sphingomyelin (d18:2/16:0, d18:1/16:1)* to glycosyl-n-stearoyl-sphingosine (d18:1/18:0)

Numerator Metabolite

Metabolite Accession: GCST90199947
Name: sphingomyelin (d18:2/16:0, d18:1/16:1)*
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):
0.154
Position:
8283819
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
9.279
Reference Allele:
A
-log10(P):
-45.516
MAF:
0.462
Beta (Num):
0.038
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: rs686548

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.142
Position:
12973521
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
-8.765
Reference Allele:
T
-log10(P):
-40.818
MAF:
0.387
Beta (Num):
-0.075
Novel Locus:
Yes ✔️
SE (Num):
0.015
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 biosynthesis

Denominator Metabolite Explanation:

Sphingolipid biosynthesis

Ratio Explanation:

This ratio may reflect CERS4's influence on ceramide utilization, directing precursors toward either sphingomyelin or glycosylsphingosine synthesis, thereby altering membrane and signaling lipid pools.4[1], 5[2], 6[3]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered CERS4 function, supported by eQTL colocalization, likely shifts the balance of specific sphingolipids.1[1], 2[2], 3[3] This dysregulation is linked to polyneuropathy, cholelithiasis, and gout, potentially through impacts on nerve cell membranes, cholesterol metabolism, and inflammatory pathways which are known to involve sphingolipids.7[4], 8[5], 9[6], 10[7], 11[8]

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