2,3-dihydroxy-5-methylthio-4-pentenoate (dmtpa)* to creatinine

Numerator Metabolite

Structure of 2,3-dihydroxy-5-methylthio-4-pentenoate (dmtpa)*
Metabolite Accession: GCST90200233
Name: 2,3-dihydroxy-5-methylthio-4-pentenoate (dmtpa)*
Hmdb Id: HMDB0240388
Super Pathway: NA
Sub Pathway: NA
Inchikey: XMZBEAXQGSBWLG

Denominator Metabolite

Structure of creatinine
Metabolite Accession: GCST90200366
Name: creatinine
Hmdb Id: HMDB0000562
Super Pathway: NA
Sub Pathway: NA
Inchikey: DDRJAANPRJIHGJ

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):
-0.120
Position:
211540507
SE (Ratio):
0.015
Effect Allele:
A
Z-score (Ratio):
-8.100
Reference Allele:
C
-log10(P):
-35.135
MAF:
0.310
Beta (Num):
-0.076
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.044
SE (Den):
0.014
No CNV overlap
rQTL cluster:
140
Reaction Distance:
NA
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

Methionine salvage pathway.6[1], 7[2]

Denominator Metabolite Explanation:

Creatine synthesis, degradation.8[1], 9[2], 10[3], 11[4]

Ratio Explanation:

An elevated ratio may indicate increased dmtpa, a uremic toxin associated with kidney disease12[1], 13[2], relative to creatinine, which is used to estimate renal function.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CPS1 missense variants may alter nitrogen and one-carbon metabolism, impacting the methionine salvage pathway and production of dmtpa, a metabolite associated with decreased kidney function, cholelithiasis, and chronic kidney disease.14[1], 12[2], 15[3], 13[4], 16[5], 17[6]

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