rs897453

This is a protein-altering variant in the PEMT gene.

▶

GWAS Catalog Trait Associations (1)

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

BMI-adjusted waist-hip ratio

Justice AE et al. “Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution.” Nature Genetics 51(3):452-469 (2019)
Allele C
OR 0.03
p 1.0e-10
N 288,492
Large GWAS
European
Christakoudi S et al. “GWAS of allometric body-shape indices in UK Biobank identifies loci suggesting associations with morphogenesis, organogenesis, adrenal cell renewal and cancer.” Scientific Reports 11(1):10688 (2021)
Allele C
OR 0.02
p 1.0e-9
N 219,872
Major Consortium StudyLarge GWAS
European
▶

Research that mentions this SNP (2)

▶
A distinct and replicable variant of the squamous cell carcinoma gene inositol polyphosphate‐5‐phosphatase modifies the susceptibility of arsenic‐associated skin lesions in Bangladesh
AssociationN=4,222Wei Jie Seow et al.(2015)· Cancer

A case-control study of 540 cases and 400 controls in Bangladesh examined 25 candidate SNPs in inflammation, one-carbon metabolism, and skin cancer genes for associations with arsenic-induced skin lesions. Six SNPs showed significant gene-environment interactions with water arsenic exposure (PEMT rs2278952 P=0.004, rs897453 P=0.05; DHFR rs1650697 P=0.02; IL10 rs3024496 P=0.04; INPP5A rs1133400 P=0.03; XPC rs2228000 P=0.01), and the INPP5A rs1133400 interaction was successfully replicated in an independent population of 488 cases and 2,794 controls (P=0.03).

Traits studied:Arsenic-induced skin lesionsBasal cell carcinoma (BCC)Bowen's diseaseHyperkeratosisKeratosisMelanosisSquamous cell carcinoma (SCC)
PubMedDOIMetascience Observatory
▶
Folate and vitamin B12-related genes and risk for omphalocele
AssociationN=930James L. Mills et al.(2012)· Human Genetics

Case-control study of 169 omphalocele cases and 761 controls examining variants in folate, vitamin B12, and homocysteine metabolism genes. Variants in transcobalamin receptor (TCblR) rs2232775 (Q8R) and methylenetetrahydrofolate reductase (MTHFR) rs1801131 (1298A>C) were significantly associated with omphalocele (TCblR OR=3.20, p=0.0017; MTHFR OR=2.04, p=0.028). Additional race-ethnicity-specific associations were found with TCN2, BHMT rs3733890, and FOLH1 variants, suggesting disruption of methylation reactions as a potential risk factor.

Traits studied:Omphalocele
PubMedDOIMetascience Observatory

About PEMT

Phosphatidylcholine (PC) is the most abundant mammalian phospholipid. This gene encodes an enzyme which converts phosphatidylethanolamine to phosphatidylcholine by sequential methylation in the liver. Another distinct synthetic pathway in nucleated cells converts intracellular choline to phosphatidylcholine by a three-step process. The protein isoforms encoded by this gene localize to the endoplasmic reticulum and mitochondria-associated membranes. Alternate splicing of this gene results in multiple transcript variants encoding different isoforms. [provided by RefSeq, May 2012]

View all PEMT variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

Community Wiki

No community notes yet for this variant. Sign in to start one.

Comments

Sign in to join the discussion.

Loading comments…