glycosyl ceramide (d18:2/24:1, d18:1/24:2)* to lactosyl-n-nervonoyl-sphingosine (d18:1/24:1)*

Numerator Metabolite

Metabolite Accession: GCST90200118
Name: glycosyl ceramide (d18:2/24:1, d18:1/24:2)*
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

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: rs3752246

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Clumped rQTL variant

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SNP Summary

Chr:
19
Beta (Ratio):
0.374
Position:
1056492
SE (Ratio):
0.017
Effect Allele:
G
Z-score (Ratio):
21.922
Reference Allele:
C
-log10(P):
-243.592
MAF:
0.175
Beta (Num):
0.004
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
-0.370
SE (Den):
0.020
No CNV overlap
rQTL cluster:
12
Reaction Distance:
NA
Closest Genes:
ABCA7 HMHA1 CNN2 POLR2E TMEM259

Region: rs35818294

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Clumped rQTL variant

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SNP Summary

Chr:
4
Beta (Ratio):
0.327
Position:
47545141
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
18.973
Reference Allele:
C
-log10(P):
-183.162
MAF:
0.177
Beta (Num):
0.311
Novel Locus:
No
SE (Num):
0.019
Beta (Den):
-0.016
SE (Den):
0.020
No CNV overlap
rQTL cluster:
126
Reaction Distance:
NA
Closest Genes:
ATP10D CORIN COMMD8 GABRB1 NFXL1

Region: rs1045989

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Clumped rQTL variant

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SNP Summary

Chr:
9
Beta (Ratio):
-0.112
Position:
114696488
SE (Ratio):
0.013
Effect Allele:
A
Z-score (Ratio):
-8.348
Reference Allele:
C
-log10(P):
-37.207
MAF:
0.417
Beta (Num):
-0.051
Novel Locus:
Yes ✔️
SE (Num):
0.015
Beta (Den):
0.061
SE (Den):
0.016
No CNV overlap
rQTL cluster:
80
Reaction Distance:
NA
Closest Genes:
UGCG SUSD1 C9orf84 GNG10 DNAJC25-GNG10

LLM Analysis

Numerator Metabolite Explanation:

Sphingolipid metabolism.4[1], 5[2], 6[3]

Denominator Metabolite Explanation:

Sphingolipid metabolism.7[1], 8[2], 9[3]

Ratio Explanation:

This ratio reflects the conversion of glucosylceramide to lactosylceramide, a key step in glycosphingolipid synthesis.7[1], 10[2] ATP10D function may modulate substrate availability.1[3]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

Altered ATP10D expression likely modifies the GlcCer/LacCer ratio, impacting cell membrane composition and signaling.1[1], 11[2] This plausibly affects red blood cell characteristics, monocyte counts, and glucose metabolism (HbA1c), consistent with ATP10D's known functions in insulin sensitivity.12[3], 13[4], 14[5]

Phenotype Driver:

Gene-centric:ATP10D

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