rs4986970

This is a variant in the LCAT gene that changes a serine to an alanine.

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GWAS Catalog Trait Associations (81)

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

total lipids in large LDL

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 0.11
p 4.0e-83
N 450,015
Large GWAS
multi-ancestry

cholesteryl esters in 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 0.09
p 3.0e-77
N 450,015
Large GWAS
multi-ancestry

HDL cholesterol change 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 0.09
p 7.0e-77
N 450,015
Large GWAS
multi-ancestry

free cholesterol to total lipids in medium HDL percentage

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 0.09
p 2.0e-73
N 450,015
Large GWAS
multi-ancestry
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele T
OR 0.10
p 3.0e-16
N 88,329
Large GWAS
European

cholesteryl esters in large 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 0.08
p 4.0e-69
N 450,015
Large GWAS
multi-ancestry

concentration of large 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 0.08
p 7.0e-69
N 450,015
Large GWAS
multi-ancestry

cholesteryl esters to total lipids in large LDL percentage

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 0.10
p 2.0e-68
N 450,015
Large GWAS
multi-ancestry
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele T
OR 0.12
p 1.0e-21
N 88,329
Large GWAS
European

cholesterol in large 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 0.08
p 1.0e-66
N 450,015
Large GWAS
multi-ancestry
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele T
OR 0.08
p 2.0e-12
N 88,329
Large GWAS
European

free cholesterol in 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 0.08
p 1.0e-65
N 450,015
Large GWAS
multi-ancestry
Davyson E et al. “Metabolomic Investigation of Major Depressive Disorder Identifies a Potentially Causal Association With Polyunsaturated Fatty Acids.” Biological Psychiatry 94(8):630-639 (2023)
Allele T
OR 0.08
p 1.0e-12
N 88,329
Large GWAS
European
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ClinVar annotation

Uncertain Significance★☆☆☆
1 submitter4 publications
View on ClinVar →
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Research that mentions this SNP (1)

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Strategies and issues in the detection of pathway enrichment in genome-wide association studies
MethodsN=28,191Mun-Gwan Hong et al.(2009)· Human Genetics

This methodological study develops ProxyGeneLD software for converting genome-wide SNP association data to pathway-enriched gene sets and validates it on multiple large GWAS datasets. The authors demonstrate successful replication of pathway enrichment for plasma HDL levels (with CETP and ABCA1 in lipid metabolism pathways) across independent samples and identify positional gene clustering as a major source of spurious enrichment in pathway analyses of GWAS data.

Traits studied:Crohn's diseasePlasma HDL cholesterolPlasma LDL cholesterolPlasma triglyceride levelsType 2 diabetes
PubMedDOIMetascience Observatory

About LCAT

This gene encodes the extracellular cholesterol esterifying enzyme, lecithin-cholesterol acyltransferase. The esterification of cholesterol is required for cholesterol transport. Mutations in this gene have been found to cause fish-eye disease as well as LCAT deficiency. [provided by RefSeq, Jul 2008]

View all LCAT variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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