picolinate to glycosyl-n-(2-hydroxynervonoyl)-sphingosine (d18:1/24:1(2oh))*

Numerator Metabolite

Structure of picolinate
Metabolite Accession: GCST90200282
Name: picolinate
Hmdb Id: HMDB0002243
Super Pathway: NA
Sub Pathway: NA
Inchikey: SIOXPEMLGUPBBT

Denominator Metabolite

Metabolite Accession: GCST90200117
Name: glycosyl-n-(2-hydroxynervonoyl)-sphingosine (d18:1/24:1(2oh))*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs1047891

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Clumped rQTL variant

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SNP Summary

Chr:
2
Beta (Ratio):
-0.213
Position:
211540507
SE (Ratio):
0.024
Effect Allele:
A
Z-score (Ratio):
-9.020
Reference Allele:
C
-log10(P):
-43.118
MAF:
0.306
Beta (Num):
-0.105
Novel Locus:
No
SE (Num):
0.018
Beta (Den):
0.108
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:

Tryptophan metabolism.5[1]

Denominator Metabolite Explanation:

Sphingolipid metabolism.6[1], 7[2], 8[3], 9[4]

Ratio Explanation:

This ratio reflects a balance between tryptophan catabolism (picolinate) and sphingolipid metabolism (glycosyl-sphingosine), which may be altered by systemic dysfunction from CPS1 deficiency.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

The CPS1 variant impairs urea cycle function, leading to liver and kidney stress associated with cholelithiasis and chronic kidney disease.10[1], 11[2] This organ damage likely alters systemic picolinate and sphingolipid levels, which are implicated in kidney disease and gallstone formation.6[3], 7[4], 12[5], 13[6], 14[7], 15[8]

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