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rs6025

From SNPedia

Orientationminus
Stabilizedminus
Geno Mag Summary
(A;A) 7 11.4x higher risk of thrombosis
(A;G) 4.1 3.5-4.4x risk of thrombosis
(G;G) 0 normal/common risk of thrombosis
ReferenceGRCh38 38.1/141
Chromosome1
Position169549811
GeneF5
is asnp
is mentioned by
dbSNPrs6025
dbSNP (old)rs6025
ClinGenrs6025
ebirs6025
HLIrs6025
Exacrs6025
Gnomadrs6025
Varsomers6025
Maprs6025
PheGenIrs6025
Biobankrs6025
1000 genomesrs6025
hgdprs6025
ensemblrs6025
gopubmedrs6025
geneviewrs6025
scholarrs6025
googlers6025
pharmgkbrs6025
gwascentralrs6025
openSNPrs6025
23andMers6025
23andMe allrs6025
SNP Nexus

SNPshotrs6025
SNPdbers6025
MSV3drs6025
GWAS Ctlgrs6025
GMAF0.005969
Max Magnitude7
? (A;A) (A;G) (G;G) 28
rs6025 represents a SNP in the Factor V F5 gene, encoding a change in the protein from an arginine at position 506 to a glutamine. The resulting rs6025(A) allele encodes a mutation known as the Leiden mutation, R506Q.

See the OMIM entry

In a 2017 study using UK Biobank, based on 3290 VTE cases and 116 868 controls, the odds ratio for a polymorphism involving the minor risk allele was 3.5. They also found higher odds for venous thromboembolism in overweight individuals (+1.57 for every 1 SD higher BMI). [PMID 28373160OA-icon.png]

In a 2013 meta-analysis of 31 databases, the analysis of Factor V rs6025 variants was based on 9,081 cases and 17,513 controls. The polymorphic variant risk for Venous Thromboembolism was overall OR: 4.38. The risk was greater in younger subjects (<45 years old, OR: 5.43; ≥45 years old, OR: 3.71). Slightly higher risk appeared in men (OR: 5.06) and in women taking oral contraceptives (OR: 6.10). The AG polymorphic variant was associated with recurrent thrombosis (recurrent VTE event, OR: 5.81; no recurrence reported, OR: 3.95). The higher risks were for venous thrombosis without evidence of pulmonary embolism (OR: 4.49) or a cerebral venous sinus thrombosis (OR: 4.14). The AA homozygous variant was rarer, and its risk was significantly higher at 11.45 but was based on fewer individuals (116 subjects among cases and 24 controls). Independent risk was seen in variants of the PT20210A or Factor 2 SNP at i3002432 (also known as rs1799963 ) [PMID 23900608OA-icon.png]

Other studies have come to similar conclusions. In a 2004 study of over 9,000 Caucasian adults in the Danish population, rs6025(A;G) and rs6025(A;A) genotypes had 2.7x and 18x higher risk for venous thromboembolism, respectively, than rs6025(G;G) individuals. The lowest absolute 10-year risks for venous thromboembolism for (A;G) and (A;A) genotypes were 0.7% (CI: 0.5% to 1.0%) and 3% (CI: 1% to 8%) for nonsmokers younger than 40 years of age with a body mass index below 25 kg/m2, and the corresponding highest risks were 10% (CI: 7% to 14%) and 51% (CI: 13% to 100%) for overweight smokers over 60.[PMID 14996674]

In a study done in the year 2000 on 119 women, it was found that women who are pregnant and rs6025(A) carriers could be at risk for obstetric complications, including pre-eclampsia or venous thromboembolism, especially if they were also prothrombin rs1799963 heterozygotes and/or have a family history of thrombosis. They concluded that if you assume an overall risk rate of 1 in 1500 pregnancies, the risk of thrombosis among rs6025(A) carriers by itself would be 0.2 percent (1 in 500); among carriers of the prothrombin rs1799963(A) by itself, would be 0.5 percent (1 in 200); and among carriers of both variant SNPs, 4.6 percent (about 1 in 20).[PMID 10666427]

