1-palmitoyl-2-palmitoleoyl-gpc (16:0/16:1)* to 1-myristoyl-2-palmitoyl-gpc (14:0/16:0)

Numerator Metabolite

Structure of 1-palmitoyl-2-palmitoleoyl-gpc (16:0/16:1)*
Metabolite Accession: GCST90200038
Name: 1-palmitoyl-2-palmitoleoyl-gpc (16:0/16:1)*
Hmdb Id: HMDB0007969
Super Pathway: NA
Sub Pathway: NA
Inchikey: QIBZFHLFHCIUOT

Denominator Metabolite

Structure of 1-myristoyl-2-palmitoyl-gpc (14:0/16:0)
Metabolite Accession: GCST90199653
Name: 1-myristoyl-2-palmitoyl-gpc (14:0/16:0)
Hmdb Id: HMDB0007869
Super Pathway: NA
Sub Pathway: NA
Inchikey: RFVFQQWKPSOBED

Associated Genomic Regions

Region: rs603424

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Clumped rQTL variant

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SNP Summary

Chr:
10
Beta (Ratio):
-0.125
Position:
102075479
SE (Ratio):
0.013
Effect Allele:
A
Z-score (Ratio):
-9.530
Reference Allele:
G
-log10(P):
-47.902
MAF:
0.176
Beta (Num):
-0.079
Novel Locus:
Yes ✔️
SE (Num):
0.020
Beta (Den):
0.046
SE (Den):
0.020
No CNV overlap
rQTL cluster:
67
Reaction Distance:
NA
Closest Genes:
PKD2L1 BLOC1S2 SCD CWF19L1 CHUK

Region: rs174561

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Clumped rQTL variant

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SNP Summary

Chr:
11
Beta (Ratio):
0.085
Position:
61582708
SE (Ratio):
0.011
Effect Allele:
C
Z-score (Ratio):
7.854
Reference Allele:
T
-log10(P):
-33.147
MAF:
0.303
Beta (Num):
0.064
Novel Locus:
Yes ✔️
SE (Num):
0.017
Beta (Den):
-0.022
SE (Den):
0.017
No CNV overlap
rQTL cluster:
62
Reaction Distance:
NA
Closest Genes:
FADS1 FADS2 FEN1 TMEM258 MYRF

Region: rs3134950

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Clumped rQTL variant

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SNP Summary

Chr:
6
Beta (Ratio):
0.081
Position:
32127477
SE (Ratio):
0.010
Effect Allele:
C
Z-score (Ratio):
7.879
Reference Allele:
A
-log10(P):
-33.343
MAF:
0.372
Beta (Num):
0.025
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
-0.056
SE (Den):
0.016
No CNV overlap
rQTL cluster:
107
Reaction Distance:
NA
Closest Genes:
PPT2 PPT2-EGFL8 EGFL8 PRRT1 AGPAT1

LLM Analysis

Numerator Metabolite Explanation:

Phospholipid biosynthesis, fatty acid desaturation.5[1], 6[2]

Denominator Metabolite Explanation:

Phospholipid biosynthesis.7[1], 8[2], 9[3]

Ratio Explanation:

This ratio directly reflects SCD enzymatic activity, comparing a phospholipid containing its product (palmitoleate, 16:1) to one with its precursor substrate (palmitate, 16:0).1[1], 4[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Genetic variation in the SCD gene alters desaturase activity, impacting the saturated to monounsaturated fatty acid balance.1[1], 4[2] This dysregulation is a known factor in developing cholelithiasis, type 2 diabetes, and ischaemic heart disease.10[3], 11[4], 12[5]

Phenotype Driver:

Gene-centric:SCD

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