1-palmitoyl-gpe (16:0) to threonine

Numerator Metabolite

Structure of 1-palmitoyl-gpe (16:0)
Metabolite Accession: GCST90199792
Name: 1-palmitoyl-gpe (16:0)
Hmdb Id: HMDB0011503
Super Pathway: NA
Sub Pathway: NA
Inchikey: YVYMBNSKXOXSKW

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):
0.211
Position:
27730940
SE (Ratio):
0.021
Effect Allele:
T
Z-score (Ratio):
9.920
Reference Allele:
C
-log10(P):
-51.736
MAF:
0.412
Beta (Num):
0.087
Novel Locus:
No
SE (Num):
0.016
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, Phospholipid biosynthesis.4[1], 5[2], 6[3], 7[4]

Denominator Metabolite Explanation:

Amino acid metabolism, Threonine degradation.8[1], 9[2], 10[3]

Ratio Explanation:

The ratio of 1-palmitoyl-gpe (16:0), a lipid membrane component, to threonine reflects the interplay between lipid metabolism and amino acid utilization, influenced by GCKR's regulatory role.2[1], 11[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

GCKR variants alter glucokinase regulation, impacting hepatic glucose and lipid metabolism.2[1], 12[2], 13[3] This systemic dysregulation is reflected in the 1-palmitoyl-gpe to threonine ratio and contributes to the increased risk of associated phenotypes like type 2 diabetes, hypercholesterolemia, and cholelithiasis.14[4], 15[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