2r,3r-dihydroxybutyrate to serine

Numerator Metabolite

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

Denominator Metabolite

Structure of serine
Metabolite Accession: GCST90200415
Name: serine
Hmdb Id: HMDB0000187
Super Pathway: NA
Sub Pathway: NA
Inchikey: MTCFGRXMJLQNBG

Associated Genomic Regions

Region: rs1047891

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Clumped rQTL variant

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SNP Summary

Chr:
2
Beta (Ratio):
-0.357
Position:
211540507
SE (Ratio):
0.025
Effect Allele:
A
Z-score (Ratio):
-14.229
Reference Allele:
C
-log10(P):
-104.116
MAF:
0.310
Beta (Num):
-0.152
Novel Locus:
No
SE (Num):
0.017
Beta (Den):
0.205
SE (Den):
0.016
No CNV overlap
rQTL cluster:
140
Reaction Distance:
NA
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

Fatty acid and amino acid metabolism.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Glycine, serine, and threonine metabolism; one-carbon metabolism.7[1], 8[2], 9[3], 10[4]

Ratio Explanation:

A high ratio may reflect impaired CPS1 function, leading to altered nitrogen and amino acid metabolism, although a direct link is not established.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

CPS1 dysfunction can lead to hyperammonemia and altered amino acid levels.1[1], 2[2], 3[3] This systemic metabolic disturbance, including changes in serine which is linked to kidney function11[4], 12[5], 13[6], 14[7], 15[8], could contribute to renal failure and cholelithiasis, both associated with CPS1 variants.16[9], 17[10], 18[11], 19[12], 20[13], 21[14]

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