculopathy on chromosome 10q26.
[PMID 17210853] Neovascular age-related macular degeneration and its association with LOC387715 and complement factor H polymorphism.
[PMID 17325155] The LOC387715 polymorphism and age-related macular degeneration: replication in three case-control samples.
[PMID 17327825] An update on the genetics of age-related macular degeneration.
[PMID 17347568] The LOC387715 gene, smoking, body mass index, environmental associations with advanced age-related macular degeneration.
[PMID 17426452] HTRA1 variant confers similar risks to geographic atrophy and neovascular age-related macular degeneration.
[PMID 17438519] HTRA1 promoter polymorphism predisposes Japanese to age-related macular degeneration.
[PMID 17692272] LOC387715/HTRA1 variants in polypoidal choroidal vasculopathy and age-related macular degeneration in a Japanese population.
[PMID 17903296] Genome-wide association with bone mass and geometry in the Framingham Heart Study.
[PMID 17903296] Genome-wide association with bone mass and geometry in the Framingham Heart Study.
[PMID 17917691] Genetic markers and biomarkers for age-related macular degeneration.
[PMID 18043728] Haplotypes in the complement factor H (CFH) gene: associations with drusen and advanced age-related macular degeneration.
[PMID 18061132] Phenotype analysis of patients with the risk variant LOC387715 (A69S) in age-related macular degeneration.
[PMID 18079691] PLEKHA1-LOC387715-HTRA1 polymorphisms and exudative age-related macular degeneration in the French population.
[PMID 18162041] Neovascular age-related macular degeneration risk based on CFH, LOC387715/HTRA1, and smoking.
[PMID 18248681] Prevalence of common disease-associated variants in Asian Indians.
[PMID 18301036] HTRA1 polymorphism in dry and wet age-related macular degeneration.
[PMID 18423869] CFH and LOC387715/ARMS2 genotypes and treatment with antioxidants and zinc for age-related macular degeneration.
[PMID 18436811] Variants in the 10q26 gene cluster (LOC387715 and HTRA1) exhibit enhanced risk of age-related macular degeneration along with CFH in Indian patients.
[PMID 18493315] C2 and CFB genes in age-related maculopathy and joint action with CFH and LOC387715 genes.
[PMID 18515590] Association analysis of CFH, C2, BF, and HTRA1 gene polymorphisms in Chinese patients with polypoidal choroidal vasculopathy.
[PMID 18535016] Rhesus monkeys and humans share common susceptibility genes for age-related macular disease.
[PMID 18601744] Combining identity by descent and association in genetic case-control studies.
[PMID 18682812] Association of CFH, LOC387715, and HTRA1 polymorphisms with exudative age-related macular degeneration in a northern Chinese population.
[PMID 18688167] Polymorphisms in the LOC387715/ARMS2 putative gene and the risk for Alzheimer's disease.
[PMID 19026761] Molecular pathology of age-related macular degeneration.
[PMID 19048105] Multifactor effects and evidence of potential interaction between complement factor H Y402H and LOC387715 A69S in age-related macular degeneration.
[PMID 19065273] Sequence variants in HTRA1 and LOC387715/ARMS2 and phenotype and response to photodynamic therapy in neovascular age-related macular degeneration in populations from Israel.
[PMID 19169232] Variations in five genes and the severity of age-related macular degeneration: results from the Muenster aging and retina study.
[PMID 19202148] Assessing susceptibility to age-related macular degeneration with proteomic and genomic biomarkers.
[PMID 19661236] Plasma complement components and activation fragments: associations with age-related macular degeneration genotypes and phenotypes.
[PMID 19806217] rs5888 variant of SCARB1 gene is a possible susceptibility factor for age-related macular degeneration.
[PMID 19823576] CFH, C3 and ARMS2 are significant risk loci for susceptibility but not for disease progression of geographic atrophy due to AMD.
[PMID 19958499] A particle swarm based hybrid system for imbalanced medical data sampling.
[PMID 20140183] Genetic and functional dissection of HTRA1 and LOC387715 in age-related macular degeneration.
[PMID 20157618] Complement component 3: an assessment of association with AMD and analysis of gene-gene and gene-environment interactions in a Northern Irish cohort.
[PMID 20339564] Risk factors for age-related maculopathy.
[PMID 20346514] C-reactive protein and CFH, ARMS2/HTRA1 gene variants are independently associated with risk of macular degeneration.
[PMID 20378180] Three major loci involved in age-related macular degeneration are also associated with polypoidal choroidal vasculopathy.
[PMID 20456446] LOC387715/HTRA1 polymorphisms, smoking and combined effects on exudative age-related macular degeneration in a Korean population.
[PMID 20664794] Age-related macular degeneration-associated variants at chromosome 10q26 do not significantly alter ARMS2 and HTRA1 transcript levels in the human retina.
[PMID 20689796] Monozygotic twins with polypoidal choroidal vasuculopathy.
[PMID 20881291] Persons with age-related maculopathy risk genotypes and clinically normal eyes have reduced mesopic vision.
[PMID 21203342] Elevated C-reactive protein levels and ARMS2/HTRA1 gene variants in subjects without age-related macular degeneration.
[PMID 21397333] Role of complement factor H I62V and age-related maculopathy susceptibility 2 A69S variants in the clinical expression of polypoidal choroidal vasculopathy.
[PMID 21402993] Assessing susceptibility to age-related macular degeneration with genetic markers and environmental factors.
[PMID 21455292] Using genetic variation and environmental risk factor data to identify individuals at high risk for age-related macular degeneration.
[PMID 21896867] Associations of complement factor H (CFH) and age-related maculopathy susceptibility 2 (ARMS2) genotypes with subtypes of polypoidal choroidal vasculopathy.
