rs10948059

This is a regulatory region variant variant in the GNMT gene.

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GWAS Catalog Trait Associations (6)

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

total lipids in small HDL measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele T
OR 0.03
p 1.0e-43
N 450,015
Large GWAS
multi-ancestry

cholesterol in small HDL measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele T
OR 0.02
p 6.0e-31
N 450,015
Large GWAS
multi-ancestry

concentration of small HDL particles measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele T
OR 0.02
p 6.0e-30
N 450,015
Large GWAS
multi-ancestry

free cholesterol in small HDL measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele T
OR 0.02
p 8.0e-21
N 450,015
Large GWAS
multi-ancestry

choline measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele T
OR 0.01
p 5.0e-13
N 450,015
Large GWAS
multi-ancestry

high density lipoprotein cholesterol measurement

Hoffmann TJ et al. “A large electronic-health-record-based genome-wide study of serum lipids.” Nature Genetics 50(3):401-413 (2018)
Allele C
OR —
β 0.023
p 1.0e-9
N 94,674
Large GWAS
multi-ancestry
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ClinVar annotation

Benign★☆☆☆
1 submitter
View on ClinVar →
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Research that mentions this SNP (1)

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Evaluation of 64 candidate single nucleotide polymorphisms as risk factors for neural tube defects in a large Irish study population
AssociationN=2,079Tonia C. Carter et al.(2011)· American Journal of Medical Genetics Part A

This case-control and family-based study evaluated 64 SNPs in 34 genes for associations with spina bifida in 558 Irish case-families and 994 controls. Spina bifida was significantly associated with LEPR rs1805134 (GRR: 1.5, P = 0.0264) and COMT rs737865 (GRR: 1.4, P = 0.0206), with additional confirmations of previous findings in MTHFR 677C>T and other genes, suggesting roles for leptin signaling and methylation pathways in neural tube defect pathogenesis.

Traits studied:Neural tube defectsSpina bifida
PubMedDOIMetascience Observatory

About GNMT

The protein encoded by this gene is an enzyme that catalyzes the conversion of S-adenosyl-L-methionine (along with glycine) to S-adenosyl-L-homocysteine and sarcosine. This protein is found in the cytoplasm and acts as a homotetramer. Defects in this gene are a cause of GNMT deficiency (hypermethioninemia). Alternative splicing results in multiple transcript variants. Naturally occurring readthrough transcription occurs between the upstream CNPY3 (canopy FGF signaling regulator 3) gene and this gene and is represented with GeneID:107080644. [provided by RefSeq, Jan 2016]

View all GNMT variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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