sphingomyelin (d18:1/18:1, d18:2/18:0) to sphingomyelin (d18:0/18:0, d19:0/17:0)*

Numerator Metabolite

Structure of sphingomyelin (d18:1/18:1, d18:2/18:0)
Metabolite Accession: GCST90199878
Name: sphingomyelin (d18:1/18:1, d18:2/18:0)
Hmdb Id: HMDB0012101
Super Pathway: NA
Sub Pathway: NA
Inchikey: NBEADXWAAWCCDG

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: rs7970695

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Clumped rQTL variant

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SNP Summary

Chr:
12
Beta (Ratio):
-0.159
Position:
121423376
SE (Ratio):
0.016
Effect Allele:
G
Z-score (Ratio):
-10.072
Reference Allele:
A
-log10(P):
-53.269
MAF:
0.382
Beta (Num):
-0.087
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.072
SE (Den):
0.016
No CNV overlap
rQTL cluster:
49
Reaction Distance:
NA
Closest Genes:
HNF1A AC079602.1 C12orf43 OASL SPPL3

Region: rs680379

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Clumped rQTL variant

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SNP Summary

Chr:
20
Beta (Ratio):
-0.163
Position:
12969400
SE (Ratio):
0.016
Effect Allele:
A
Z-score (Ratio):
-10.393
Reference Allele:
G
-log10(P):
-56.584
MAF:
0.385
Beta (Num):
-0.032
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.131
SE (Den):
0.016
No CNV overlap
rQTL cluster:
5
Reaction Distance:
NA
Closest Genes:
SPTLC3 ISM1 TASP1 ESF1 NDUFAF5

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.3[1], 4[2]

Denominator Metabolite Explanation:

Sphingolipid metabolism.5[1], 6[2]

Ratio Explanation:

This ratio reflects the balance between unsaturated and saturated sphingomyelins, likely influenced by the substrate preference of the SPTLC3-containing enzyme complex during synthesis.1[1], 7[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

SPTLC3 variation alters sphingolipid composition, affecting the balance between saturated and unsaturated species. This dysregulation is linked to increased risk for myocardial infarction and cholelithiasis, likely by impacting mitochondrial function in the heart and cholesterol metabolism related to gallstones.8[1], 9[2], 10[3], 11[4], 12[5]

Phenotype Driver:

Gene-centric:SPTLC3

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