1-palmitoyl-2-linoleoyl-gpc (16:0/18:2) to dihomo-linolenate (20:3n3 or n6)

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 dihomo-linolenate (20:3n3 or n6)
Metabolite Accession: GCST90199820
Name: dihomo-linolenate (20:3n3 or n6)
Hmdb Id: HMDB0002925
Super Pathway: NA
Sub Pathway: NA
Inchikey: AHANXAKGNAKFSK

Associated Genomic Regions

Region: rs12928099

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):
-0.197
Position:
15150505
SE (Ratio):
0.023
Effect Allele:
A
Z-score (Ratio):
-8.636
Reference Allele:
C
-log10(P):
-39.681
MAF:
0.291
Beta (Num):
-0.097
Novel Locus:
Yes ✔️
SE (Num):
0.017
Beta (Den):
0.100
SE (Den):
0.016
No CNV overlap
rQTL cluster:
34
Reaction Distance:
NA
Closest Genes:
PDXDC1 NTAN1 RRN3 NPIPA1 NOMO1

LLM Analysis

Numerator Metabolite Explanation:

Glycerophospholipid metabolism, Phosphatidylcholine biosynthesis.6[1], 7[2]

Denominator Metabolite Explanation:

Linoleic acid and alpha-linolenic acid metabolism.8[1], 9[2]

Ratio Explanation:

The ratio may reflect the balance between phospholipid synthesis and polyunsaturated fatty acid metabolism, although a direct enzymatic link with PDXDC1 is not established.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Genetic variation near PDXDC1 is associated with altered triglyceride and HDL-C levels, a key feature of dyslipidemia.3[1], 4[2], 10[3] The ratio of a major phospholipid to a polyunsaturated fatty acid may reflect changes in lipid composition that contribute to this phenotype.

Phenotype Driver:

Gene-centric:PDXDC1

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