sphingomyelin (d18:1/22:2, d18:2/22:1, d16:1/24:2)* to 1,2-dipalmitoyl-gpc (16:0/16:0)

Numerator Metabolite

Metabolite Accession: GCST90200013
Name: sphingomyelin (d18:1/22:2, d18:2/22:1, d16:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Denominator Metabolite

Structure of 1,2-dipalmitoyl-gpc (16:0/16:0)
Metabolite Accession: GCST90199660
Name: 1,2-dipalmitoyl-gpc (16:0/16:0)
Hmdb Id: HMDB0000564
Super Pathway: NA
Sub Pathway: NA
Inchikey: KILNVBDSWZSGLL

Associated Genomic Regions

Region: rs102275

Click a 'Plot' button in the tables to the right to view a locus plot here.

Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
0.294
Position:
61557803
SE (Ratio):
0.018
Effect Allele:
C
Z-score (Ratio):
16.692
Reference Allele:
T
-log10(P):
-142.360
MAF:
0.347
Beta (Num):
0.073
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
-0.221
SE (Den):
0.016
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
TMEM258 MYRF FEN1 FADS2 FADS1

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism, ceramide synthesis.4[1], 5[2]

Denominator Metabolite Explanation:

Glycerophospholipid metabolism, Kennedy pathway.6[1], 7[2]

Ratio Explanation:

The ratio reflects FADS1-mediated desaturation activity leading to polyunsaturated sphingomyelins relative to the synthesis of saturated dipalmitoyl-GPC, a major membrane phospholipid.8[1], 9[2], 7[3]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

Genetic variation in FADS1 alters fatty acid desaturation, changing the balance of polyunsaturated sphingomyelins to saturated phospholipids.10[1], 11[2], 12[3], 13[4] This lipid profile shift is strongly associated with dyslipidemia, gallstone formation (cholelithiasis), and increased risk for type 2 diabetes and cardiovascular disease.10[5], 8[6], 14[7], 15[8], 16[9]

Phenotype Driver:

Gene-centric:FADS1

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