lignoceroyl sphingomyelin (d18:1/24:0) to palmitoyl dihydrosphingomyelin (d18:0/16:0)*

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

Structure of palmitoyl dihydrosphingomyelin (d18:0/16:0)*
Metabolite Accession: GCST90200035
Name: palmitoyl dihydrosphingomyelin (d18:0/16:0)*
Hmdb Id: HMDB0010168
Super Pathway: NA
Sub Pathway: NA
Inchikey: QHZIGNLCLJPLCU

Associated Genomic Regions

Region: rs680379

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):
-0.135
Position:
12969400
SE (Ratio):
0.014
Effect Allele:
A
Z-score (Ratio):
-9.624
Reference Allele:
G
-log10(P):
-48.808
MAF:
0.385
Beta (Num):
-0.093
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.042
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 metabolism.5[1], 6[2]

Denominator Metabolite Explanation:

Sphingolipid de novo synthesis.7[1], 8[2], 9[3]

Ratio Explanation:

This ratio compares a very-long-chain sphingomyelin to its precursor, reflecting sphingolipid biosynthesis and elongation, processes ISM1 may influence through its role in lipid metabolism.2[1], 10[2], 6[3]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1's role in suppressing hepatic lipid synthesis could alter sphingolipid metabolism, a pathway linked to cholelithiasis.1[1], 11[2], 12[3], 2[4] Changes in sphingolipid profiles, including specific ceramides and sphingomyelins, are observed in patients with cholelithiasis and are associated with elevated Alanine aminotransferase (ALT).11[5], 12[6], 13[7]

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