1-palmitoyl-2-linoleoyl-gpc (16:0/18:2) to arachidoylcarnitine (c20)*

Numerator Metabolite

Structure of 1-palmitoyl-2-linoleoyl-gpc (16:0/18:2)
Metabolite Accession: GCST90200330
Name: 1-palmitoyl-2-linoleoyl-gpc (16:0/18:2)
Hmdb Id: HMDB0007973
Super Pathway: NA
Sub Pathway: NA
Inchikey: JLPULHDHAOZNQI

Denominator Metabolite

Structure of arachidoylcarnitine (c20)*
Metabolite Accession: GCST90200135
Name: arachidoylcarnitine (c20)*
Hmdb Id: HMDB0006460
Super Pathway: NA
Sub Pathway: NA
Inchikey: SVJLJQBGUITFLI

Associated Genomic Regions

Region: rs4500751

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

Clumped rQTL variant

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SNP Summary

Chr:
16
Beta (Ratio):
0.162
Position:
15140211
SE (Ratio):
0.020
Effect Allele:
T
Z-score (Ratio):
8.011
Reference Allele:
C
-log10(P):
-34.411
MAF:
0.311
Beta (Num):
0.095
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
-0.068
SE (Den):
0.017
No CNV overlap
rQTL cluster:
34
Reaction Distance:
NA
Closest Genes:
PDXDC1 NTAN1 RRN3 NPIPA1 NOMO1

LLM Analysis

Numerator Metabolite Explanation:

Glycerophospholipid metabolism, Fatty acid metabolism.3[1]

Denominator Metabolite Explanation:

Fatty acid metabolism, Carnitine shuttle.4[1], 5[2], 6[3]

Ratio Explanation:

The ratio reflects the balance between glycerophospholipid synthesis and fatty acid beta-oxidation, potentially influenced by FADS-mediated fatty acid availability.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Genetic variants in the FADS cluster (FADS1/FADS2) alter fatty acid desaturation, influencing the composition of lipids like 1-palmitoyl-2-linoleoyl-gpc.7[1], 8[2], 9[3], 10[4] This altered lipid profile, particularly related to arachidonic acid, is associated with an increased risk of cholelithiasis (gallstones), a recognized phenotype linked to FADS variants.11[5], 12[6], 13[7], 14[8], 15[9]

Phenotype Driver:

Gene-centric:FADS1/FADS2

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