tricosanoyl sphingomyelin (d18:1/23:0)* to glycosyl ceramide (d18:1/20:0, d16:1/22:0)*

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: GCST90200145
Name: glycosyl ceramide (d18:1/20:0, d16:1/22:0)*
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):
0.219
Position:
8283819
SE (Ratio):
0.016
Effect Allele:
C
Z-score (Ratio):
13.818
Reference Allele:
A
-log10(P):
-98.332
MAF:
0.462
Beta (Num):
0.035
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.184
SE (Den):
0.016
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs686548

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):
-0.164
Position:
12973521
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
-10.570
Reference Allele:
T
-log10(P):
-58.453
MAF:
0.386
Beta (Num):
-0.049
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.115
SE (Den):
0.016
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid synthesis

Denominator Metabolite Explanation:

Sphingolipid metabolism

Ratio Explanation:

This ratio may reflect the balance between distinct ceramide utilization pathways, where CERS4-derived ceramides are directed towards sphingomyelin or glycosylceramide synthesis.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CERS4's role in synthesizing specific ceramides could influence downstream metabolic pathways. Altered CERS4 activity may affect the balance of sphingomyelin and glycosylceramide, potentially contributing to the associated phenotypes of polyneuropathy, cholelithiasis, and gout through disruptions in lipid signaling and metabolism.

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