stearoyl sphingomyelin (d18:1/18:0) to tricosanoyl sphingomyelin (d18:1/23:0)*

Numerator Metabolite

Structure of stearoyl sphingomyelin (d18:1/18:0)
Metabolite Accession: GCST90200335
Name: stearoyl sphingomyelin (d18:1/18:0)
Hmdb Id: HMDB0001348
Super Pathway: NA
Sub Pathway: NA
Inchikey: LKQLRGMMMAHREN

Denominator 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

Associated Genomic Regions

Region: rs1466448

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
-0.285
Position:
8289519
SE (Ratio):
0.019
Effect Allele:
C
Z-score (Ratio):
-14.713
Reference Allele:
A
-log10(P):
-111.162
MAF:
0.191
Beta (Num):
-0.230
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
0.055
SE (Den):
0.018
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs680379

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):
0.141
Position:
12969400
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
8.889
Reference Allele:
G
-log10(P):
-41.930
MAF:
0.385
Beta (Num):
0.092
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
-0.049
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:

This ratio reflects CERS4 activity, which synthesizes the C18:0 ceramide precursor for the numerator but not the C23:0 precursor for the denominator.6[1], 2[2], 3[3]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variants altering CERS4 expression likely modify the balance of sphingomyelin species.7[1] This altered sphingolipid profile is associated with cholelithiasis and elevated ALT, potentially by affecting cholesterol crystallization in bile.8[2], 9[3], 10[4], 11[5]

Phenotype Driver:

Gene-centric:CERS4

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