Rs2165241

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Orientationplus
Geno Mag Summary
(C;C) 0 normal
(C;T) 2.2 4.4x increased risk of exfoliation glaucoma
(T;T) 2.3 >10x increased risk of exfoliation glaucoma
ReferenceGRCh38 38.1/141
Chromosome15
Position73929861
GeneLOXL1, RNASEH2B
is asnp
is mentioned by
dbSNPrs2165241
Exacrs2165241
PheGenIrs2165241
nextbiors2165241
hapmaprs2165241
1000 genomesrs2165241
hgdprs2165241
ensemblrs2165241
gopubmedrs2165241
geneviewrs2165241
scholarrs2165241
googlers2165241
pharmgkbrs2165241
gwascentralrs2165241
openSNPrs2165241
23andMers2165241
23andMe allrs2165241
SNP Nexus

SNPshotrs2165241
SNPdbers2165241
MSV3drs2165241
GMAF0.3136
? (C;C) (C;T) (T;T) 28
This SNP, located in an intron of the LOXL1 gene, was initially reported to be associated with exfoliation glaucoma. However, it was shown in the same study to no longer be significant once two other SNPs, which cause actual changes in the LOXL1 protein, were identified.

More specifically, the risk allele rs2165241(T) was found to be associated with glaucoma only because it effectively predicted (with 90% probability) the actual high-risk haplotype consisting of rs1048661(G) and rs3825942(C), as oriented with respect to their entries in dbSNP. [PMID 17690259]

However, a meta-analysis published in 2010 concluded that it's likely that SNPs rs1048661 and rs2165241 are not directly implicated in the pathogenesis of glaucoma; only the nearby rs3825942 seemed to be the disease-associated SNP.[PMID 20142848OA-icon.png]

[PMID 18287813] rs2165241 was significantly associated with XFG and XFS (p=4.13x10e-9 for an additive model, heterozygote odds ratio = 4.42 (CI: 2.3-8.5), homozygote odds ratio = 34.19 (CI: 4.48-261), with the rs2165241 (T) allele being the risk allele, found in 83.1% of cases versus 52.4% in controls, based on a study of 62 Caucasian patients. Significant association was also found for rs3825942 (p=1.89x10e-6).

[PMID 18385788OA-icon.png] rs1048661 (G), rs3825942 (G), and rs2165241 (T) are highly associated with XFS and XFG in American and European populations. The GGT haplotype constitutes a major risk haplotype for exfoliation.

[PMID 18385063] Confirmed as risk for pseudoexfoliation (PEX) and pseudoexfoliation glaucoma (PEXG) in populations of German and Italian descent.

Rs2165241
PubMed [PMID 17690259]
Affy Probeset SNP_A-8476188
Affy Orientation reverse
On GW 5.0 0
Alleles A/B A/G
Ancestral C
Population EU(Scand.)
Allele T
Case Freq.
Control Freq.
Odds Ratio Het
Odds Ratio Hom
Odds Ratio All 1.96
Disease Glaucoma (GC)


rs2165241 increases susceptibility to Exfoliation glaucoma 3.62 times for carriers of the T allele [PMID 17690259]

rs2165241 increases susceptibility to Glaucoma 1.96 times for carriers of the T allele [PMID 17690259]

rs2165241 increases susceptibility to Primary open-angle glaucoma 1.04 times for carriers of the T allele [PMID 17690259]

OMIM153456
DescLYSYL OXIDASE-LIKE 1; LOXL1
Variant
Relatedalso
[PMID 19936304OA-icon.png] Evaluation of LOXL1 polymorphisms in exfoliation syndrome in a Chinese population

[PMID 20051886] Lack of Association of Polymorphisms in Elastin With Pseudoexfoliation Syndrome and Glaucoma

OMIM153456
Desc
Variant0003
Relatedalso
OMIM177650
Desc
Variant
Relatedalso
[PMID 21510775OA-icon.png] Lack of association between LOXL1 gene polymorphisms and primary open angle glaucoma in the Saudi Arabian population


[PMID 21970694] Prevalence of high-risk alleles in the LOXL1 gene and its association with pseudoexfoliation syndrome and exfoliation glaucoma in a Latin American population


[PMID 22194657OA-icon.png] Analysis of LOXL1 gene variants in Japanese patients with branch retinal vein occlusion


[PMID 22765198] TT polymorphism in rs2165241 and rs1048661 region in lysyl oxidase like-1 gene may have a role in stress urinary incontinence physiopathology


[PMID 18223248] The LOXL1 gene variations are not associated with primary open-angle and primary angle-closure glaucomas.


