lignoceroyl sphingomyelin (d18:1/24:0) to glycosyl ceramide (d18:1/23:1, d17:1/24:1)*

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: GCST90200119
Name: glycosyl ceramide (d18:1/23:1, d17:1/24:1)*
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):
-0.205
Position:
12959398
SE (Ratio):
0.024
Effect Allele:
T
Z-score (Ratio):
-8.496
Reference Allele:
C
-log10(P):
-38.467
MAF:
0.386
Beta (Num):
-0.094
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.110
SE (Den):
0.020
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism.6[1], 7[2]

Ratio Explanation:

The ratio of lignoceroyl sphingomyelin to glycosyl ceramide reflects the balance within sphingolipid metabolism, potentially influenced by ISM1's role in broader lipid homeostasis.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

ISM1's regulation of lipid metabolism may alter sphingolipid pools, including sphingomyelin.1[1], 8[2] Altered sphingomyelin levels are linked to cholelithiasis risk, partly mediated by changes in LDL cholesterol, providing a plausible link between the gene, ratio, and observed phenotypes.9[3], 10[4]

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