1-palmitoyl-2-stearoyl-gpc (16:0/18:0) to sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*

Numerator Metabolite

Structure of 1-palmitoyl-2-stearoyl-gpc (16:0/18:0)
Metabolite Accession: GCST90200041
Name: 1-palmitoyl-2-stearoyl-gpc (16:0/18:0)
Hmdb Id: HMDB0007970
Super Pathway: NA
Sub Pathway: NA
Inchikey: PZNPLUBHRSSFHT

Denominator Metabolite

Structure of sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Metabolite Accession: GCST90200017
Name: sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: LQINJRUGTUOHGS

Associated Genomic Regions

Region: rs364585

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):
-0.137
Position:
12962718
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
-7.881
Reference Allele:
G
-log10(P):
-33.359
MAF:
0.384
Beta (Num):
-0.055
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.083
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:

Glycerophospholipid biosynthesis

Denominator Metabolite Explanation:

Sphingolipid metabolism.3[1], 4[2]

Ratio Explanation:

The ratio of 1-palmitoyl-2-stearoyl-gpc to sphingomyelin reflects the balance between glycerophospholipid and sphingolipid pools, with phosphatidylcholine serving as a phosphocholine donor for sphingomyelin synthesis.5[1], 6[2]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

ISM1, a secreted adipokine, is linked to cholelithiasis and altered LDL-cholesterol and ALT levels.7[1], 8[2], 9[3] Its function in suppressing hepatic lipid synthesis and modulating lipid metabolism likely influences bile composition and lipid profiles, contributing to the observed phenotypes.1[4], 2[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