sphingomyelin (d18:2/24:1, d18:1/24:2)* to glycosyl ceramide (d18:1/20:0, d16:1/22:0)*

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: 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):
0.242
Position:
8283819
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
13.826
Reference Allele:
A
-log10(P):
-98.438
MAF:
0.462
Beta (Num):
0.058
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: rs1321940

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.183
Position:
12959885
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
-10.678
Reference Allele:
G
-log10(P):
-59.616
MAF:
0.386
Beta (Num):
-0.067
Novel Locus:
No
SE (Num):
0.014
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 metabolism, ceramide synthesis.3[1], 4[2]

Denominator Metabolite Explanation:

Glycosphingolipid metabolism, ceramide metabolism.5[1], 6[2]

Ratio Explanation:

CERS4 synthesizes ceramides, which can be converted to either sphingomyelin or glycosylceramides, thus influencing the balance between these two lipid classes.3[1]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CERS4 variation influences the sphingomyelin to glycosyl ceramide ratio. Altered levels of these lipids, particularly sphingomyelin, have been linked to cholelithiasis and LDL cholesterol levels, and changes in ceramide metabolism can impact pathways related to gout and neuropathy.7[1], 8[2], 9[3], 10[4]

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