stearoyl sphingomyelin (d18:1/18:0) to lignoceroyl sphingomyelin (d18:1/24:0)

Numerator Metabolite

Structure of stearoyl sphingomyelin (d18:1/18:0)
Metabolite Accession: GCST90200335
Name: stearoyl sphingomyelin (d18:1/18:0)
Hmdb Id: HMDB0001348
Super Pathway: NA
Sub Pathway: NA
Inchikey: LKQLRGMMMAHREN

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: rs4814176

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):
0.186
Position:
12959398
SE (Ratio):
0.019
Effect Allele:
T
Z-score (Ratio):
9.565
Reference Allele:
C
-log10(P):
-48.237
MAF:
0.386
Beta (Num):
0.092
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
-0.094
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 metabolism3[1], 4[2], 5[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism3[1], 4[2], 5[3]

Ratio Explanation:

The ratio reflects the relative abundance of a common versus a very-long-chain sphingomyelin, potentially indicating alterations in ceramide synthase activity or substrate availability.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Elevated ISM1 may alter sphingolipid metabolism, contributing to changes in LDL-cholesterol and bile composition. This dysregulation is associated with an increased risk of cholelithiasis, potentially mediated by LDL levels, and elevated ALT, indicating liver stress.6[1], 7[2]

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