Have questions? Visit https://www.reddit.com/r/SNPedia

rs10490924

From SNPedia

age related macular degeneration
Orientationplus
Stabilizedplus
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
ReferenceGRCh38 38.1/141
Chromosome10
Position122454932
GeneARMS2
is asnp
is mentioned by
dbSNPrs10490924
ebirs10490924
HLIrs10490924
Exacrs10490924
Varsomers10490924
Maprs10490924
PheGenIrs10490924
hapmaprs10490924
1000 genomesrs10490924
hgdprs10490924
ensemblrs10490924
gopubmedrs10490924
geneviewrs10490924
scholarrs10490924
googlers10490924
pharmgkbrs10490924
gwascentralrs10490924
openSNPrs10490924
23andMers10490924
23andMe allrs10490924
SNP Nexus

SNPshotrs10490924
SNPdbers10490924
MSV3drs10490924
GWAS Ctlgrs10490924
GMAF0.2736
Max Magnitude3.5
? (G;G) (G;T) (T;T) 28
CPMC Logo.png

This SNP has been recognized by the Coriell Personalized Medicine Collaborative ICOB.
Additional information is available here

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 16642439OA-icon.png]

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 21122828OA-icon.png]

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 17884985OA-icon.png] A likely biological mechanism is that the A69S change in the LOC387715/ARMS2 protein affects its presumptive function in mitochondria.

[PMID 18164066OA-icon.png] 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 18682806OA-icon.png] An analysis of the joint effects of rs1061170, rs11200638 and rs10490924 on AMD

Neighborrs11200638
Distance6096


[PMID 19268887] ARMS2 (LOC387715) Variants in Japanese Patients with Exudative Age-related Macular Degeneration and Polypoidal Choroidal Vasculopathy.

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

[PMID 19255159OA-icon.png] Age-Related Macular Degeneration Associated ARMS2 is not a Mitochondrial but Cytosolic Protein.

OMIM611313
DescLOC387715 GENE
Variant
Relatedalso
OMIM610149
DescMACULAR DEGENERATION, AGE-RELATED, 7; ARMD7
Variant
Relatedalso
OMIM602194
DescHTRA SERINE PEPTIDASE 1; HTRA1
Variant
Relatedalso

[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 19796758OA-icon.png] 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 20157352OA-icon.png] Genetic analysis of typical wet-type age-related macular degeneration and polypoidal choroidal vasculopathy in Japanese population


[PMID 20182747OA-icon.png] Analysis of the indel at the ARMS2 3'UTR in age-related macular degeneration


[PMID 20381870OA-icon.png] Progression of Geographic Atrophy and Genotype in Age-Related Macular Degeneration

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 5E-119
Odds Ratio None None

[PMID 20664795OA-icon.png] 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 20861866OA-icon.png]
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 21067572OA-icon.png] Association Analysis of Nine Candidate Gene Polymorphisms in Indian Patients with Type 2 Diabetic Retinopathy

OMIM611313
Desc
Variant0001
Relatedalso


[PMID 21621535] No association between the T280M polymorphism of the CX3CR1 gene and exudative AMD

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 T
P-val 0
Odds Ratio 2.9400 [NR]


[PMID 21825189OA-icon.png] 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 22049084OA-icon.png] HTRA1 regulates angiogenesis through TGF-? family member GDF6


[PMID 22509112OA-icon.png] 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 22699975OA-icon.png] 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
Variation info
Gene ARMS2
CLNDBN Age-related macular degeneration 8 not provided
Reversed 0
HGVS NC_000010.10:g.124214448G>T
CLNSRC OMIM Allelic Variant
CLNACC RCV000001030.3, RCV000190307.1,



[PMID 16080115OA-icon.png] 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 17325155OA-icon.png] The LOC387715 polymorphism and age-related macular degeneration: replication in three case-control samples.

[PMID 17327825OA-icon.png] 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 17438519OA-icon.png] 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 17903296OA-icon.png] Genome-wide association with bone mass and geometry in the Framingham Heart Study.

[PMID 17903296OA-icon.png] Genome-wide association with bone mass and geometry in the Framingham Heart Study.

[PMID 17917691OA-icon.png] Genetic markers and biomarkers for age-related macular degeneration.

[PMID 18043728OA-icon.png] 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 18162041OA-icon.png] Neovascular age-related macular degeneration risk based on CFH, LOC387715/HTRA1, and smoking.

[PMID 18248681OA-icon.png] 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 18493315OA-icon.png] 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 18535016OA-icon.png] Rhesus monkeys and humans share common susceptibility genes for age-related macular disease.

[PMID 18601744OA-icon.png] Combining identity by descent and association in genetic case-control studies.

[PMID 18682812OA-icon.png] 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 19026761OA-icon.png] Molecular pathology of age-related macular degeneration.

[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 19065273OA-icon.png] 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 19202148OA-icon.png] Assessing susceptibility to age-related macular degeneration with proteomic and genomic biomarkers.

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

[PMID 19806217OA-icon.png] rs5888 variant of SCARB1 gene is a possible susceptibility factor for age-related macular degeneration.

[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 19958499OA-icon.png] A particle swarm based hybrid system for imbalanced medical data sampling.

[PMID 20140183OA-icon.png] Genetic and functional dissection of HTRA1 and LOC387715 in age-related macular degeneration.

[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.

[PMID 20339564OA-icon.png] Risk factors for age-related maculopathy.

[PMID 20346514OA-icon.png] C-reactive protein and CFH, ARMS2/HTRA1 gene variants are independently associated with risk of macular degeneration.

[PMID 20378180OA-icon.png] 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 20664794OA-icon.png] Age-related macular degeneration-associated variants at chromosome 10q26 do not significantly alter ARMS2 and HTRA1 transcript levels in the human retina.

[PMID 20689796OA-icon.png] Monozygotic twins with polypoidal choroidal vasuculopathy.

[PMID 20881291OA-icon.png] Persons with age-related maculopathy risk genotypes and clinically normal eyes have reduced mesopic vision.

[PMID 21203342OA-icon.png] 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 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 21896867] Associations of complement factor H (CFH) and age-related maculopathy susceptibility 2 (ARMS2) genotypes with subtypes of polypoidal choroidal vasculopathy.

[PMID 22293892OA-icon.png] 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 22705344OA-icon.png]
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 22694956OA-icon.png]
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


GET Evidence
ARMS2-A69S
aa_change Ala69Ser
aa_change_short A69S
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.207428
summary associated wuth polypoidal choroidal vasculopathy (PCV) and age-related macular degeneration (AMD)



[PMID 23337555OA-icon.png] 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 23302509OA-icon.png] 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 23644223OA-icon.png] Variants at chromosome 10q26 locus and the expression of HTRA1 in the retina

GWAS snp
PMID [PMID 23455636OA-icon.png]
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 23938121OA-icon.png] Associations of Candidate Genes to Age-Related Macular Degeneration Among Racial/Ethnic Groups in the Multi-Ethnic Study of Atherosclerosis

GWAS snp
PMID [PMID 23577725OA-icon.png]
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 23204795OA-icon.png] 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 24067115OA-icon.png] 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 24974817OA-icon.png] 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.