sphingomyelin (d18:2/24:1, d18:1/24:2)* to sphingomyelin (d18:1/19:0, d19:1/18:0)*

Numerator Metabolite

Metabolite Accession: GCST90200040
Name: sphingomyelin (d18:2/24:1, d18:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Metabolite Accession: GCST90200131
Name: sphingomyelin (d18:1/19:0, d19:1/18:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs1466448

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.266
Position:
8289519
SE (Ratio):
0.020
Effect Allele:
C
Z-score (Ratio):
13.209
Reference Allele:
A
-log10(P):
-90.054
MAF:
0.192
Beta (Num):
0.075
Novel Locus:
No
SE (Num):
0.018
Beta (Den):
-0.191
SE (Den):
0.018
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs364585

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.268
Position:
12962718
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
-16.345
Reference Allele:
G
-log10(P):
-136.599
MAF:
0.384
Beta (Num):
-0.068
Novel Locus:
No
SE (Num):
0.014
Beta (Den):
0.199
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:

The ratio reflects differential activity of ceramide and sphingomyelin synthesis enzymes. SPTLC3 influences the sphingoid backbone, while CERS4 determines the N-acyl chain length.5[1], 2[2], 6[3]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Genetic variants in SPTLC3 are associated with altered plasma sphingolipid profiles and risk for cholelithiasis.7[1], 8[2], 9[3] Altered sphingomyelin composition, influenced by SPTLC3 and potentially CERS4 activity, may affect cholesterol solubility in bile and LDL metabolism, contributing to gallstone formation and changes in LDL-C and ALT.10[4], 11[5], 12[6], 13[7], 14[8]

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