stearoyl sphingomyelin (d18:1/18:0) to sphingomyelin (d18:0/20:0, d16:0/22:0)*

Numerator Metabolite

Structure of stearoyl sphingomyelin (d18:1/18:0)
Metabolite Accession: GCST90200335
Name: stearoyl sphingomyelin (d18:1/18:0)
Hmdb Id: HMDB0001348
Super Pathway: NA
Sub Pathway: NA
Inchikey: LKQLRGMMMAHREN

Denominator Metabolite

Metabolite Accession: GCST90200123
Name: sphingomyelin (d18:0/20:0, d16:0/22:0)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs10916301

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Clumped rQTL variant

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SNP Summary

Chr:
1
Beta (Ratio):
0.160
Position:
224294870
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
9.788
Reference Allele:
T
-log10(P):
-50.416
MAF:
0.400
Beta (Num):
0.045
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.115
SE (Den):
0.015
No CNV overlap
rQTL cluster:
153
Reaction Distance:
NA
Closest Genes:
FBXO28 DEGS1 AC138393.1 NVL CNIH4

Region: rs2244608

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Clumped rQTL variant

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SNP Summary

Chr:
12
Beta (Ratio):
-0.187
Position:
121416988
SE (Ratio):
0.017
Effect Allele:
G
Z-score (Ratio):
-10.806
Reference Allele:
A
-log10(P):
-61.002
MAF:
0.318
Beta (Num):
-0.072
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.115
SE (Den):
0.016
No CNV overlap
rQTL cluster:
49
Reaction Distance:
NA
Closest Genes:
HNF1A AC079602.1 C12orf43 OASL SPPL3

Region: rs17101394

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
0.250
Position:
64232386
SE (Ratio):
0.022
Effect Allele:
A
Z-score (Ratio):
11.582
Reference Allele:
G
-log10(P):
-69.750
MAF:
0.165
Beta (Num):
0.179
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
-0.071
SE (Den):
0.020
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid de novo biosynthesis

Denominator Metabolite Explanation:

Sphingolipid de novo biosynthesis

Ratio Explanation:

The ratio of stearoyl sphingomyelin (d18:1/18:0) to sphingomyelin (d18:0/...) reflects DEGS1 enzyme activity, which converts dihydroceramides (d18:0 backbone) to ceramides (d18:1 backbone).4[1], 7[2]

Ratio Evidence:

canonical reaction catalyzed by the enzyme

Gene Ratio Phenotype Relationship:

Altered DEGS1 activity, reflected by the sphingomyelin ratio, is linked to dyslipidemia and an increased risk for cardiovascular diseases, including atherosclerosis and coronary heart disease, potentially through effects on ceramide and sphingomyelin levels in lipoproteins and vascular tissue.8[1], 9[2], 10[3], 11[4]

Phenotype Driver:

Gene-centric:DEGS1

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