pregnanediol-3-glucuronide to 5alpha-pregnan-3beta,20alpha-diol monosulfate (2)

Numerator Metabolite

Structure of pregnanediol-3-glucuronide
Metabolite Accession: GCST90199917
Name: pregnanediol-3-glucuronide
Hmdb Id: HMDB0010318
Super Pathway: NA
Sub Pathway: NA
Inchikey: ZFFFJLDTCLJDHL

Denominator Metabolite

Metabolite Accession: GCST90199854
Name: 5alpha-pregnan-3beta,20alpha-diol monosulfate (2)
Hmdb Id: NA
Super Pathway: NA
Sub Pathway: NA
Inchikey: NA

Associated Genomic Regions

Region: rs3750568

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Clumped rQTL variant

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SNP Summary

Chr:
10
Beta (Ratio):
-0.159
Position:
5247631
SE (Ratio):
0.017
Effect Allele:
A
Z-score (Ratio):
-9.141
Reference Allele:
G
-log10(P):
-44.229
MAF:
0.149
Beta (Num):
-0.050
Novel Locus:
Yes ✔️
SE (Num):
0.022
Beta (Den):
0.109
SE (Den):
0.022
No CNV overlap
rQTL cluster:
76
Reaction Distance:
NA
Closest Genes:
AKR1C4 AKR1CL1 AKR1C3 UCN3 AKR1C2

Region: rs4881413

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Clumped rQTL variant

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SNP Summary

Chr:
10
Beta (Ratio):
-0.156
Position:
5258450
SE (Ratio):
0.017
Effect Allele:
T
Z-score (Ratio):
-8.949
Reference Allele:
G
-log10(P):
-42.472
MAF:
0.150
Beta (Num):
-0.047
Novel Locus:
Yes ✔️
SE (Num):
0.022
Beta (Den):
0.109
SE (Den):
0.022
No CNV overlap
rQTL cluster:
217
Reaction Distance:
NA
Closest Genes:
AKR1C4 AKR1CL1 AKR1C3 UCN3 TUBAL3

Region: rs2151901

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Clumped rQTL variant

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SNP Summary

Chr:
10
Beta (Ratio):
-0.156
Position:
5262965
SE (Ratio):
0.017
Effect Allele:
C
Z-score (Ratio):
-8.946
Reference Allele:
A
-log10(P):
-42.445
MAF:
0.150
Beta (Num):
-0.047
Novel Locus:
Yes ✔️
SE (Num):
0.022
Beta (Den):
0.109
SE (Den):
0.022
No CNV overlap
rQTL cluster:
285
Reaction Distance:
NA
Closest Genes:
AKR1C4 AKR1CL1 AKR1C3 UCN3 TUBAL3

Region: rs4148415

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Clumped rQTL variant

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SNP Summary

Chr:
17
Beta (Ratio):
-0.108
Position:
48752600
SE (Ratio):
0.013
Effect Allele:
T
Z-score (Ratio):
-8.373
Reference Allele:
C
-log10(P):
-37.422
MAF:
0.355
Beta (Num):
-0.102
Novel Locus:
Yes ✔️
SE (Num):
0.016
Beta (Den):
0.005
SE (Den):
0.016
No CNV overlap
rQTL cluster:
19
Reaction Distance:
NA
Closest Genes:
ABCC3 ANKRD40 LUC7L3 CACNA1G SPATA20

LLM Analysis

Numerator Metabolite Explanation:

Progesterone metabolism, Steroid biosynthesis

Denominator Metabolite Explanation:

Steroid hormone metabolism, Androgen and estrogen metabolism

Ratio Explanation:

The ratio reflects the balance between progesterone inactivation via glucuronidation and the formation of other sulfated pregnane-diol isomers, influenced by AKR1C4 and ABCC3 activity.

Ratio Evidence:

metabolites not in a pathway but enzyme catalyzes one metabolite

Gene Ratio Phenotype Relationship:

AKR1C4 variation alters steroid metabolism, impacting liver function and systemic metabolic traits. Specifically, altered AKR1C4 function is linked to changes in triglycerides, GGT, and bilirubin, likely through its role in bile acid and steroid hormone homeostasis, while ABCC3 influences the transport of these steroid conjugates.2[1], 4[2], 5[3], 6[4]

Phenotype Driver:

Gene-centric:AKR1C4

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