sphingomyelin (d18:2/16:0, d18:1/16:1)* to n-palmitoyl-heptadecasphingosine (d17:1/16:0)*

Numerator Metabolite

Metabolite Accession: GCST90199947
Name: sphingomyelin (d18:2/16:0, d18:1/16:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Metabolite Accession: GCST90200115
Name: n-palmitoyl-heptadecasphingosine (d17:1/16:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs364585

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.175
Position:
12962718
SE (Ratio):
0.018
Effect Allele:
A
Z-score (Ratio):
-9.563
Reference Allele:
G
-log10(P):
-48.221
MAF:
0.384
Beta (Num):
-0.074
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.101
SE (Den):
0.017
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], 6[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism.4[1], 7[2]

Ratio Explanation:

The ratio of sphingomyelin to its precursor ceramide reflects sphingolipid biosynthesis activity.4[1], 5[2], 8[3] ISM1, an adipokine, may influence this ratio, impacting lipid homeostasis.1[4], 2[5]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Elevated ISM1 protein levels are linked to higher LDL, ALT, and cholelithiasis risk.1[1], 3[2] ISM1 is a secreted protein associated with metabolic changes, including disruptions in sphingolipid balance, which may contribute to the pathophysiology of gallstone disease, potentially mediated by changes in LDL cholesterol.1[3], 9[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