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rs401681

From SNPedia

Orientationplus
Stabilizedplus
Geno Mag Summary
(C;C) 1.5 ~1.2x increased risk for several types of cancer
(C;T) 1.5 ~1.2x increased risk for several types of cancer
(T;T) normal
ReferenceGRCh38 38.1/141
Chromosome5
Position1321972
GeneCLPTM1L
is asnp
is mentioned by
dbSNPrs401681
ebirs401681
HLIrs401681
Exacrs401681
Varsomers401681
Maprs401681
PheGenIrs401681
hapmaprs401681
1000 genomesrs401681
hgdprs401681
ensemblrs401681
gopubmedrs401681
geneviewrs401681
scholarrs401681
googlers401681
pharmgkbrs401681
gwascentralrs401681
openSNPrs401681
23andMers401681
23andMe allrs401681
SNP Nexus

SNPshotrs401681
SNPdbers401681
MSV3drs401681
GWAS Ctlgrs401681
GMAF0.4435
Max Magnitude1.5
? (C;C) (C;T) (T;T) 28
CPMC Logo.png

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

rs401681 is a SNP in the CLPTM1-like CLPTM1 gene.

The following studies span several types of cancer, and over 30,000 cases and 45,000 controls.

deCODE press release reports rs401681 linked to basal cell carcinoma and many cancers for individuals with shorter telomeres, whereas those with long telomeres are at greater risk of melanoma. Neighboring rs2736098 also increases risk of cancer by affecting telomerase reverse transcriptase. The risk of these different cancers conferred by these two SNPs appears to be independent.

[PMID 19151717OA-icon.png] 23andMe blog rs2736098 and rs401681 linked to many cancers, including susceptibility to pancreatic cancer [PMID 20101243OA-icon.png]

However, a very large study (encompassing thousands of cases and controls) found no association between rs401681 and either (1) mean telomere length, or, (2) breast cancer, colorectal cancer, or melanoma.[PMID 20570912OA-icon.png]

[PMID 18978787OA-icon.png] lung cancer rs401681 P = 7.90 x 10(-9)


[PMID 19465454] The TERT-CLPTM1L lung cancer susceptibility variant associates with higher DNA adduct formation in the lung

[PMID 19578363OA-icon.png] New common variants affecting susceptibility to basal cell carcinoma

OMIM605462
DescBASAL CELL CARCINOMA, MULTIPLE
Variant
Relatedalso
OMIM612571
DescLUNG CANCER SUSCEPTIBILITY 3; LNCR3
Variant
Relatedalso
OMIM155600
DescMELANOMA, CUTANEOUS MALIGNANT; CMM
Variant
Relatedalso


GWAS snp
PMID [PMID 20101243OA-icon.png]
Trait Pancreatic cancer
Title A genome-wide association study identifies pancreatic cancer susceptibility loci on chromosomes 13q22.1, 1q32.1 and 5p15.33
Risk Allele T
P-val 7E-7
Odds Ratio 1.19 [1.11-1.27]



GWAS snp
PMID [PMID 20972438OA-icon.png]
Trait
Title A multi-stage genome-wide association study of bladder cancer identifies multiple susceptibility loci
Risk Allele C
P-val 5E-7
Odds Ratio 1.1100 [1.07-1.16]
GWAS snp
PMID [PMID 21160077OA-icon.png]
Trait
Title Genetic Correction of PSA Values Using Sequence Variants Associated with PSA Levels
Risk Allele C
P-val 1E-10
Odds Ratio 7.0000 [NR] % increase
OMIM260350
Desc
Variant
Relatedalso
OMIM613059
Desc
Variant
Relatedalso
GWAS snp
PMID [PMID 21983787OA-icon.png]
Trait
Title Genome-wide association study identifies three new melanoma susceptibility loci.
Risk Allele A
P-val 3E-8
Odds Ratio 1.2000 None


[PMID 22404340] Replication of results of genome-wide association studies on lung cancer susceptibility loci in a Korean population


[PMID 18978790OA-icon.png] Lung cancer susceptibility locus at 5p15.33.


[PMID 19423719OA-icon.png] Update in lung cancer 2008.


[PMID 19654303OA-icon.png] Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study.


[PMID 19774073OA-icon.png] Genetic epidemiology of glioblastoma multiforme: confirmatory and new findings from analyses of human leukocyte antigen alleles and motifs.


