palmitoyl sphingomyelin (d18:1/16:0) to sphingomyelin (d18:1/17:0, d17:1/18:0, d19:1/16:0)

Numerator Metabolite

Structure of palmitoyl sphingomyelin (d18:1/16:0)
Metabolite Accession: GCST90199876
Name: palmitoyl sphingomyelin (d18:1/16:0)
Hmdb Id: HMDB0010169
Super Pathway: NA
Sub Pathway: NA
Inchikey: RWKUXQNLWDTSLO

Denominator Metabolite

Metabolite Accession: GCST90200047
Name: sphingomyelin (d18:1/17:0, d17:1/18:0, d19:1/16:0)
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs1466448

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.129
Position:
8289519
SE (Ratio):
0.016
Effect Allele:
C
Z-score (Ratio):
7.903
Reference Allele:
A
-log10(P):
-33.536
MAF:
0.191
Beta (Num):
0.058
Novel Locus:
Yes ✔️
SE (Num):
0.019
Beta (Den):
-0.071
SE (Den):
0.019
No CNV overlap
rQTL cluster:
11
Reaction Distance:
NA
Closest Genes:
CERS4 FBN3 CD320 NDUFA7 NDUFA7

Region: rs364585

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.111
Position:
12962718
SE (Ratio):
0.013
Effect Allele:
A
Z-score (Ratio):
-8.346
Reference Allele:
G
-log10(P):
-37.187
MAF:
0.384
Beta (Num):
-0.024
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.086
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 synthesis3[1], 4[2]

Denominator Metabolite Explanation:

Sphingolipid synthesis5[1], 6[2]

Ratio Explanation:

This ratio contrasts a common even-chain sphingomyelin with less abundant odd-chain sphingomyelins, potentially reflecting alterations in the substrate availability for ceramide synthesis.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Genetic variants in ISM1, a regulator of lipid metabolism, may alter the balance between even- and odd-chain sphingomyelin synthesis.2[1] This dysregulation is associated with cholelithiasis and changes in ALT and LDL-cholesterol, possibly through altered bile composition or liver inflammation.7[2], 8[3], 9[4]

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