n-palmitoylglycine to homoarginine

Numerator Metabolite

Structure of n-palmitoylglycine
Metabolite Accession: GCST90199923
Name: n-palmitoylglycine
Hmdb Id: HMDB0013034
Super Pathway: NA
Sub Pathway: NA
Inchikey: KVTFEOAKFFQCCX

Denominator Metabolite

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

Associated Genomic Regions

Region: rs1047891

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
2
Beta (Ratio):
0.514
Position:
211540507
SE (Ratio):
0.024
Effect Allele:
A
Z-score (Ratio):
21.470
Reference Allele:
C
-log10(P):
-233.767
MAF:
0.310
Beta (Num):
0.247
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.267
SE (Den):
0.015
No CNV overlap
rQTL cluster:
140
Reaction Distance:
NA
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

N-acyl-alpha amino acid biosynthesis.3[1]

Denominator Metabolite Explanation:

Urea cycle, Arginine and proline metabolism.4[1]

Ratio Explanation:

The ratio may reflect a balance between fatty acid metabolism (n-palmitoylglycine) and urea cycle function (homoarginine), potentially influenced by CPS1 activity.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

A CPS1 missense variant could impair urea cycle function, leading to altered homoarginine levels.2[1], 4[2], 5[3] This, combined with changes in n-palmitoylglycine, may contribute to the pathophysiology of cholelithiasis and renal disease, conditions associated with metabolic dysregulation.6[4], 7[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