tricosanoyl sphingomyelin (d18:1/23:0)* to sphingomyelin (d17:1/14:0, d16:1/15:0)*

Numerator Metabolite

Structure of tricosanoyl sphingomyelin (d18:1/23:0)*
Metabolite Accession: GCST90200034
Name: tricosanoyl sphingomyelin (d18:1/23:0)*
Hmdb Id: HMDB0012105
Super Pathway: NA
Sub Pathway: NA
Inchikey: SXZWBNWTCVLZJN

Denominator Metabolite

Metabolite Accession: GCST90200169
Name: sphingomyelin (d17:1/14:0, d16:1/15:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs686548

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
20
Beta (Ratio):
-0.130
Position:
12973521
SE (Ratio):
0.013
Effect Allele:
A
Z-score (Ratio):
-9.927
Reference Allele:
T
-log10(P):
-51.802
MAF:
0.386
Beta (Num):
-0.049
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.081
SE (Den):
0.014
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], 7[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism.8[1], 5[2], 6[3]

Ratio Explanation:

The ratio reflects the balance of two distinct sphingomyelin species, both part of the broader sphingolipid metabolic network.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Elevated ISM1 levels, a secreted protein involved in lipid metabolism, may influence sphingomyelin profiles. This alteration, coupled with ISM1's functions, could contribute to an increased risk of cholelithiasis and affect LDL-cholesterol and ALT levels, though the direct causal link is not fully established.1[1], 9[2], 10[3], 11[4], 12[5]

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