1-palmitoleoyl-gpc (16:1)* to threonine

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 threonine
Metabolite Accession: GCST90200432
Name: threonine
Hmdb Id: HMDB0000167
Super Pathway: NA
Sub Pathway: NA
Inchikey: AYFVYJQAPQTCCC

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):
0.212
Position:
27730940
SE (Ratio):
0.022
Effect Allele:
T
Z-score (Ratio):
9.750
Reference Allele:
C
-log10(P):
-50.043
MAF:
0.413
Beta (Num):
0.088
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.124
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, de novo lipogenesis.5[1], 6[2]

Denominator Metabolite Explanation:

Amino acid metabolism, Glycine, serine and threonine metabolism.7[1], 8[2], 9[3]

Ratio Explanation:

The ratio reflects GCKR's influence on hepatic metabolism, shunting glucose towards lipid synthesis (increasing the numerator) and away from amino acid pathways (decreasing the denominator).1[1], 10[2], 5[3], 6[4]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

GCKR variants alter hepatic glucose utilization, impacting downstream lipid and amino acid pathways.1[1], 10[2] This metabolic shift is linked to dyslipidemia, type 2 diabetes, and related disorders like cholelithiasis and gout, which are strongly associated with GCKR function.1[3], 11[4], 12[5]

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