1-linolenoyl-gpc (18:3)* to 1-(1-enyl-palmitoyl)-2-linoleoyl-gpc (p-16:0/18:2)*

Numerator Metabolite

Structure of 1-linolenoyl-gpc (18:3)*
Metabolite Accession: GCST90199958
Name: 1-linolenoyl-gpc (18:3)*
Hmdb Id: HMDB0010388
Super Pathway: NA
Sub Pathway: NA
Inchikey: WKQNRCYKYCKESD

Denominator Metabolite

Structure of 1-(1-enyl-palmitoyl)-2-linoleoyl-gpc (p-16:0/18:2)*
Metabolite Accession: GCST90200060
Name: 1-(1-enyl-palmitoyl)-2-linoleoyl-gpc (p-16:0/18:2)*
Hmdb Id: HMDB0011211
Super Pathway: NA
Sub Pathway: NA
Inchikey: QLEHHUPUHJPURI

Associated Genomic Regions

Region: rs1260326

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:
2
Beta (Ratio):
0.171
Position:
27730940
SE (Ratio):
0.020
Effect Allele:
T
Z-score (Ratio):
8.692
Reference Allele:
C
-log10(P):
-40.178
MAF:
0.413
Beta (Num):
0.084
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
-0.087
SE (Den):
0.015
No CNV overlap
rQTL cluster:
152
Reaction Distance:
NA
Closest Genes:
GCKR FNDC4 IFT172 AC109829.1 KRTCAP3

LLM Analysis

Numerator Metabolite Explanation:

Glycerophospholipid metabolism, Lysophospholipid biosynthesis.4[1], 5[2]

Denominator Metabolite Explanation:

Ether lipid metabolism, Plasmalogen biosynthesis.6[1], 7[2]

Ratio Explanation:

The ratio contrasts a lysophospholipid with a plasmalogen, reflecting altered phospholipid turnover downstream of GCKR-mediated changes in hepatic glucose and lipid metabolism.1[1], 2[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Variation in GCKR, a key regulator of hepatic glucose and lipid metabolism, drives phenotypes like Type 2 diabetes, dyslipidemia, and cholelithiasis.1[1], 2[2], 8[3], 9[4] The altered phospholipid ratio is a downstream biomarker of this systemic metabolic dysregulation.

Phenotype Driver:

Gene-centric:GCKR

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