serine to threonine

Numerator Metabolite

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

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):
0.328
Position:
211540507
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
19.587
Reference Allele:
C
-log10(P):
-195.029
MAF:
0.310
Beta (Num):
0.205
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.123
SE (Den):
0.017
No CNV overlap
rQTL cluster:
140
Reaction Distance:
2.0
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

Glycolysis, One-carbon metabolism.7[1], 8[2], 9[3]

Denominator Metabolite Explanation:

Amino acid degradation, One-carbon metabolism.10[1], 11[2], 12[3]

Ratio Explanation:

CPS1 dysfunction alters nitrogen metabolism; serine and threonine are involved in interconnected amino acid and one-carbon pathways, but are not directly processed by CPS1.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Reduced CPS1 function from genetic variants likely impairs ammonia detoxification, contributing to systemic metabolic stress. This, rather than the serine/threonine ratio itself, is associated with kidney disease and may influence the bile composition, contributing to cholelithiasis.4[1], 13[2], 14[3], 15[4], 16[5]

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