creatine to threonine

Numerator Metabolite

Structure of creatine
Metabolite Accession: GCST90200323
Name: creatine
Hmdb Id: HMDB0000064
Super Pathway: NA
Sub Pathway: NA
Inchikey: CVSVTCORWBXHQV

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: rs1047891

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):
0.327
Position:
211540507
SE (Ratio):
0.022
Effect Allele:
A
Z-score (Ratio):
15.011
Reference Allele:
C
-log10(P):
-115.601
MAF:
0.310
Beta (Num):
0.204
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.123
SE (Den):
0.017
No CNV overlap
rQTL cluster:
140
Reaction Distance:
5.0
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

Creatine-phosphate shuttle, Amino acid metabolism5[1], 6[2], 7[3]

Denominator Metabolite Explanation:

Amino acid metabolism, Protein synthesis8[1], 9[2], 10[3]

Ratio Explanation:

CPS1 is key in nitrogen metabolism; altered function could impact the availability of precursors like arginine and glycine for creatine synthesis, relative to threonine levels.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

A CPS1 missense variant may alter nitrogen balance, affecting creatine synthesis. This change, reflected in the creatine/threonine ratio, could link to kidney-related phenotypes (renal failure, chronic kidney disease, cholelithiasis) as CPS1 function is tied to renal health and nitrogenous waste clearance.11[1], 12[2]

Phenotype Driver:

Gene-centric:CPS1

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