sphingomyelin (d18:2/24:1, d18:1/24:2)* to n-palmitoyl-heptadecasphingosine (d17:1/16:0)*

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: GCST90200115
Name: n-palmitoyl-heptadecasphingosine (d17:1/16:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs364585

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.169
Position:
12962718
SE (Ratio):
0.020
Effect Allele:
A
Z-score (Ratio):
-8.525
Reference Allele:
G
-log10(P):
-38.716
MAF:
0.384
Beta (Num):
-0.068
Novel Locus:
Yes ✔️
SE (Num):
0.014
Beta (Den):
0.101
SE (Den):
0.017
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.5[1]

Denominator Metabolite Explanation:

Ceramide (de novo) synthesis, Sphingolipid metabolism.5[1], 6[2], 7[3]

Ratio Explanation:

The ratio reflects sphingomyelin synthesis from ceramide precursors; lower levels may indicate altered sphingolipid metabolism, potentially influenced by ISM1's regulatory roles.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Elevated LDL-cholesterol is a risk factor for cholelithiasis.8[1], 9[2] Altered sphingolipid metabolism, potentially modulated by ISM1, can influence both LDL levels and is independently associated with gallstone formation, suggesting a link between ISM1, dyslipidemia, and cholelithiasis.10[3], 11[4], 12[5]

Phenotype Driver:

Gene-centric:ISM1

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