n-palmitoyl-sphinganine (d18:0/16:0) to glycosyl ceramide (d18:1/23:1, d17:1/24:1)*

Numerator Metabolite

Structure of n-palmitoyl-sphinganine (d18:0/16:0)
Metabolite Accession: GCST90200064
Name: n-palmitoyl-sphinganine (d18:0/16:0)
Hmdb Id: HMDB11760
Super Pathway: NA
Sub Pathway: NA
Inchikey: GCGTXOVNNFGTPQ

Denominator Metabolite

Metabolite Accession: GCST90200119
Name: glycosyl ceramide (d18:1/23:1, d17:1/24:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs17101394

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:
14
Beta (Ratio):
-0.269
Position:
64232386
SE (Ratio):
0.032
Effect Allele:
A
Z-score (Ratio):
-8.462
Reference Allele:
G
-log10(P):
-38.178
MAF:
0.164
Beta (Num):
-0.112
Novel Locus:
Yes ✔️
SE (Num):
0.021
Beta (Den):
0.157
SE (Den):
0.025
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid biosynthesis, Ceramide synthesis.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Glycosphingolipid biosynthesis.7[1], 8[2], 9[3]

Ratio Explanation:

This ratio may reflect the rate of de novo dihydroceramide synthesis (numerator) relative to its downstream conversion into complex glycosphingolipids (denominator).10[1], 11[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered SGPP1 activity likely modifies sphingolipid pools, including dihydroceramides.2[1], 12[2], 13[3] Elevated dihydroceramides are associated with insulin resistance and impaired glucose metabolism, providing a plausible link to increased HbA1c and triglyceride levels, which are markers for metabolic dysfunction.14[4], 15[5], 16[6]

Phenotype Driver:

Gene-centric:SGPP1

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