1-palmitoyl-2-stearoyl-gpc (16:0/18:0) to sphingomyelin (d17:1/14:0, d16:1/15:0)*

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

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: 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):
-0.134
Position:
12962718
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
-8.283
Reference Allele:
G
-log10(P):
-36.658
MAF:
0.384
Beta (Num):
-0.055
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.080
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:

Glycerophospholipid metabolism, Phosphatidylcholine biosynthesis.4[1]

Denominator Metabolite Explanation:

Sphingolipid metabolism.5[1], 6[2], 7[3]

Ratio Explanation:

This ratio reflects the balance between glycerophospholipid and sphingolipid pools.5[1], 4[2] The pQTL-implicated gene ISM1 may regulate this balance, impacting cell membrane composition.1[3], 2[4]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Genetic variation associated with ISM1 may alter the PC/SM ratio, disrupting biliary lipid composition and cholesterol solubility.8[1], 9[2] This promotes cholelithiasis (gallstones) and is consistent with associated elevations in LDL-C and ALT.10[3], 8[4], 11[5]

Phenotype Driver:

Metabolite-centric[both]

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