arginine to serine

Numerator Metabolite

Structure of arginine
Metabolite Accession: GCST90200372
Name: arginine
Hmdb Id: HMDB0000517
Super Pathway: NA
Sub Pathway: NA
Inchikey: ODKSFYDXXFIFQN

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):
-0.295
Position:
211540507
SE (Ratio):
0.020
Effect Allele:
A
Z-score (Ratio):
-14.532
Reference Allele:
C
-log10(P):
-108.499
MAF:
0.309
Beta (Num):
-0.090
Novel Locus:
No
SE (Num):
0.017
Beta (Den):
0.205
SE (Den):
0.016
No CNV overlap
rQTL cluster:
140
Reaction Distance:
3.0
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

Region: rs56335308

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Clumped rQTL variant

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SNP Summary

Chr:
8
Beta (Ratio):
-0.469
Position:
17419461
SE (Ratio):
0.060
Effect Allele:
A
Z-score (Ratio):
-7.796
Reference Allele:
G
-log10(P):
-32.685
MAF:
0.025
Beta (Num):
-0.238
Novel Locus:
Yes ✔️
SE (Num):
0.050
Beta (Den):
0.232
SE (Den):
0.048
No CNV overlap
rQTL cluster:
86
Reaction Distance:
3.0
Closest Genes:
SLC7A2 PDGFRL MTUS1 MTMR7 VPS37A

LLM Analysis

Numerator Metabolite Explanation:

Urea cycle, Nitric oxide synthesis5[1], 6[2]

Denominator Metabolite Explanation:

Glycolysis, One-carbon metabolism7[1], 8[2]

Ratio Explanation:

The ratio may reflect urea cycle dysfunction (arginine/CPS1) relative to glycolysis (serine), with elevated levels potentially indicating decreased arginine utilization or synthesis impairment by CPS1.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CPS1 gene variants can impair the urea cycle, altering arginine levels.3[1], 4[2] This metabolic disruption contributes to ammonia accumulation and is linked to hypertension and renal failure, as evidenced by associations with BUN and serum creatinine.9[3], 10[4]

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