5-methylthioadenosine (mta) to glycosyl-n-(2-hydroxynervonoyl)-sphingosine (d18:1/24:1(2oh))*

Numerator Metabolite

Structure of 5-methylthioadenosine (mta)
Metabolite Accession: GCST90200359
Name: 5-methylthioadenosine (mta)
Hmdb Id: HMDB0001173
Super Pathway: NA
Sub Pathway: NA
Inchikey: WUUGFSXJNOTRMR

Denominator Metabolite

Metabolite Accession: GCST90200117
Name: glycosyl-n-(2-hydroxynervonoyl)-sphingosine (d18:1/24:1(2oh))*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs1047891

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:
2
Beta (Ratio):
-0.215
Position:
211540507
SE (Ratio):
0.023
Effect Allele:
A
Z-score (Ratio):
-9.483
Reference Allele:
C
-log10(P):
-47.448
MAF:
0.310
Beta (Num):
-0.107
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.108
SE (Den):
0.016
No CNV overlap
rQTL cluster:
140
Reaction Distance:
NA
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

Methionine salvage, polyamine synthesis.8[1], 9[2], 10[3], 11[4], 12[5]

Denominator Metabolite Explanation:

Sphingolipid metabolism.13[1]

Ratio Explanation:

The ratio may reflect altered urea cycle function (CPS1) and unrelated changes in sphingolipid metabolism, but a direct functional link is not established.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CPS1 dysfunction, suggested by the missense variant, can impair the urea cycle, leading to ammonia buildup and contributing to kidney disease.1[1], 2[2], 4[3], 14[4], 15[5] The association with cholelithiasis might be a secondary effect of the overall metabolic disturbance.6[6], 7[7]

Phenotype Driver:

Gene-centric:CPS1

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