glycosyl-n-behenoyl-sphingadienine (d18:2/22:0)* to lactosyl-n-nervonoyl-sphingosine (d18:1/24:1)*

Numerator Metabolite

Metabolite Accession: GCST90200105
Name: glycosyl-n-behenoyl-sphingadienine (d18:2/22:0)*
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):
0.019
Effect Allele:
G
Z-score (Ratio):
19.744
Reference Allele:
C
-log10(P):
-198.131
MAF:
0.175
Beta (Num):
0.003
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):
0.317
Position:
47545141
SE (Ratio):
0.019
Effect Allele:
A
Z-score (Ratio):
16.554
Reference Allele:
C
-log10(P):
-140.060
MAF:
0.177
Beta (Num):
0.300
Novel Locus:
No
SE (Num):
0.020
Beta (Den):
-0.016
SE (Den):
0.020
No CNV overlap
rQTL cluster:
126
Reaction Distance:
NA
Closest Genes:
ATP10D CORIN COMMD8 GABRB1 NFXL1

LLM Analysis

Numerator Metabolite Explanation:

Glycosphingolipid metabolism.4[1]

Denominator Metabolite Explanation:

Glycosphingolipid metabolism.4[1], 5[2]

Ratio Explanation:

The ratio reflects the balance between a monoglycosylated ceramide (numerator) and a diglycosylated ceramide (denominator), a conversion process potentially influenced by ATP10D-mediated substrate transport.4[1], 1[2]

Ratio Evidence:

reaction where the ratio is shared through a pathway

Gene Ratio Phenotype Relationship:

ATP10D dysfunction likely alters red blood cell membrane composition by disrupting glycosphingolipid homeostasis.6[1], 7[2] This can impact red blood cell integrity, turnover, and function, leading to the observed changes in hematological traits like MCHC, RBC count, Hb, and HbA1c.8[3]

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