sphingomyelin (d18:2/24:1, d18:1/24:2)* to glycosyl-n-stearoyl-sphingosine (d18:1/18:0)

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: GCST90199846
Name: glycosyl-n-stearoyl-sphingosine (d18:1/18:0)
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs1871194

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.173
Position:
8283819
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
10.342
Reference Allele:
A
-log10(P):
-56.047
MAF:
0.462
Beta (Num):
0.058
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.115
SE (Den):
0.016
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs1321940

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.135
Position:
12959885
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
-8.203
Reference Allele:
G
-log10(P):
-35.987
MAF:
0.386
Beta (Num):
-0.067
Novel Locus:
Yes ✔️
SE (Num):
0.014
Beta (Den):
0.067
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.3[1], 4[2]

Denominator Metabolite Explanation:

Sphingolipid/glycosphingolipid metabolism.5[1], 6[2]

Ratio Explanation:

The ratio reflects ceramide synthesis (CERS4) versus its glycosylation. An altered ratio may indicate a shift in sphingolipid composition, affecting downstream signaling and membrane structure.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CERS4 variants are associated with altered sphingolipid levels.7[1] Dysregulated sphingolipid metabolism, particularly involving ceramides and related species, is linked to cholelithiasis, gout, and neuropathies, potentially through inflammatory pathways and altered cell signaling.8[2], 9[3], 10[4], 11[5], 7[6]

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