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

Numerator Metabolite

Structure of sphingomyelin (d18:1/24:1, d18:2/24:0)*
Metabolite Accession: GCST90199972
Name: sphingomyelin (d18:1/24:1, d18:2/24:0)*
Hmdb Id: HMDB0012107
Super Pathway: NA
Sub Pathway: NA
Inchikey: WKZHECFHXLTOLJ

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):
0.235
Position:
8283819
SE (Ratio):
0.018
Effect Allele:
C
Z-score (Ratio):
13.275
Reference Allele:
A
-log10(P):
-90.936
MAF:
0.461
Beta (Num):
0.051
Novel Locus:
No
SE (Num):
0.016
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):
-0.163
Position:
12959885
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
-9.408
Reference Allele:
G
-log10(P):
-46.737
MAF:
0.386
Beta (Num):
-0.047
Novel Locus:
No
SE (Num):
0.016
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.4[1], 5[2]

Denominator Metabolite Explanation:

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

Ratio Explanation:

The ratio reflects the balance between two major ceramide-derived sphingolipids. CERS4 generates the ceramide precursors for both pathways.1[1], 7[2], 8[3], 9[4]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CERS4 variants are associated with altered levels of sphingomyelin and glycosylceramide precursors, as well as with cholelithiasis.7[1], 10[2] Dysregulation of sphingolipid metabolism, potentially influenced by CERS4, may contribute to gallstone formation by altering bile composition.11[3], 12[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