1-palmitoleoyl-2-linolenoyl-gpc (16:1/18:3)* to threonine

Numerator Metabolite

Structure of 1-palmitoleoyl-2-linolenoyl-gpc (16:1/18:3)*
Metabolite Accession: GCST90200102
Name: 1-palmitoleoyl-2-linolenoyl-gpc (16:1/18:3)*
Hmdb Id: HMDB0008008
Super Pathway: NA
Sub Pathway: NA
Inchikey: MMUCLZZSNHBNFL

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

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
2
Beta (Ratio):
0.217
Position:
27730940
SE (Ratio):
0.022
Effect Allele:
T
Z-score (Ratio):
9.940
Reference Allele:
C
-log10(P):
-51.938
MAF:
0.412
Beta (Num):
0.093
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:

Phosphatidylcholine biosynthesis, Glycerophospholipid metabolism

Denominator Metabolite Explanation:

Threonine degradation, Amino acid metabolism.11[1], 12[2], 13[3], 14[4], 15[5]

Ratio Explanation:

Elevated ratio may indicate dysregulation in both lipid and amino acid metabolism, potentially driven by GCKR's influence on glucose and lipid pathways.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

GCKR variants alter glucose and lipid metabolism, influencing circulating levels of phosphatidylcholines and threonine, contributing to phenotypes like type 2 diabetes and liver disease.2[1], 3[2], 6[3]

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