sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)* to 1-palmitoyl-gpe (16:0)

Numerator Metabolite

Structure of sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Metabolite Accession: GCST90200017
Name: sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: LQINJRUGTUOHGS

Denominator Metabolite

Structure of 1-palmitoyl-gpe (16:0)
Metabolite Accession: GCST90199792
Name: 1-palmitoyl-gpe (16:0)
Hmdb Id: HMDB0011503
Super Pathway: NA
Sub Pathway: NA
Inchikey: YVYMBNSKXOXSKW

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):
-0.177
Position:
27730940
SE (Ratio):
0.021
Effect Allele:
T
Z-score (Ratio):
-8.606
Reference Allele:
C
-log10(P):
-39.423
MAF:
0.413
Beta (Num):
-0.090
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.087
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 synthesis and catabolism.5[1], 6[2], 7[3], 8[4], 9[5]

Denominator Metabolite Explanation:

Glycerophospholipid metabolism.10[1]

Ratio Explanation:

The ratio may reflect a shift in lipid metabolism, potentially influenced by GCKR's role in glucose sensing and subsequent effects on lipid synthesis.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

GCKR variants alter glucose and lipid metabolism, predisposing individuals to type 2 diabetes and cholelithiasis.2[1], 3[2], 4[3], 11[4], 12[5], 13[6] The altered sphingomyelin to glycerophospholipid ratio may reflect these metabolic disturbances, contributing to the observed phenotypes.

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