Free for academic non-profit institutions. Other users need a Commercial license

Aliases for PEPD Gene

Aliases for PEPD Gene

  • Peptidase D 2 3 4 5
  • Prolidase 2 3 4
  • Proline Dipeptidase 3 4
  • X-Pro Dipeptidase 3 4
  • Imidodipeptidase 3 4
  • Testicular Tissue Protein Li 138 3
  • Aminoacyl-L-Proline Hydrolase 3
  • Xaa-Pro Dipeptidase 3
  • EC 4
  • PRD 4

External Ids for PEPD Gene

Previous GeneCards Identifiers for PEPD Gene

  • GC19M034495
  • GC19M034326
  • GC19M038553
  • GC19M038569
  • GC19M033877
  • GC19M030378

Summaries for PEPD Gene

Entrez Gene Summary for PEPD Gene

  • 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]

GeneCards Summary for PEPD Gene

PEPD (Peptidase D) is a Protein Coding gene. Diseases associated with PEPD include Prolidase Deficiency and Bacterial Vaginosis. Gene Ontology (GO) annotations related to this gene include peptidase activity and aminopeptidase activity.

UniProtKB/Swiss-Prot for PEPD Gene

  • Splits dipeptides with a prolyl or hydroxyprolyl residue in the C-terminal position. Plays an important role in collagen metabolism because the high level of iminoacids in collagen.

Gene Wiki entry for PEPD Gene

Additional gene information for PEPD Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PEPD Gene

Genomics for PEPD Gene

GeneHancer (GH) Regulatory Elements for PEPD Gene

Promoters and enhancers for PEPD Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19I033519 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 557 +0.7 697 2.5 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF548 KLF13 SP3 SP5 MXD4 PEPD GC19M033516 LOC105372370 GPATCH1 LSM14A CEP89 KIAA0355 FAAP24 WDR88 ENSG00000267219
GH19I033388 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 14.4 +128.6 128573 10.5 FOXA2 MLX ZFP64 ARID4B FEZF1 DMAP1 YY1 SLC30A9 SP5 NFYC CEP89 GPATCH1 LSM14A PDCD5 ENSG00000267219 CHST8 PEPD WDR88 KIAA0355 CEBPG
GH19I033296 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 9 +220.5 220487 10.6 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF213 ZNF416 ZNF143 CEBPA-AS1 CEBPA ENSG00000267580 GC19M033302 ENSG00000267727 GPATCH1 ZNF507 CEP89 LSM14A KIAA0355
GH19I033472 Enhancer 0.9 ENCODE 23.8 +48.4 48440 2.3 PKNOX1 INSM2 KLF17 ZNF76 FEZF1 ZNF2 ZEB1 ZNF335 GLIS2 ZNF366 GPATCH1 PEPD CEP89 LSM14A KIAA0355 GC19P033457 GC19M033516
GH19I033485 Enhancer 0.7 FANTOM5 ENCODE 21.7 +35.0 35037 2 GLIS2 GLIS1 SCRT2 ZIC2 PEPD SLC7A10 GC19P033457 GC19M033516
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PEPD on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PEPD gene promoter:

Genomic Locations for PEPD Gene

Genomic Locations for PEPD Gene
134,945 bases
Minus strand

Genomic View for PEPD Gene

Genes around PEPD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PEPD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PEPD Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PEPD Gene

Proteins for PEPD Gene

  • Protein details for PEPD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Xaa-Pro dipeptidase
    Protein Accession:
    Secondary Accessions:
    • A8K3Z1
    • A8K416
    • A8K696
    • A8MX47
    • B4DDB7
    • B4DGJ1
    • E9PCE8
    • Q8TBN9
    • Q9BT75

    Protein attributes for PEPD Gene

    493 amino acids
    Molecular mass:
    54548 Da
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PEPD Gene

    Alternative splice isoforms for PEPD Gene


neXtProt entry for PEPD Gene

Post-translational modifications for PEPD Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PEPD Gene

Domains & Families for PEPD Gene

Gene Families for PEPD Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for PEPD Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase M24B family. Eukaryotic-type prolidase subfamily.
  • Belongs to the peptidase M24B family. Eukaryotic-type prolidase subfamily.
genes like me logo Genes that share domains with PEPD: view

Function for PEPD Gene

Molecular function for PEPD Gene

GENATLAS Biochemistry:
peptidase D
UniProtKB/Swiss-Prot CatalyticActivity:
Hydrolysis of Xaa- -Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on Pro- -Pro.
UniProtKB/Swiss-Prot Function:
Splits dipeptides with a prolyl or hydroxyprolyl residue in the C-terminal position. Plays an important role in collagen metabolism because the high level of iminoacids in collagen.

