n6-methyllysine to n6,n6-dimethyllysine

Numerator Metabolite

Structure of n6-methyllysine
Metabolite Accession: GCST90200689
Name: n6-methyllysine
Hmdb Id: HMDB0002038
Super Pathway: NA
Sub Pathway: NA
Inchikey: PQNASZJZHFPQLE

Denominator Metabolite

Structure of n6,n6-dimethyllysine
Metabolite Accession: GCST90200696
Name: n6,n6-dimethyllysine
Hmdb Id: HMDB0013287
Super Pathway: NA
Sub Pathway: NA
Inchikey: XXEWFEBMSGLYBY

Associated Genomic Regions

Region: rs7252778

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:
19
Beta (Ratio):
-0.128
Position:
33360369
SE (Ratio):
0.007
Effect Allele:
C
Z-score (Ratio):
-18.063
Reference Allele:
A
-log10(P):
-166.266
MAF:
0.396
Beta (Num):
-0.142
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
-0.014
SE (Den):
0.016
No CNV overlap
rQTL cluster:
9
Reaction Distance:
NA
Closest Genes:
SLC7A9 CEP89 TDRD12 C19orf40 RHPN2

LLM Analysis

Numerator Metabolite Explanation:

Lysine degradation, Protein methylation.5[1], 6[2], 7[3]

Denominator Metabolite Explanation:

Lysine degradation, Carnitine biosynthesis.8[1], 9[2]

Ratio Explanation:

This ratio reflects the sequential methylation of lysine, where n6-methyllysine is a precursor to n6,n6-dimethyllysine, a key step in post-translational modifications and carnitine biosynthesis.5[1], 8[2], 10[3]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

A variant in SLC7A9, a renal amino acid transporter for lysine, is associated with gout, altered red blood cell counts, and kidney function markers.11[1], 12[2], 13[3] Altered lysine transport likely impacts downstream lysine metabolism and related phenotypes like gout.14[4], 15[5], 16[6]

Phenotype Driver:

Gene-centric:SLC7A9

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