serine to betaine

Numerator Metabolite

Structure of serine
Metabolite Accession: GCST90200415
Name: serine
Hmdb Id: HMDB0000187
Super Pathway: NA
Sub Pathway: NA
Inchikey: MTCFGRXMJLQNBG

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

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):
0.361
Position:
211540507
SE (Ratio):
0.020
Effect Allele:
A
Z-score (Ratio):
17.676
Reference Allele:
C
-log10(P):
-159.326
MAF:
0.310
Beta (Num):
0.205
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.156
SE (Den):
0.016
No CNV overlap
rQTL cluster:
140
Reaction Distance:
3.0
Closest Genes:
CPS1 LANCL1 MYL1 ACADL KANSL1L

LLM Analysis

Numerator Metabolite Explanation:

Glycolysis, One-carbon metabolism, Gluconeogenesis.5[1], 6[2], 7[3], 8[4]

Denominator Metabolite Explanation:

Choline oxidation, Methionine cycle.9[1], 10[2], 11[3], 12[4]

Ratio Explanation:

CPS1 dysfunction can alter nitrogen balance, potentially impacting glycine levels, which is interconnected with betaine through one-carbon metabolism, thus affecting this ratio.13[1], 14[2], 15[3], 16[4]

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

CPS1 variants are associated with altered nitrogen metabolism and ammonia detoxification, directly impacting kidney function.17[1], 18[2], 19[3] The subsequent changes in glycine and betaine, key players in methyl group metabolism and osmoregulation, further link to renal and cholelithiasis phenotypes.13[4], 17[5], 20[6]

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