tricosanoyl sphingomyelin (d18:1/23:0)* to sphingomyelin (d18:1/21:0, d17:1/22:0, d16:1/23:0)*

Numerator Metabolite

Structure of tricosanoyl sphingomyelin (d18:1/23:0)*
Metabolite Accession: GCST90200034
Name: tricosanoyl sphingomyelin (d18:1/23:0)*
Hmdb Id: HMDB0012105
Super Pathway: NA
Sub Pathway: NA
Inchikey: SXZWBNWTCVLZJN

Denominator Metabolite

Metabolite Accession: GCST90200053
Name: sphingomyelin (d18:1/21:0, d17:1/22:0, d16:1/23:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs8008068

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
14
Beta (Ratio):
-0.287
Position:
64233717
SE (Ratio):
0.014
Effect Allele:
G
Z-score (Ratio):
-20.594
Reference Allele:
A
-log10(P):
-215.312
MAF:
0.166
Beta (Num):
0.022
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
0.309
SE (Den):
0.019
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

Region: rs4814176

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

Loading Ratio Plot...

Loading Numerator Plot...

Loading Denominator Plot...

SNP Summary

Chr:
20
Beta (Ratio):
-0.205
Position:
12959398
SE (Ratio):
0.011
Effect Allele:
T
Z-score (Ratio):
-18.933
Reference Allele:
C
-log10(P):
-182.396
MAF:
0.386
Beta (Num):
-0.048
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.156
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 metabolism.4[1], 5[2]

Denominator Metabolite Explanation:

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

Ratio Explanation:

The ratio reflects altered SPTLC3 activity, comparing a very-long-chain (C23:0) sphingomyelin to other long-chain sphingomyelins, indicating a shift in sphingolipid composition.6[1], 7[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Variants in SPTLC3 are associated with altered sphingolipid profiles and a risk of cholelithiasis.8[1], 9[2], 10[3] Altered sphingolipid and ceramide levels can impact lipoprotein metabolism and bile composition, providing a plausible mechanism for the development of gallstones and dyslipidemia.11[4], 12[5], 13[6]

Phenotype Driver:

Gene-centric:SPTLC3

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