homoarginine to serine

Numerator Metabolite

Structure of homoarginine
Metabolite Accession: GCST90199675
Name: homoarginine
Hmdb Id: HMDB0000670
Super Pathway: NA
Sub Pathway: NA
Inchikey: QUOGESRFPZDMMT

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

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):
-0.472
Position:
211540507
SE (Ratio):
0.023
Effect Allele:
A
Z-score (Ratio):
-20.598
Reference Allele:
C
-log10(P):
-215.385
MAF:
0.309
Beta (Num):
-0.267
Novel Locus:
No
SE (Num):
0.015
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:

Urea cycle, Nitric oxide metabolism.8[1], 9[2], 10[3], 11[4]

Denominator Metabolite Explanation:

Glycolysis, One-carbon metabolism, Folate cycle.12[1], 13[2], 14[3]

Ratio Explanation:

A dysfunctional CPS1 disrupts nitrogen homeostasis, reflected by the ratio of homoarginine (urea cycle-related) to serine, an amino acid involved in separate but connected metabolic pathways.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Impaired CPS1 function leads to hyperammonemia, which is toxic and can cause renal dysfunction.15[1], 16[2], 17[3] Low homoarginine, a consequence of altered urea cycle flux, is also independently associated with kidney and cardiovascular disease, while low CPS1 expression is linked to cholelithiasis.11[4], 18[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