1-palmitoleoyl-gpc (16:1)* to gamma-glutamylthreonine

Numerator Metabolite

Structure of 1-palmitoleoyl-gpc (16:1)*
Metabolite Accession: GCST90199777
Name: 1-palmitoleoyl-gpc (16:1)*
Hmdb Id: HMDB0010383
Super Pathway: NA
Sub Pathway: NA
Inchikey: LFUDDCMNKWEORN

Denominator Metabolite

Structure of gamma-glutamylthreonine
Metabolite Accession: GCST90199749
Name: gamma-glutamylthreonine
Hmdb Id: HMDB0029159
Super Pathway: NA
Sub Pathway: NA
Inchikey: GWNXFCYUJXASDX

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):
0.195
Position:
27730940
SE (Ratio):
0.022
Effect Allele:
T
Z-score (Ratio):
9.025
Reference Allele:
C
-log10(P):
-43.159
MAF:
0.413
Beta (Num):
0.088
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.106
SE (Den):
0.016
No CNV overlap
rQTL cluster:
152
Reaction Distance:
NA
Closest Genes:
GCKR FNDC4 IFT172 AC109829.1 KRTCAP3

LLM Analysis

Numerator Metabolite Explanation:

Glycerophospholipid metabolism, Lysophospholipid signaling.7[1], 8[2]

Denominator Metabolite Explanation:

Gamma-glutamyl cycle, Glutathione metabolism.9[1], 10[2], 11[3]

Ratio Explanation:

The ratio may reflect the balance between hepatic lipid metabolism (1-palmitoleoyl-GPC) and amino acid/oxidative stress status (gamma-glutamylthreonine), modulated by GCKR's regulatory role.12[1], 13[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

GCKR variants alter hepatic glucose and lipid metabolism, which influences both the lysophosphatidylcholine numerator and the gamma-glutamylthreonine denominator.2[1], 12[2], 13[3] This widespread metabolic dysregulation contributes to phenotypes like hypercholesterolemia, T2D, and cholelithiasis.4[4], 6[5], 14[6], 15[7]

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