[PMID 19836008OA-icon.png] A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma.


[PMID 19916168OA-icon.png] Genome-wide association studies--a summary for the clinical gastroenterologist.


[PMID 20445798OA-icon.png] Chromosome 5p Region SNPs Are Associated with Risk of NSCLC among Women.


[PMID 20628624OA-icon.png] Evaluation of candidate stromal epithelial cross-talk genes identifies association between risk of serous ovarian cancer and TERT, a cancer susceptibility "hot-spot".


[PMID 20802237OA-icon.png] Genetic variations in TERT-CLPTM1L genes and risk of squamous cell carcinoma of the head and neck.


[PMID 21081471OA-icon.png] Genetic variations on chromosomes 5p15 and 15q25 and bladder cancer risk: findings from the Los Angeles-Shanghai bladder case-control study.


[PMID 21116649OA-icon.png] Genetic variants in telomere-maintaining genes and skin cancer risk.


[PMID 21332924OA-icon.png] Absence of association of a single-nucleotide polymorphism in the TERT-CLPTM1L locus with age-related phenotypes in a large multicohort study: the HALCyon programme.


[PMID 22370939] Multiple variants of TERT and CLPTM1L constitute risk factors for lung adenocarcinoma.


GET Evidence
rs401681
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.390625
summary



Prostate-Specific Antigen


[PMID 23393597OA-icon.png] Replication and Predictive Value of SNPs Associated with Melanoma and Pigmentation Traits in a Southern European Case-Control Study


[PMID 24039754OA-icon.png] The impact of polymorphic variations in the 5p15, 6p12, 6p21 and 15q25 Loci on the risk and prognosis of portuguese patients with non-small cell lung cancer


[PMID 24386361OA-icon.png] Genetic Variant rs401681 at 5p15.33 Modifies Susceptibility to Lung Cancer but Not Esophageal Squamous Cell Carcinoma


[PMID 24577890] Association between CLPTM1L-TERT rs401681 polymorphism and pancreatic cancer risk among Chinese Han population


[PMID 22893025] Association between TERT-CLPTM1L rs401681[C] allele and NMSC cancer risk: a meta-analysis including 45,184 subjects.


[PMID 23433592OA-icon.png] Genetic polymorphisms of TERT and CLPTM1L and risk of lung cancer--a case-control study in a Chinese population.


[PMID 23535824OA-icon.png] Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression.


[PMID 24761905] Genetic Variations in TERT-CLPTM1L Genes and Risk of Lung Cancer in a Chinese Population

GWAS snp
PMID [PMID 24163127OA-icon.png]
Trait Bladder cancer
Title Genome-wide association study identifies multiple loci associated with bladder cancer risk.
Risk Allele C
P-val 4E-11
Odds Ratio 1.12 [1.08-1.16]


[PMID 24861918] Genetic polymorphisms of TERT and CLPTM1L and risk of lung cancer: a case-control study in northeast Chinese male population


[PMID 24907075] Association between CLPTM1L polymorphisms (rs402710 and rs401681) and lung cancer susceptibility: evidence from 27 case-control studies


[PMID 25007268OA-icon.png] TERT-CLPTM1L Rs401681 C>T Polymorphism Was Associated with a Decreased Risk of Esophageal Cancer in a Chinese Population


[PMID 24615522] Quantitative assessment of common genetic variants on chromosome 5p15 and lung cancer risk


[PMID 25159867] Common variants modify the age of onset for basal cell carcinomas in Gorlin syndrome

GWAS snp
PMID [PMID 24403052OA-icon.png]
Trait Basal cell carcinoma
Title Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma.
Risk Allele C
P-val 2E-12
Odds Ratio 1.23 [1.16-1.30]


[PMID 25457634] Long telomere length and a TERT-CLPTM1 locus polymorphism association with melanoma risk


[PMID 25837821] Inherited genetic variants associated with occurrence of multiple primary melanoma


[PMID 26304507] Association of gastrointestinal gland cancer susceptibility loci with esophageal carcinoma among the Chinese Han population: a case-control study


[PMID 26590902] Fine-mapping of chromosome 5p15.33 based on a targeted deep sequencing and high density genotyping identifies novel lung cancer susceptibility loci