palmitoyl sphingomyelin (d18:1/16:0) to sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*

Numerator Metabolite

Structure of palmitoyl sphingomyelin (d18:1/16:0)
Metabolite Accession: GCST90199876
Name: palmitoyl sphingomyelin (d18:1/16:0)
Hmdb Id: HMDB0010169
Super Pathway: NA
Sub Pathway: NA
Inchikey: RWKUXQNLWDTSLO

Denominator Metabolite

Structure of sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Metabolite Accession: GCST90200017
Name: sphingomyelin (d17:1/16:0, d18:1/15:0, d16:1/17:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: LQINJRUGTUOHGS

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):
-0.107
Position:
12962718
SE (Ratio):
0.012
Effect Allele:
A
Z-score (Ratio):
-8.586
Reference Allele:
G
-log10(P):
-39.253
MAF:
0.384
Beta (Num):
-0.024
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.083
SE (Den):
0.015
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid biosynthesis

Denominator Metabolite Explanation:

Sphingolipid biosynthesis

Ratio Explanation:

This ratio reflects the substrate preference of serine palmitoyltransferase (SPTLC3), comparing the synthesis of common even-chain sphingomyelins to atypical odd-chain sphingomyelins.

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

SPTLC3 variants alter sphingolipid composition, impacting the ratio of typical to atypical sphingomyelins.3[1], 4[2] Altered sphingolipid profiles, including those of sphingomyelin, are linked to dyslipidemia and increased cholesterol saturation in bile, which are primary risk factors for developing cholelithiasis (gallstones) and elevated ALT.3[3], 5[4]

Phenotype Driver:

Metabolite-centric[both]

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