3-methylglutarylcarnitine (2) to gamma-glutamylthreonine

Numerator Metabolite

Structure of 3-methylglutarylcarnitine (2)
Metabolite Accession: GCST90199971
Name: 3-methylglutarylcarnitine (2)
Hmdb Id: HMDB0000552
Super Pathway: NA
Sub Pathway: NA
Inchikey: HFCPFJNSBPQJDP

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

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
2
Beta (Ratio):
0.185
Position:
27730940
SE (Ratio):
0.021
Effect Allele:
T
Z-score (Ratio):
8.960
Reference Allele:
C
-log10(P):
-42.571
MAF:
0.413
Beta (Num):
0.079
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:

Leucine catabolism, fatty acid metabolism.5[1], 6[2]

Denominator Metabolite Explanation:

Gamma-glutamyl cycle, protein catabolism.7[1], 8[2], 9[3]

Ratio Explanation:

GCKR variants are associated with gamma-glutamylthreonine levels, suggesting a link between glucose/lipid regulation and gamma-glutamyl metabolism, though the direct mechanism influencing both metabolites remains undefined.10[1]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

GCKR variants are associated with altered glucose and lipid metabolism, increasing risk for type 2 diabetes, hypercholesterolemia, and cholelithiasis.2[1], 11[2], 12[3], 13[4] GCKR's regulatory role likely drives these phenotypes, with the metabolite ratio reflecting downstream metabolic shifts in glucose, lipid, and amino acid pathways.

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