A 2006 review article of 10 previous studies found that women who are rs6025(A) carriers also are at increased risk for venous thromboembolism and perhaps ischemic stroke when they take combined oral contraceptives (i.e. "the pill"). A 2006 literature meta-analysis from a total of 10 studies concluded that "good" evidence existed for a greater risk of venous thromboembolism (risk ratios of 1.3-25.1) and cerebral vein or cerebral sinus thrombosis when comparing heterozygotes taking such contraceptives to heterozygotes who did not.[PMID 16413847]

Additionally, a 2004 meta-analysis involving 18,000 cases and 58,000 controls found an increased risk for ischemic stroke for rs6025(A) carriers. The odds ratio based on a study of ~4,500 patients was 1.33, CI: 1.12-1.58.[PMID 15534175]

Although preliminary, a 2010 study found that women taking tamoxifen as part of their treatment for early-stage breast cancer, those who had a thromboembolic event were nearly five times more likely to have a rs6025(A) allele compared to those who did not have a TE. The authors suggest that postmenopausal women should be evaluated for the rs6025(A) SNP before being given a prescription for tamoxifen if the result would affect the decision.[PMID 20554945OA-icon.png]

A related editorial pointed out that tamoxifen on its own is known to increase the risk of thromboembolic events 2-4 fold.[PMID 20554943]

According to a 1999 Blood journal article, coexistence of the R2 polymorphism rs1800595 with factor V Leiden increased the risk for venous thrombosis approximately to a 16-fold increased risk. The average age of the first thrombotic event is six years younger in individuals who are heterozygous for both factor V Leiden and the R2 polymorphism than in those with factor V Leiden alone. [1]

Another 1999 study concluded that heterozygotes for rs6025 and rs1799963 have an increased risk of recurrent deep venous thrombosis after a first episode and are therefore candidates for lifelong anticoagulation treatment. [PMID 10477778]


Venter snp
Source plos
Gene F5
allele C
frequency 0.992
sift TOLERATED
HuRef 1103675256965
Disease Association Defects in F5 are the cause of resistance to activated protein C (APCR) (MIM:188055). APCR is a form of thrombophilia. The APCR mutation is found in about 5% of the population which suggest that a slight thrombotic tendency may confer some advantage in fetal implantation.



[PMID 19415820OA-icon.png] The effect of nine common polymorphisms in coagulation factor genes (F2, F5, F7, F12 and F13 ) on the effectiveness of statins: the GenHAT study


[PMID 19786296] Platelet glycoprotein GP VI 13254C allele is an independent risk factor of premature myocardial infarction



[PMID 21291465] The association of genetic polymorphisms with cerebral palsy: a meta-analysis

OMIM612309
Desc
Variant0001
Relatedalso
[PMID 21564075] Resistance to activated protein C is a risk factor for pregnancy-related venous thrombosis in the absence of the F5 rs6025 (factor V Leiden) polymorphism


[PMID 21332313] Sequence variations in the FII, FV, F13A1, FGB and PAI-1 genes are associated with differences in myocardial perfusion


[PMID 21659962OA-icon.png] Replication of genetic associations in the inflammation, complement, and coagulation pathways with intraventricular hemorrhage in LBW preterm neonates


[PMID 22198364] The association of inherited thrombophilia and intrauterine fetal death: a case-control study


[PMID 21913742] Genetic predictors of response to photodynamictherapy


[PMID 21955043OA-icon.png] Validation of single nucleotide polymorphisms associated with acute rejection in kidney transplant recipients using a large multi-center cohort


[PMID 22421107] The G534E-polymorphism of the gene encoding the Factor VII-activating protease is a risk factor for venous thrombosis and recurrent events


[PMID 22707612OA-icon.png] Genetic Risk Factors for Thrombosis in Systemic Lupus Erythematosus


ClinVar
Risk Rs6025(G;G)
Alt Rs6025(G;G)
Reference Rs6025(A;A)
Significance Other
Disease Thrombophilia due to factor V Leiden Ischemic stroke Budd-Chiari syndrome Recurrent abortion Factor V deficiency Thrombophilia due to activated protein C resistance hormonal contraceptives for systemic use response - Toxicity/ADR
Variation info
Gene F5
CLNDBN Thrombophilia due to factor V Leiden Ischemic stroke, susceptibility to Budd-Chiari syndrome, susceptibility to Recurrent abortion Factor V deficiency Thrombophilia due to activated protein C resistance hormonal contraceptives for systemic use response - Toxicity/ADR
Reversed 1
HGVS NC_000001.10:g.169519049T\x3d; NC_000001.10:g.169519049T>C
CLNSRC OMIM Allelic Variant UniProtKB (protein) PharmGKB Clinical Annotation
CLNACC RCV000000674.2, RCV000000675.3, RCV000000676.2, RCV000023935.2, RCV000205002.4, RCV000454249.1, RCV000211384.1,



[PMID 16846490OA-icon.png] Lemierre's syndrome and genetic polymorphisms: a case report.

