stearoyl sphingomyelin (d18:1/18:0) to sphingomyelin (d18:0/18:0, d19:0/17:0)*

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

Structure of sphingomyelin (d18:0/18:0, d19:0/17:0)*
Metabolite Accession: GCST90200056
Name: sphingomyelin (d18:0/18:0, d19:0/17:0)*
Hmdb Id: HMDB0012087
Super Pathway: NA
Sub Pathway: NA
Inchikey: JCELSEVNSMXGKA

Associated Genomic Regions

Region: rs11065384

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Clumped rQTL variant

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SNP Summary

Chr:
12
Beta (Ratio):
-0.159
Position:
121423285
SE (Ratio):
0.015
Effect Allele:
T
Z-score (Ratio):
-10.604
Reference Allele:
C
-log10(P):
-58.818
MAF:
0.310
Beta (Num):
-0.075
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.084
SE (Den):
0.017
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):
0.258
Position:
64232386
SE (Ratio):
0.019
Effect Allele:
A
Z-score (Ratio):
13.820
Reference Allele:
G
-log10(P):
-98.349
MAF:
0.165
Beta (Num):
0.179
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
-0.079
SE (Den):
0.021
No CNV overlap
rQTL cluster:
47
Reaction Distance:
NA
Closest Genes:
SGPP1 SYNE2 WDR89 PPP2R5E ESR2

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism, fatty acid desaturation.7[1], 8[2], 9[3], 10[4]

Denominator Metabolite Explanation:

Sphingolipid metabolism.11[1], 12[2], 13[3]

Ratio Explanation:

This ratio likely reflects stearoyl-CoA desaturase (SCD) activity, converting the saturated C18:0 fatty acid in sphingomyelin to the monounsaturated C18:1 form.10[1], 14[2], 15[3]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

The HNF1A variant likely alters its transcriptional control over lipid and glucose metabolism.3[1], 5[2] This dysregulation, reflected by the sphingomyelin ratio indicating SCD activity, contributes to a broad metabolic phenotype including altered liver enzymes (GGT, ALP), dyslipidemia, and impaired glycemic control (HbA1c).16[3], 17[4], 18[5]

Phenotype Driver:

Gene-centric:HNF1A

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