3-hydroxyhexanoylcarnitine (1) to 3-hydroxybutyroylglycine**

Numerator Metabolite

Structure of 3-hydroxyhexanoylcarnitine (1)
Metabolite Accession: GCST90200228
Name: 3-hydroxyhexanoylcarnitine (1)
Hmdb Id: HMDB0013131
Super Pathway: NA
Sub Pathway: NA
Inchikey: VYEONLJQPYRKAN

Denominator Metabolite

Metabolite Accession: GCST90200174
Name: 3-hydroxybutyroylglycine**
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs640777

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
-0.132
Position:
67354986
SE (Ratio):
0.014
Effect Allele:
T
Z-score (Ratio):
-9.643
Reference Allele:
C
-log10(P):
-48.996
MAF:
0.426
Beta (Num):
-0.031
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.101
SE (Den):
0.015
No CNV overlap
rQTL cluster:
58
Reaction Distance:
NA
Closest Genes:
GSTP1 C11orf72 NDUFV1 NUDT8 TBX10

Region: rs1047891

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Clumped rQTL variant

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SNP Summary

Chr:
2
Beta (Ratio):
-0.362
Position:
211540507
SE (Ratio):
0.015
Effect Allele:
A
Z-score (Ratio):
-24.679
Reference Allele:
C
-log10(P):
-307.961
MAF:
0.310
Beta (Num):
-0.038
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.324
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:

Fatty acid beta-oxidation, Branched-chain amino acid catabolism6[1], 7[2]

Denominator Metabolite Explanation:

Acyl-Glycine metabolism, Ketone body metabolism8[1], 9[2]

Ratio Explanation:

An elevated ratio could suggest that impaired urea cycle function via a CPS1 variant leads to metabolic shifts, potentially affecting fatty acid and ketone metabolism.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

A CPS1 missense variant likely impairs the urea cycle, leading to hyperammonemia, which is associated with renal and liver stress.3[1], 10[2], 11[3] This primary defect in nitrogen metabolism can secondarily alter fatty acid and ketone body pathways, reflected in the metabolite ratio and contributing to phenotypes like cholelithiasis and renal failure.

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