1-(1-enyl-palmitoyl)-2-palmitoyl-gpc (p-16:0/16:0)* to lactosyl-n-nervonoyl-sphingosine (d18:1/24:1)*

Numerator Metabolite

Structure of 1-(1-enyl-palmitoyl)-2-palmitoyl-gpc (p-16:0/16:0)*
Metabolite Accession: GCST90200083
Name: 1-(1-enyl-palmitoyl)-2-palmitoyl-gpc (p-16:0/16:0)*
Hmdb Id: HMDB0011206
Super Pathway: NA
Sub Pathway: NA
Inchikey: PEWXKAOBUSBJLD

Denominator Metabolite

Structure of lactosyl-n-nervonoyl-sphingosine (d18:1/24:1)*
Metabolite Accession: GCST90200098
Name: lactosyl-n-nervonoyl-sphingosine (d18:1/24:1)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: MKOKWBRPIBQYJJ

Associated Genomic Regions

Region: rs1077989

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Clumped rQTL variant

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SNP Summary

Chr:
14
Beta (Ratio):
-0.386
Position:
67975822
SE (Ratio):
0.014
Effect Allele:
C
Z-score (Ratio):
-27.974
Reference Allele:
A
-log10(P):
-394.819
MAF:
0.476
Beta (Num):
-0.357
Novel Locus:
No
SE (Num):
0.015
Beta (Den):
0.029
SE (Den):
0.015
No CNV overlap
rQTL cluster:
46
Reaction Distance:
NA
Closest Genes:
TMEM229B PLEKHH1 PIGH PLEK2 ARG2

Region: rs4147929

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):
0.375
Position:
1063443
SE (Ratio):
0.018
Effect Allele:
A
Z-score (Ratio):
20.677
Reference Allele:
G
-log10(P):
-217.016
MAF:
0.174
Beta (Num):
0.011
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
-0.365
SE (Den):
0.020
No CNV overlap
rQTL cluster:
12
Reaction Distance:
NA
Closest Genes:
ABCA7 HMHA1 POLR2E CNN2 GPX4

LLM Analysis

Numerator Metabolite Explanation:

Plasmalogen biosynthesis.4[1], 5[2]

Denominator Metabolite Explanation:

Glycosphingolipid metabolism.6[1], 7[2], 8[3]

Ratio Explanation:

The ratio represents a balance between membrane phospholipids (plasmalogen) and glycosphingolipids (lactosylceramide), potentially influenced by TMEM229B's role in regulating lipid homeostasis.9[1], 2[2]

Ratio Evidence:

metabolites related through biology

Gene Ratio Phenotype Relationship:

TMEM229B is associated with altered levels of plasmalogens and lactosylceramides, both crucial components of the red blood cell membrane.9[1], 10[2] This altered lipid composition likely impacts red blood cell integrity and function, leading to the observed phenotypes like changes in RBC count, hemoglobin, and MCV.

Phenotype Driver:

Gene-centric:TMEM229B

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