3-methylglutaconate to 2r,3r-dihydroxybutyrate

Numerator Metabolite

Structure of 3-methylglutaconate
Metabolite Accession: GCST90199886
Name: 3-methylglutaconate
Hmdb Id: HMDB0000522
Super Pathway: NA
Sub Pathway: NA
Inchikey: WKRBKYFIJPGYQC

Denominator Metabolite

Structure of 2r,3r-dihydroxybutyrate
Metabolite Accession: GCST90199889
Name: 2r,3r-dihydroxybutyrate
Hmdb Id: HMDB0000498
Super Pathway: NA
Sub Pathway: NA
Inchikey: LOUGYXZSURQALL

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):
0.520
Position:
211540507
SE (Ratio):
0.021
Effect Allele:
A
Z-score (Ratio):
25.212
Reference Allele:
C
-log10(P):
-321.276
MAF:
0.309
Beta (Num):
0.367
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.152
SE (Den):
0.017
No CNV overlap
rQTL cluster:
140
Reaction Distance:
NA
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

Leucine degradation, Mevalonate shunt, Fatty acid metabolism.6[1], 7[2]

Denominator Metabolite Explanation:

Valine catabolism, Fatty acid β-oxidation. 8[1], 9[2]

Ratio Explanation:

An elevated ratio suggests disrupted mitochondrial metabolism, where both leucine/fatty acid degradation and valine catabolism may be affected, but not directly by CPS1.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Impaired CPS1 function leads to hyperammonemia and is genetically associated with chronic kidney disease and cholelithiasis. 10[1], 11[2], 12[3], 13[4], 14[5], 15[6]The altered metabolite ratio reflects broader mitochondrial stress, which likely contributes to these phenotypes.

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