lignoceroyl sphingomyelin (d18:1/24:0) to sphingomyelin (d18:1/17:0, d17:1/18:0, d19:1/16:0)

Numerator 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

Denominator Metabolite

Metabolite Accession: GCST90200047
Name: sphingomyelin (d18:1/17:0, d17:1/18:0, d19:1/16:0)
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

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):
-0.182
Position:
12959398
SE (Ratio):
0.019
Effect Allele:
T
Z-score (Ratio):
-9.717
Reference Allele:
C
-log10(P):
-49.717
MAF:
0.386
Beta (Num):
-0.094
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.087
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:

Sphingomyelin Synthesis4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Sphingomyelin Synthesis4[1], 5[2], 6[3]

Ratio Explanation:

This ratio reflects the balance of different sphingomyelin species, with lignoceroyl sphingomyelin having a very-long-chain fatty acid and the denominator having shorter, odd-chain fatty acids.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

The pQTL colocalization of ISM1 suggests it influences sphingomyelin metabolism. Altered sphingomyelin levels are associated with cholelithiasis, and ISM1 may influence this by affecting hepatic lipid synthesis and LDL cholesterol, both of which are linked to gallstone formation.7[1], 8[2], 9[3]

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