1-linolenoyl-gpc (18:3)* to 1-(1-enyl-palmitoyl)-2-oleoyl-gpc (p-16:0/18:1)*

Numerator Metabolite

Structure of 1-linolenoyl-gpc (18:3)*
Metabolite Accession: GCST90199958
Name: 1-linolenoyl-gpc (18:3)*
Hmdb Id: HMDB0010388
Super Pathway: NA
Sub Pathway: NA
Inchikey: WKQNRCYKYCKESD

Denominator Metabolite

Structure of 1-(1-enyl-palmitoyl)-2-oleoyl-gpc (p-16:0/18:1)*
Metabolite Accession: GCST90200057
Name: 1-(1-enyl-palmitoyl)-2-oleoyl-gpc (p-16:0/18:1)*
Hmdb Id: HMDB0007996
Super Pathway: NA
Sub Pathway: NA
Inchikey: MPQGNHKVOVYEEN

Associated Genomic Regions

Region: rs1260326

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

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SNP Summary

Chr:
2
Beta (Ratio):
0.175
Position:
27730940
SE (Ratio):
0.020
Effect Allele:
T
Z-score (Ratio):
8.636
Reference Allele:
C
-log10(P):
-39.683
MAF:
0.413
Beta (Num):
0.084
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
-0.090
SE (Den):
0.015
No CNV overlap
rQTL cluster:
152
Reaction Distance:
NA
Closest Genes:
GCKR FNDC4 IFT172 AC109829.1 KRTCAP3

LLM Analysis

Numerator Metabolite Explanation:

Glycerophospholipid metabolism, alpha-Linolenic acid metabolism.10[1], 11[2]

Denominator Metabolite Explanation:

Glycerophospholipid metabolism, Plasmalogen synthesis.12[1], 13[2], 14[3], 15[4], 16[5]

Ratio Explanation:

GCKR dysregulation alters hepatic lipid metabolism, potentially affecting the balance between these two distinct glycerophospholipid species, though a direct enzymatic link is not established.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

GCKR variants influence hepatic glucose and lipid metabolism, predisposing to hyperlipidemia, fatty liver, and gout.1[1], 2[2], 3[3], 6[4], 7[5], 8[6], 9[7] This altered metabolic state likely drives the observed changes in the ratio of these two phospholipids and contributes to the associated cardiometabolic phenotypes.

Phenotype Driver:

Gene-centric:GCKR

Downloads

Download the full rQTL summary statistics file for this metabolite ratio. Data contains the loci listed here. For each SNP (chromosome, effect_allele, reference_allele, pos_name, position) these columns contain the summary statistics of the ratio (beta, pgain, pval, se, z), the numerator metabolite (beta_1, pval_1, n_iids_1, effect_allele_frequency_1, se_1, z_1) and the denominator metabolite (beta_2, pval_2, n_iids_2, effect_allele_frequency_2, se_2, z_2)

Download rQTL Data