[PMID 22293892] A69S and R38X ARMS2 and Y402H CFH gene polymorphisms as risk factors for neovascular age-related macular degeneration in Poland - a brief report.
[PMID 22491416] Differentiation of exudative age-related macular degeneration and polypoidal choroidal vasculopathy in the ARMS2/HTRA1 locus.
[PMID 22618592] Association of genetic polymorphisms and age-related macular degeneration in chinese population.
| GWAS snp | |
|---|---|
| PMID | [PMID 22705344]
|
| Trait | |
| Title | Heritability and Genome-Wide Association Study to Assess Genetic Differences between Advanced Age-Related Macular Degeneration Subtypes. |
| Risk Allele | T |
| P-val | 0 |
| Odds Ratio | 3.6700 None |
| GWAS snp | |
|---|---|
| PMID | [PMID 22694956]
|
| Trait | |
| Title | Genome-wide association study of age-related macular degeneration identifies associated variants in the TNXB-FKBPL-NOTCH4 region of chromosome 6p21.3. |
| Risk Allele | T |
| P-val | 3E-72 |
| Odds Ratio | 3.0000 None |
[PMID 22977134] Single nucleotide polymorphism in the cholesterol-24S-hydroxylase (CYP46A1) gene and its association with CFH and LOC387715 gene polymorphisms in AMD
[PMID 23337555] Pharmacogenetics for Genes Associated with Age-Related Macular Degeneration in the Comparison of AMD Treatments Trials (CATT)
[PMID 23111182] Prevalence and genomic association of reticular pseudodrusen in age-related macular degeneration
[PMID 23302509] Mitochondrial DNA haplogroups confer differences in risk for age-related macular degeneration: a case control study
[PMID 23098369] ARMS2 increases the risk of early and late age-related macular degeneration in the European Eye Study
[PMID 23582991] Genetic Influences on the Outcome of Anti-Vascular Endothelial Growth Factor Treatment in Neovascular Age-related Macular Degeneration
[PMID 23644223] Variants at chromosome 10q26 locus and the expression of HTRA1 in the retina
| GWAS snp | |
|---|---|
| PMID | [PMID 23455636]
|
| Trait | Age-related macular degeneration |
| Title | Seven new loci associated with age-related macular degeneration. |
| Risk Allele | T |
| P-val | 4E-540 |
| Odds Ratio | 2.76 [2.72-2.80] |
[PMID 23938121] Associations of Candidate Genes to Age-Related Macular Degeneration Among Racial/Ethnic Groups in the Multi-Ethnic Study of Atherosclerosis
| GWAS snp | |
|---|---|
| PMID | [PMID 23577725]
|
| Trait | Age-related macular degeneration |
| Title | Genetic factors in nonsmokers with age-related macular degeneration revealed through genome-wide gene-environment interaction analysis. |
| Risk Allele | A |
| P-val | 8E-27 |
| Odds Ratio | 2.28 [1.96-2.65] |
[PMID 24332537] Incidence and Progression of Reticular Drusen in Age-Related Macular Degeneration: Findings from an Older Australian Cohort
[PMID 23103884] Age-related macular degeneration and coronary heart disease: evaluation of genetic and environmental associations.
[PMID 23204795] Pharmacogenetic influence of LOC387715/HTRA1 on the efficacy of bevacizumab treatment for age-related macular degeneration in a Korean population.
[PMID 23289807] Gene-gene interactions of CFH and LOC387715/ARMS2 with Korean exudative age-related macular degeneration patients.
[PMID 23289808] The association of age-related maculopathy susceptibility 2 (ARMS2) and complement factor H (CFH) variants with two angiographic subtypes of polypoidal choroidal vasculopathy.
[PMID 24865190] Association of Specific Genetic Polymorphisms with Age-related Macular Degeneration in a Northern Chinese Population
[PMID 24865191] Genetic Variants in the SKIV2L Gene in Exudative Age-related Macular Degeneration in the Japanese Population
[PMID 24970616] The contribution of genetic factors to phenotype and progression of drusen in early age-related macular degeneration
[PMID 24067115] Functional effect of Saffron supplementation and risk genotypes in early age-related macular degeneration: a preliminary report
[PMID 25439433] Chronic Central Serous Chorioretinopathy Is Associated with Genetic Variants Implicated in Age-Related Macular Degeneration
[PMID 24974817] No clinically significant association between CFH and ARMS2 genotypes and response to nutritional supplements: AREDS report number 38
[PMID 26067391] Differential DNA Methylation Identified in the Blood and Retina of AMD Patients
[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 26681391] Reticular Pseudodrusen and Their Association with Age-Related Macular Degeneration: The Melbourne Collaborative Cohort Study.
[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 28659708] Specific correlation between the major chromosome 10q26 haplotype conferring risk for age-related macular degeneration and the expression of HTRA1.
[PMID 29259020] Genetic risk factors for late age-related macular degeneration in India.
[PMID 29311295] CFH and ARMS2 genetic risk determines progression to neovascular age-related macular degeneration after antioxidant and zinc supplementation.
[PMID 30154790] Novel Association of High C-Reactive Protein Levels and A69S at Risk Alleles in Wet Age-Related Macular Degeneration Women.
[PMID 31916060] Investigation of genetic base in the treatment of age-related macular degeneration.
[PMID 32138827] Distribution of risk alleles in patients with age-related macular degeneration.
[PMID 31988359] Association of Irregular Pigment Epithelial Detachment in Central Serous Chorioretinopathy with Genetic Variants Implicated in Age-related Macular Degeneration.
