rs1625895

This is a intron variant variant in the TP53 gene.

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GWAS Catalog Trait Associations (6)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

sex hormone-binding globulin measurement

Sinnott-Armstrong N et al. “Genetics of 35 blood and urine biomarkers in the UK Biobank.” Nature Genetics 53(2):185-194 (2021)
Allele C
OR 0.11
p 4.0e-195
N 322,484
Major Consortium StudyLarge GWAS
multi-ancestry
Coviello AD et al. “A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation.” Plos Genetics 8(7):e1002805 (2012)
Allele C
OR 0.12
p 2.0e-21
N 21,791
Meta-analysisLarge GWAS
European

body height

Yengo L et al. “A saturated map of common genetic variants associated with human height.” Nature 610(7933):704-712 (2022)
Allele T
OR 0.02
p 5.0e-75
N 5,314,291
Large GWAS
European, Hispanic or Latin American, East Asian, African unspecified, South Asian

testosterone measurement

Sinnott-Armstrong N et al. “Genetics of 35 blood and urine biomarkers in the UK Biobank.” Nature Genetics 53(2):185-194 (2021)
Allele C
OR 0.05
p 6.0e-36
N 322,594
Major Consortium StudyLarge GWAS
multi-ancestry

HbA1c measurement

Sinnott-Armstrong N et al. “Genetics of 35 blood and urine biomarkers in the UK Biobank.” Nature Genetics 53(2):185-194 (2021)
Allele C
OR 0.03
p 3.0e-12
N 338,919
Major Consortium StudyLarge GWAS
multi-ancestry

total cholesterol measurement

Sinnott-Armstrong N et al. “Genetics of 35 blood and urine biomarkers in the UK Biobank.” Nature Genetics 53(2):185-194 (2021)
Allele C
OR 0.02
p 7.0e-10
N 355,858
Major Consortium StudyLarge GWAS
multi-ancestry

aspartate aminotransferase measurement

Sinnott-Armstrong N et al. “Genetics of 35 blood and urine biomarkers in the UK Biobank.” Nature Genetics 53(2):185-194 (2021)
Allele C
OR 0.02
p 5.0e-9
N 354,541
Major Consortium StudyLarge GWAS
multi-ancestry
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ClinVar annotation

Benign★★★☆
5 submitters1 publication

Hereditary cancer-predisposing syndrome; Li-Fraumeni syndrome 1 (LFS); not specified

View on ClinVar →
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Research that mentions this SNP (4)

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Associations of polymorphisms in the genes of FGFR2, FGF1, and RBFOX2 with breast cancer risk by estrogen/progesterone receptor status
AssociationN=2,416Yu‐Ling Cen et al.(2013)· Molecular Carcinogenesis

A hospital-based case-control study in rural and urban India (1,204 cases; 1,212 controls) examined genetic and lifestyle risk factors for breast cancer. Four SNPs in FGFR2 (rs1219648, rs2420946, rs2981575, rs2981582) showed positive associations with breast cancer (ORs 1.32-1.47). Additional SNPs in obesity and metabolic genes (rs374748 in FBN2, rs2922763 in HNF4G, rs2116830 in KCNMA1, rs11121832 in MTHFR, rs16886165 in MAP3K1, rs11594610 in TCF7L2, rs2274459 in MLN) were associated with increased breast cancer risk. Waist-to-hip ratio ≥0.95 showed strong association (OR 3.78; 95% CI 2.92-4.89), and women living first 20 years in rural areas showed protective effect (OR 0.77).

Traits studied:Breast cancerBreast cancer riskER+/PR+ breast cancerER/PR negative breast cancerTriple negative breast cancer
PubMedDOIMetascience Observatory
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Association between TP53 gene ARG72PRO polymorphism and chromosome aberrations in human cancers
AssociationN=914Nicolay V. Litviakov et al.(2010)· Molecular Carcinogenesis

Hospital-based case-control study of 453 breast cancer patients and 461 controls in a Spanish population examining TP53 polymorphisms. The Arg72Pro (Ex4 ± 119G/C, rs1042522) TP53 polymorphism was significantly associated with increased breast cancer risk (OR=1.34, 95% CI 1.03-1.75, p=0.029). The two-locus interaction between this TP53 variant and -710 C/T VEGFR1 showed even stronger association (OR=1.44, 95% CI 1.10-1.88, p=0.0083). Pro/Pro carriers at rs1042522 also showed poor disease-free survival (p=0.013).

Traits studied:Breast cancer
PubMedDOIMetascience Observatory
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Construction of a high resolution linkage disequilibrium map to evaluate common genetic variation inTP53and neural tube defect risk in an Irish population
AssociationN=2,561Faith Pangilinan et al.(2008)· American Journal of Medical Genetics Part A

This case-control and family-based association study evaluated 21 TP53 variants and 1 MDM2 variant (rs2279744) in 549 Irish NTD cases, 532 mothers, 481 fathers, and 999 controls. Three TP53 noncoding variants showed associations with neural tube defect risk: rs1625895 (intron 6, GG genotype, OR=1.37, p=0.02), the intron 1 VNTR (135/135 genotype, maternal effect, OR=1.86, p=0.01), and rs1614984 (maternal TT genotype, RR=0.58, p=0.02). However, these associations did not remain significant after multiple testing correction. The functional R72P variant (rs1042522) showed no association with NTD risk.

Traits studied:NTDNeural tube defects
PubMedDOIMetascience Observatory
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Common genetic variation in TP53 and its flanking genes, WDR79 and ATP1B2, and susceptibility to breast cancer
AssociationN=8,046Montserrat Garcia‐Closas et al.(2007)· International Journal of Cancer

Case-control study of 731 Norwegian and 1,995 Polish breast cancer cases with 1,124 and 2,296 controls respectively, investigating common genetic variation in TP53 and flanking genes WDR79 and ATP1B2. No significant overall TP53 SNP associations with breast cancer risk were found, but WDR79 rs2287499 (R68G) showed increased risk (OR=1.60 for GG vs CC, p-trend=0.01). Notably, rs2287499 and rs17887200 (TP53) were associated specifically with ER-negative breast cancers (OR=1.42 and 1.48 respectively, p-trend<0.01), but not ER-positive tumors.

Traits studied:Breast cancerER-negative breast cancerER-positive breast cancer
PubMedDOIMetascience Observatory

About TP53

This gene encodes a tumor suppressor protein containing transcriptional activation, DNA binding, and oligomerization domains. The encoded protein responds to diverse cellular stresses to regulate expression of target genes, thereby inducing cell cycle arrest, apoptosis, senescence, DNA repair, or changes in metabolism. Mutations in this gene are associated with a variety of human cancers, including hereditary cancers such as Li-Fraumeni syndrome. Alternative splicing of this gene and the use of alternate promoters result in multiple transcript variants and isoforms. Additional isoforms have also been shown to result from the use of alternate translation initiation codons from identical transcript variants (PMIDs: 12032546, 20937277). [provided by RefSeq, Dec 2016]

View all TP53 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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