n-palmitoyl-sphinganine (d18:0/16:0) to ceramide (d18:1/14:0, d16:1/16:0)*

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: GCST90200116
Name: ceramide (d18:1/14:0, d16:1/16:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs4902243

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):
-0.366
Position:
64234243
SE (Ratio):
0.026
Effect Allele:
G
Z-score (Ratio):
-13.952
Reference Allele:
A
-log10(P):
-100.197
MAF:
0.165
Beta (Num):
-0.110
Novel Locus:
No
SE (Num):
0.021
Beta (Den):
0.256
SE (Den):
0.022
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

De novo ceramide biosynthesis.3[1], 4[2]

Denominator Metabolite Explanation:

De novo ceramide biosynthesis.3[1], 4[2]

Ratio Explanation:

This ratio reflects the conversion of dihydroceramide (n-palmitoyl-sphinganine) to ceramide, a critical step in de novo sphingolipid synthesis, regulated by dihydroceramide desaturase.5[1], 6[2], 7[3]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered SGPP1 activity can disrupt the balance of sphingolipid precursors, impacting ceramide levels.1[1], 2[2] Dysregulated ceramide metabolism is linked to lipoprotein disorders and insulin resistance (affecting HbA1c and triglycerides), consistent with the observed phenotypes.8[3]

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