sphingomyelin (d18:1/14:0, d16:1/16:0)* to palmitoyl sphingomyelin (d18:1/16:0)

Numerator Metabolite

Structure of sphingomyelin (d18:1/14:0, d16:1/16:0)*
Metabolite Accession: GCST90199945
Name: sphingomyelin (d18:1/14:0, d16:1/16:0)*
Hmdb Id: HMDB0012097
Super Pathway: NA
Sub Pathway: NA
Inchikey: KYICBZWZQPCUMO

Denominator Metabolite

Structure of palmitoyl sphingomyelin (d18:1/16:0)
Metabolite Accession: GCST90199876
Name: palmitoyl sphingomyelin (d18:1/16:0)
Hmdb Id: HMDB0010169
Super Pathway: NA
Sub Pathway: NA
Inchikey: RWKUXQNLWDTSLO

Associated Genomic Regions

Region: rs4814175

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):
0.141
Position:
12959094
SE (Ratio):
0.014
Effect Allele:
A
Z-score (Ratio):
9.849
Reference Allele:
T
-log10(P):
-51.027
MAF:
0.387
Beta (Num):
0.118
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.024
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 de novo biosynthesis, ceramide synthesis.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Sphingolipid de novo biosynthesis, ceramide synthesis.4[1], 5[2], 6[3]

Ratio Explanation:

This ratio reflects the balance of sphingomyelin species with different N-acyl fatty acid chains (C14:0/C16:1 vs. C16:0), potentially influenced by ISM1's regulation of lipid metabolism.1[1]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Genetic variants linked to ISM1, a protein that suppresses hepatic lipid synthesis and is associated with LDL-C and ALT levels, likely alter sphingomyelin composition, contributing to the cholesterol dysregulation and liver stress seen in cholelithiasis.1[1], 7[2], 3[3], 8[4], 9[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