[PMID 18254956OA-icon.png] DNA sequence variants in the LOXL1 gene are associated with pseudoexfoliation glaucoma in a U.S. clinic-based population with broad ethnic diversity.


[PMID 18334928OA-icon.png] Analysis of LOXL1 polymorphisms in a United States population with pseudoexfoliation glaucoma.


[PMID 18334947OA-icon.png] Association of non-synonymous single nucleotide polymorphisms in the LOXL1 gene with pseudoexfoliation syndrome in India.


[PMID 18421074OA-icon.png] Lack of association between LOXL1 variants and primary open-angle glaucoma in three different populations.


[PMID 18450598] Association of LOXL1 gene polymorphisms with pseudoexfoliation in the Japanese.


[PMID 18618003OA-icon.png] Exfoliation syndrome and exfoliation glaucoma-associated LOXL1 variations are not involved in pigment dispersion syndrome and pigmentary glaucoma.


[PMID 18648524OA-icon.png] Evaluation of LOXL1 polymorphisms in eyes with exfoliation glaucoma in Japanese.


[PMID 18958304OA-icon.png] LOXL1 variants in elderly Japanese patients with exfoliation syndrome/glaucoma, primary open-angle glaucoma, normal tension glaucoma, and cataract.


[PMID 19098994OA-icon.png] Evaluation of LOXL1 polymorphisms in primary open-angle glaucoma in southern and northern Chinese.


[PMID 19112534OA-icon.png] Lack of association of polymorphisms in homocysteine metabolism genes with pseudoexfoliation syndrome and glaucoma.


[PMID 19343041] Association of LOXL1 gene with Finnish exfoliation syndrome patients.


[PMID 19503743OA-icon.png] Association of LOXL1 polymorphisms with pseudoexfoliation in the Chinese.


[PMID 19801603OA-icon.png] Rapid inexpensive genome-wide association using pooled whole blood.


[PMID 20431720OA-icon.png] Major LOXL1 risk allele is reversed in exfoliation glaucoma in a black South African population.


[PMID 20661439OA-icon.png] Ancestry-shift refinement mapping of the C6orf97-ESR1 breast cancer susceptibility locus.


[PMID 21150032OA-icon.png] Complex genetic mechanisms in glaucoma: an overview.


[PMID 21559813] No association of LOXL1 gene polymorphisms with Alzheimer's disease.


[PMID 23441117OA-icon.png] Evaluation of lysyl oxidase-like 1 gene polymorphisms in pseudoexfoliation syndrome in a Korean population


[PMID 23869164OA-icon.png] Association of lysyl oxidase-like 1 gene common sequence variants in Greek patients with pseudoexfoliation syndrome and pseudoexfoliation glaucoma


[PMID 24068861OA-icon.png] The T allele of lysyl oxidase-like 1 rs41435250 is a novel risk factor for pseudoexfoliation syndrome and pseudoexfoliation glaucoma independently and through intragenic epistatic interaction


[PMID 24603551OA-icon.png] Association between Polymorphisms in Lysyl Oxidase-Like 1 and Susceptibility to Pseudoexfoliation Syndrome and Pseudoexfoliation Glaucoma


[PMID 24892565] Association of lysyl oxidase-like 1 gene polymorphisms in pseudoexfoliation syndrome and pseudoexfoliation glaucoma in a Spanish population


[PMID 24893574] Genetic polymorphism related to exfoliative glaucoma is also associated with primary open-angle glaucoma risk


[PMID 24967207OA-icon.png] Lack of association between lysyl oxidase-like 1 polymorphisms and primary open angle glaucoma: a meta-analysis


[PMID 25304275] LOXL1 Gene Polymorphism With Exfoliation Syndrome/Exfoliation Glaucoma: A Meta-Analysis