1-palmitoyl-2-linoleoyl-gpc (16:0/18:2) to 1-stearoyl-2-linoleoyl-gpi (18:0/18:2)

Numerator Metabolite

Structure of 1-palmitoyl-2-linoleoyl-gpc (16:0/18:2)
Metabolite Accession: GCST90200330
Name: 1-palmitoyl-2-linoleoyl-gpc (16:0/18:2)
Hmdb Id: HMDB0007973
Super Pathway: NA
Sub Pathway: NA
Inchikey: JLPULHDHAOZNQI

Denominator Metabolite

Structure of 1-stearoyl-2-linoleoyl-gpi (18:0/18:2)
Metabolite Accession: GCST90200067
Name: 1-stearoyl-2-linoleoyl-gpi (18:0/18:2)
Hmdb Id: HMDB0009809
Super Pathway: NA
Sub Pathway: NA
Inchikey: KZVRAFHIKMDULK

Associated Genomic Regions

Region: rs173539

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Clumped rQTL variant

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SNP Summary

Chr:
16
Beta (Ratio):
0.121
Position:
56988044
SE (Ratio):
0.014
Effect Allele:
T
Z-score (Ratio):
8.510
Reference Allele:
C
-log10(P):
-38.593
MAF:
0.334
Beta (Num):
0.090
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
-0.031
SE (Den):
0.016
No CNV overlap
rQTL cluster:
26
Reaction Distance:
NA
Closest Genes:
CETP HERPUD1 NLRC5 SLC12A3 NUP93

Region: rs8736

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):
-0.223
Position:
54677189
SE (Ratio):
0.014
Effect Allele:
T
Z-score (Ratio):
-16.021
Reference Allele:
C
-log10(P):
-131.341
MAF:
0.435
Beta (Num):
-0.013
Novel Locus:
No
SE (Num):
0.016
Beta (Den):
0.210
SE (Den):
0.015
No CNV overlap
rQTL cluster:
6
Reaction Distance:
NA
Closest Genes:
MBOAT7 TMC4 LENG1 TSEN34 CNOT3

LLM Analysis

Numerator Metabolite Explanation:

Glycerophospholipid metabolism

Denominator Metabolite Explanation:

Phosphatidylinositol biosynthesis

Ratio Explanation:

This ratio contrasts a major phosphatidylcholine (PC) with a phosphatidylinositol (PI), suggesting an alteration in glycerophospholipid head group metabolism, potentially influenced by TMC4's role in membrane transport.

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

Genetic variants in TMC4 are linked to changes in the PC to PI ratio; this altered membrane lipid profile is causally associated with an increased risk for macular degeneration, as evidenced by Mendelian randomization.5[1]

Phenotype Driver:

Metabolite-centric[both]

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