[PMID 17048007OA-icon.png] Association of warfarin dose with genes involved in its action and metabolism.

[PMID 17107626OA-icon.png] Comparison of PrASE and Pyrosequencing for SNP Genotyping.

[PMID 17677000OA-icon.png] Combined effects of thrombosis pathway gene variants predict cardiovascular events.

[PMID 18513389OA-icon.png] New application of intelligent agents in sporadic amyotrophic lateral sclerosis identifies unexpected specific genetic background.

[PMID 18752569] Factor V Leiden is associated with pre-eclampsia but not with fetal growth restriction: a genetic association study and meta-analysis.

[PMID 18936436OA-icon.png] Prevalence in the United States of selected candidate gene variants: Third National Health and Nutrition Examination Survey, 1991-1994.

[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 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 19536175OA-icon.png] Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study.

[PMID 19538716OA-icon.png] Thrombotic genetic risk factors and warfarin pharmacogenetic variants in Sao Miguel's healthy population (Azores).

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

[PMID 19591822] Prevalence of genetic thrombophilic polymorphisms in the Sri Lankan population--implications for association study design and clinical genetic testing services.

[PMID 20031567OA-icon.png] An evaluation of candidate genes of inflammation and thrombosis in relation to the risk of venous thromboembolism: The Women's Genome Health Study.

[PMID 20352152] Association of common genetic variations and idiopathic venous thromboembolism. Results from EDITh, a hospital-based case-control study.

[PMID 21422408] Clotting factor gene polymorphisms and colorectal cancer risk.

[PMID 22388798OA-icon.png] Gene panels to help identify subgroups at high and low risk of coronary heart disease among those randomized to antihypertensive treatment: the GenHAT study.

[PMID 22540831] Candidate gene study of genetic thrombophilic polymorphisms in pre-eclampsia and recurrent pregnancy loss in Sinhalese women.

GWAS snp
PMID [PMID 22672568OA-icon.png]
Trait
Title A genome-wide association study of venous thromboembolism identifies risk variants in chromosomes 1q24.2 and 9q.
Risk Allele T
P-val 2E-22
Odds Ratio 3.5700 None


[PMID 23015030] Differential haemostatic risk factors for pregnancy related deep vein thrombosis and pulmonary embolism. A population-based case-control study


[PMID 23018527] Necessity and risks of arterial blood sampling in healthy volunteer studies


GET Evidence
F5-Q534R
aa_change Gln534Arg
aa_change_short Q534R
impact pharmacogenetic
qualified_impact Insufficiently evaluated pharmacogenetic
overall_frequency 0.978063
summary



[PMID 23132613] Genetic association studies in pre-eclampsia: systematic meta-analyses and field synopsis


[PMID 23150947] Single nucleotide polymorphisms and the risk of venous thrombosis: results from a Danish case-cohort study


[PMID 23274712OA-icon.png] Genetic polymorphisms and the risk of myocardial infarction in patients under 45 years of age.


[PMID 23533563OA-icon.png] Novel risk factors for premature peripheral arterial occlusive disease in non-diabetic patients: a case-control study.


[PMID 24908450OA-icon.png] A genetic association study of D-dimer levels with 50K SNPs from a candidate gene chip in four ethnic groups


[PMID 25028703] Maternal Genotype and Severe Preeclampsia: A HuGE Review


[PMID 25119470OA-icon.png] Single Nucleotide Polymorphisms Other than Factor V Leiden Are Associated with Coagulopathy and Osteonecrosis of the Femoral Head in Chinese Patients


[PMID 25210051] Genetic Variations Associated with Recurrent Venous Thrombosis


[PMID 24816905OA-icon.png] Single nucleotide variants in the protein C pathway and mortality in dialysis patients

Placental Abruption

Oral Contraceptives, HRT and Risk of VTE