n-stearoyl-sphingosine (d18:1/18:0)* to lignoceroyl sphingomyelin (d18:1/24:0)

Numerator Metabolite

Structure of n-stearoyl-sphingosine (d18:1/18:0)*
Metabolite Accession: GCST90200341
Name: n-stearoyl-sphingosine (d18:1/18:0)*
Hmdb Id: HMDB0004950
Super Pathway: NA
Sub Pathway: NA
Inchikey: VODZWWMEJITOND

Denominator Metabolite

Structure of lignoceroyl sphingomyelin (d18:1/24:0)
Metabolite Accession: GCST90200020
Name: lignoceroyl sphingomyelin (d18:1/24:0)
Hmdb Id: HMDB0011697
Super Pathway: NA
Sub Pathway: NA
Inchikey: QEDPUVGSSDPBMD

Associated Genomic Regions

Region: rs364585

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:
20
Beta (Ratio):
0.210
Position:
12962718
SE (Ratio):
0.021
Effect Allele:
A
Z-score (Ratio):
9.978
Reference Allele:
G
-log10(P):
-52.311
MAF:
0.384
Beta (Num):
0.117
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.093
SE (Den):
0.015
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

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

Denominator Metabolite Explanation:

Sphingolipid metabolism.7[1], 8[2], 9[3]

Ratio Explanation:

This ratio may reflect the balance between ceramide synthesis and its conversion to sphingomyelin, with potential ISM1 influence on overall lipid metabolism.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Altered ISM1 function may influence sphingolipid metabolism, contributing to changes in bile composition and increasing the risk of cholelithiasis.10[1], 11[2], 12[3], 13[4] This is supported by associations with elevated Alanine aminotransferase (ALT) and LDL-cholesterol, which are also linked to liver function and gallstone disease.

Phenotype Driver:

Gene-centric:ISM1

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