palmitoyl sphingomyelin (d18:1/16:0) to 1-palmitoyl-gpc (16:0)

Numerator Metabolite

Structure of palmitoyl sphingomyelin (d18:1/16:0)
Metabolite Accession: GCST90199876
Name: palmitoyl sphingomyelin (d18:1/16:0)
Hmdb Id: HMDB0010169
Super Pathway: NA
Sub Pathway: NA
Inchikey: RWKUXQNLWDTSLO

Denominator Metabolite

Structure of 1-palmitoyl-gpc (16:0)
Metabolite Accession: GCST90199733
Name: 1-palmitoyl-gpc (16:0)
Hmdb Id: HMDB0010382
Super Pathway: NA
Sub Pathway: NA
Inchikey: ASWBNKHCZGQVJV

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):
-0.152
Position:
27730940
SE (Ratio):
0.018
Effect Allele:
T
Z-score (Ratio):
-8.289
Reference Allele:
C
-log10(P):
-36.707
MAF:
0.413
Beta (Num):
-0.082
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.070
SE (Den):
0.016
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], 8[2], 9[3]

Ratio Explanation:

An increased ratio of palmitoyl sphingomyelin to 1-palmitoyl-gpc suggests a shift in lipid metabolism, potentially from GCKR-influenced altered glucose and lipid homeostasis.1[1], 3[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

GCKR variants are associated with altered glucose/lipid metabolism and phenotypes like type 2 diabetes and hypercholesterolaemia.1[1], 2[2], 3[3] This dysregulation likely affects the balance between sphingolipid and glycerophospholipid pools, leading to the observed ratio change and contributing to cardiometabolic diseases.

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