n-palmitoyl-sphingosine (d18:1/16:0) to n-palmitoyl-sphinganine (d18:0/16:0)

Numerator Metabolite

Structure of n-palmitoyl-sphingosine (d18:1/16:0)
Metabolite Accession: GCST90200336
Name: n-palmitoyl-sphingosine (d18:1/16:0)
Hmdb Id: HMDB0004949
Super Pathway: NA
Sub Pathway: NA
Inchikey: YDNKGFDKKRUKPY

Denominator 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

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):
0.172
Position:
64232386
SE (Ratio):
0.020
Effect Allele:
A
Z-score (Ratio):
8.697
Reference Allele:
G
-log10(P):
-40.219
MAF:
0.164
Beta (Num):
0.060
Novel Locus:
Yes ✔️
SE (Num):
0.021
Beta (Den):
-0.112
SE (Den):
0.021
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism, de novo ceramide synthesis.4[1], 5[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism, de novo ceramide synthesis.4[1], 6[2]

Ratio Explanation:

The ratio of n-palmitoyl-sphingosine to its precursor n-palmitoyl-sphinganine reflects the activity of dihydroceramide desaturase (DEGS1) in the ceramide synthesis pathway.4[1], 7[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered SGPP1 function may modulate sphingolipid metabolism, reflected by the ceramide/dihydroceramide ratio.1[1], 2[2] Elevated ceramides are linked to insulin resistance and dyslipidemia, providing a plausible mechanism for the association with increased HbA1c and triglyceride levels.8[3], 9[4], 10[5], 11[6]

Phenotype Driver:

Metabolite-centric[n-palmitoyl-sphingosine (d18:1/16:0)]

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