hydroxypalmitoyl sphingomyelin (d18:1/16:0(oh))** to 1-palmitoleoyl-2-linolenoyl-gpc (16:1/18:3)*

Numerator Metabolite

Metabolite Accession: GCST90200243
Name: hydroxypalmitoyl sphingomyelin (d18:1/16:0(oh))**
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Structure of 1-palmitoleoyl-2-linolenoyl-gpc (16:1/18:3)*
Metabolite Accession: GCST90200102
Name: 1-palmitoleoyl-2-linolenoyl-gpc (16:1/18:3)*
Hmdb Id: HMDB0008008
Super Pathway: NA
Sub Pathway: NA
Inchikey: MMUCLZZSNHBNFL

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):
-0.178
Position:
27730940
SE (Ratio):
0.020
Effect Allele:
T
Z-score (Ratio):
-8.692
Reference Allele:
C
-log10(P):
-40.180
MAF:
0.412
Beta (Num):
-0.085
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.093
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:

Sphingolipid metabolism.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Glycerophospholipid metabolism.7[1]

Ratio Explanation:

This ratio of hydroxypalmitoyl sphingomyelin to palmitoleoyl-linolenoyl-GPC likely reflects the balance between sphingolipid and glycerophospholipid synthesis, which is modulated by GCKR's control over upstream glucose and lipid precursors.1[1], 8[2], 9[3]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

GCKR variants modulate hepatic glucose and lipid metabolism, altering the balance between sphingolipid and glycerophospholipid pools.1[1], 2[2], 8[3], 9[4] This systemic dyslipidemia is a known risk factor for associated phenotypes including type 2 diabetes, cholelithiasis, and ischaemic heart disease.10[5], 11[6], 12[7], 13[8]

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