rs3786897

This is a intron variant variant in the PEPD gene.

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GWAS Catalog Trait Associations (9)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

BMI-adjusted waist-hip ratio

Lotta LA et al. “Association of Genetic Variants Related to Gluteofemoral vs Abdominal Fat Distribution With Type 2 Diabetes, Coronary Disease, and Cardiovascular Risk Factors.” Jama 320(24):2553-2563 (2018)
Allele G
OR 0.03
p 5.0e-63
N 660,648
Large GWAS
European
Pulit SL et al. “Meta-analysis of genome-wide association studies for body fat distribution in 694 649 individuals of European ancestry.” Human Molecular Genetics 28(1):166-174 (2019)
Allele G
OR 0.03
p 3.0e-58
N 315,284
Meta-analysisLarge GWAS
European
Graff M et al. “Genome-wide physical activity interactions in adiposity - A meta-analysis of 200,452 adults.” Plos Genetics 13(4):e1006528 (2017)
Allele G
OR 0.03
p 4.0e-10
N 118,949
Meta-analysisLarge GWAS
multi-ancestry

waist-hip ratio

Pulit SL et al. “Meta-analysis of genome-wide association studies for body fat distribution in 694 649 individuals of European ancestry.” Human Molecular Genetics 28(1):166-174 (2019)
Allele A
OR 0.02
p 1.0e-43
N 316,772
Meta-analysisLarge GWAS
European
Lotta LA et al. “Association of Genetic Variants Related to Gluteofemoral vs Abdominal Fat Distribution With Type 2 Diabetes, Coronary Disease, and Cardiovascular Risk Factors.” Jama 320(24):2553-2563 (2018)
Allele A
OR —
p 5.0e-8
N 663,598
Large GWAS
European
Shungin D et al. “New genetic loci link adipose and insulin biology to body fat distribution.” Nature 518(7538):187-196 (2015)
Allele A
OR 0.02
p 4.0e-11
N 143,480
Large GWAS
multi-ancestry

leukocyte quantity

Jee YH et al. “Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures.” Nature Communications 16(1):4935 (2025)
Allele A
OR 0.01
p 4.0e-19
N 928,679
Large GWAS
multi-ancestry
Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)
Allele A
OR 0.01
p 7.0e-12
N 504,825
Large GWAS
multi-ancestry

BMI-adjusted waist-hip ratio, physical activity measurement

Graff M et al. “Genome-wide physical activity interactions in adiposity - A meta-analysis of 200,452 adults.” Plos Genetics 13(4):e1006528 (2017)
Allele G
OR 0.03
p 2.0e-13
N 156,653
Meta-analysisLarge GWAS
multi-ancestry

degree of unsaturation measurement

Zoodsma M et al. “A genetic map of human metabolism across the allele frequency spectrum.” Nature Genetics 57(10):2445-2455 (2025)
Allele G
OR 0.01
p 5.0e-11
N 450,015
Large GWAS
multi-ancestry

visceral adipose tissue quantity

Agrawal S et al. “Inherited basis of visceral, abdominal subcutaneous and gluteofemoral fat depots.” Nature Communications 13(1):3771 (2022)
Allele A
OR 0.04
p 6.0e-10
N 38,965
Large GWAS
European, East Asian, South Asian, African unspecified, NR

type 2 diabetes mellitus

Cho YS et al. “Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians.” Nature Genetics 44(1):67-72 (2011)
Allele A
OR 1.10
p 1.0e-8
N 18,817
Meta-analysisLarge GWAS
multi-ancestry

BMI-adjusted waist circumference

Shungin D et al. “New genetic loci link adipose and insulin biology to body fat distribution.” Nature 518(7538):187-196 (2015)
Allele G
OR 0.02
p 9.0e-9
N 143,480
Large GWAS
multi-ancestry
Graff M et al. “Genome-wide physical activity interactions in adiposity - A meta-analysis of 200,452 adults.” Plos Genetics 13(4):e1006528 (2017)
Allele G
OR 0.02
p 3.0e-8
N 122,328
Meta-analysisLarge GWAS
multi-ancestry
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ClinVar annotation

Benign★☆☆☆
1 submitter
View on ClinVar →

About PEPD

This gene encodes a member of the peptidase family. The protein forms a homodimer that hydrolyzes dipeptides or tripeptides with C-terminal proline or hydroxyproline residues. The enzyme serves an important role in the recycling of proline, and may be rate limiting for the production of collagen. Mutations in this gene result in prolidase deficiency, which is characterized by the excretion of large amount of di- and tri-peptides containing proline. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]

View all PEPD variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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