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

Numerator 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

Denominator Metabolite

Structure of betaine
Metabolite Accession: GCST90200425
Name: betaine
Hmdb Id: HMDB0000043
Super Pathway: NA
Sub Pathway: NA
Inchikey: KWIUHFFTVRNATP

Associated Genomic Regions

Region: rs1047891

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Clumped rQTL variant

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SNP Summary

Chr:
2
Beta (Ratio):
0.264
Position:
211540507
SE (Ratio):
0.023
Effect Allele:
A
Z-score (Ratio):
11.717
Reference Allele:
C
-log10(P):
-71.333
MAF:
0.311
Beta (Num):
0.108
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.156
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:

Glycosphingolipid metabolism5[1], 6[2]

Denominator Metabolite Explanation:

Betaine metabolism, One-carbon metabolism7[1], 8[2]

Ratio Explanation:

Impaired CPS1 function can disrupt nitrogen balance, potentially affecting both sphingolipid and betaine metabolism, although a direct link is not established.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

CPS1 dysfunction is linked to hyperammonemia, which can cause renal failure. Altered CPS1 activity is also associated with cholelithiasis, potentially through disrupted lipid metabolism or altered bile composition, linking the gene to the observed kidney and gallbladder phenotypes.9[1], 10[2], 11[3]

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