1-palmitoyl-2-stearoyl-gpc (16:0/18:0) to glycosyl ceramide (d18:1/20:0, d16:1/22:0)*

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: GCST90200145
Name: glycosyl ceramide (d18:1/20:0, d16:1/22:0)*
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):
-0.168
Position:
12962718
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
-9.924
Reference Allele:
G
-log10(P):
-51.771
MAF:
0.384
Beta (Num):
-0.055
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.114
SE (Den):
0.016
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Glycerophospholipid metabolism, Phospholipid biosynthesis.3[1], 4[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism, Ceramide synthesis.1[1], 5[2], 6[3]

Ratio Explanation:

The ratio reflects the balance between glycerophospholipid and sphingolipid pathways, where CERS4's activity in producing specific ceramides could influence this equilibrium.1[1], 3[2], 4[3]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CERS4 gene variation likely alters ceramide synthesis, affecting the glycosyl ceramide pool.1[1], 7[2], 8[3] This shift in lipid metabolism, particularly impacting cholesterol and bile acid pathways, is a known factor in cholelithiasis development.9[4], 10[5], 11[6], 12[7]

Phenotype Driver:

Gene-centric:CERS4

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