dihomo-linolenoyl-choline to sphingomyelin (d18:2/21:0, d16:2/23:0)*

Numerator Metabolite

Structure of dihomo-linolenoyl-choline
Metabolite Accession: GCST90200090
Name: dihomo-linolenoyl-choline
Hmdb Id: HMDB0240646
Super Pathway: NA
Sub Pathway: NA
Inchikey: CPIZQONKXRTJBX

Denominator Metabolite

Metabolite Accession: GCST90200129
Name: sphingomyelin (d18:2/21:0, d16:2/23:0)*
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):
-0.174
Position:
211540507
SE (Ratio):
0.022
Effect Allele:
A
Z-score (Ratio):
-7.801
Reference Allele:
C
-log10(P):
-32.725
MAF:
0.309
Beta (Num):
-0.098
Novel Locus:
Yes ✔️
SE (Num):
0.018
Beta (Den):
0.076
SE (Den):
0.014
No CNV overlap
rQTL cluster:
140
Reaction Distance:
NA
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

Glycerophospholipid metabolism, fatty acid metabolism.6[1], 7[2], 8[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism.9[1], 10[2], 11[3]

Ratio Explanation:

The ratio likely reflects altered membrane composition due to mitochondrial dysfunction from CPS1 variants, affecting distinct glycerophospholipid and sphingolipid pools through an indirect mechanism.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Defective CPS1 causes hyperammonemia, leading to systemic metabolic stress and mitochondrial dysfunction that can result in renal failure and cholelithiasis.12[1], 13[2], 14[3], 15[4] The altered lipid ratio is likely a secondary biomarker of this cellular stress rather than a direct cause of the phenotypes.

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