n-palmitoyl-sphinganine (d18:0/16:0) to ceramide (d18:1/17:0, d17:1/18:0)*

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: GCST90200121
Name: ceramide (d18:1/17:0, d17:1/18:0)*
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):
-0.261
Position:
64232386
SE (Ratio):
0.028
Effect Allele:
A
Z-score (Ratio):
-9.465
Reference Allele:
G
-log10(P):
-47.276
MAF:
0.164
Beta (Num):
-0.112
Novel Locus:
Yes ✔️
SE (Num):
0.021
Beta (Den):
0.148
SE (Den):
0.024
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.3[1]

Denominator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2]

Ratio Explanation:

This ratio reflects the activity of ceramide synthesis, where n-palmitoyl-sphinganine is a precursor to dihydroceramides, which are then converted to ceramides.

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered SGPP1 activity can disrupt the balance of sphingolipids, contributing to insulin resistance and dyslipidemia, which are reflected in elevated HbA1c and triglyceride levels.6[1], 7[2], 8[3], 9[4]

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