Enzyme Numbers (IUBMB) for PEPD Gene

Phenotypes From GWAS Catalog for PEPD Gene

Gene Ontology (GO) - Molecular Function for PEPD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004177 aminopeptidase activity IEA --
GO:0004181 metallocarboxypeptidase activity TAS 1972707
GO:0005515 protein binding IPI 21044950
GO:0008233 peptidase activity IEA --
GO:0008237 metallopeptidase activity IEA --
genes like me logo Genes that share ontologies with PEPD: view
genes like me logo Genes that share phenotypes with PEPD: view

Human Phenotype Ontology for PEPD Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PEPD Gene

MGI Knock Outs for PEPD:
  • Pepd tm1a(KOMP)Wtsi

Animal Model Products

CRISPR Products

miRNA for PEPD Gene

miRTarBase miRNAs that target PEPD

Inhibitory RNA Products

No data available for Transcription Factor Targets and HOMER Transcription for PEPD Gene

Localization for PEPD Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PEPD gene
Compartment Confidence
extracellular 5
cytosol 3
nucleus 2
plasma membrane 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PEPD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0070062 extracellular exosome IDA,HDA 19056867
genes like me logo Genes that share ontologies with PEPD: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PEPD Gene

Pathways & Interactions for PEPD Gene

No Data Available

Gene Ontology (GO) - Biological Process for PEPD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006508 proteolysis IEA --
GO:0006520 cellular amino acid metabolic process TAS 1972707
GO:0030574 collagen catabolic process IEA --
genes like me logo Genes that share ontologies with PEPD: view

No data available for Pathways by source and SIGNOR curated interactions for PEPD Gene

Drugs & Compounds for PEPD Gene

(27) Drugs for PEPD Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Manganese Approved Nutra 37

(11) Additional Compounds for PEPD Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • 1-(Aminoacetyl)proline
  • 1-Glycyl-L-Proline
  • 1-Glycylproline
  • GLY-pro
  • N-Glycyl-L-proline
genes like me logo Genes that share compounds with PEPD: view

Transcripts for PEPD Gene

Unigene Clusters for PEPD Gene

Peptidase D:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PEPD Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17a · 17b
SP1: - - -
SP2: -
SP3: - - - - - -
SP4: -

Relevant External Links for PEPD Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PEPD Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PEPD Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PEPD Gene

This gene is overexpressed in Kidney - Cortex (x5.5).

Protein differential expression in normal tissues from HIPED for PEPD Gene

This gene is overexpressed in Serum (11.8) and Pancreatic juice (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PEPD Gene

Protein tissue co-expression partners for PEPD Gene

NURSA nuclear receptor signaling pathways regulating expression of PEPD Gene:


SOURCE GeneReport for Unigene cluster for PEPD Gene:


Evidence on tissue expression from TISSUES for PEPD Gene

  • Nervous system(5)
  • Kidney(4.9)
  • Skin(4.6)
  • Liver(4.5)
  • Intestine(3.4)
  • Lung(2.5)
  • Blood(2.3)
  • Stomach(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PEPD Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Head and neck:
  • brain
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • middle ear
  • mouth
  • nose
  • scalp
  • skull
  • tooth
  • bronchus
  • esophagus
  • heart
  • lung
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • spleen
  • stomach
  • pelvis
  • ankle
  • digit
  • elbow
  • femur
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • nail
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • upper limb
  • wrist
  • blood
  • blood vessel
  • coagulation system
  • hair
  • lymph node
  • peripheral nervous system
  • red blood cell
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with PEPD: view

No data available for mRNA Expression by UniProt/SwissProt for PEPD Gene

Orthologs for PEPD Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PEPD Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PEPD 33 34
  • 99.1 (n)
(Canis familiaris)
Mammalia PEPD 33 34
  • 89.93 (n)
(Bos Taurus)
Mammalia PEPD 33 34
  • 89.32 (n)
(Rattus norvegicus)
Mammalia Pepd 33
  • 84.96 (n)
(Mus musculus)
Mammalia Pepd 33 16 34
  • 84.18 (n)
(Monodelphis domestica)
Mammalia PEPD 34
  • 84 (a)
(Ornithorhynchus anatinus)
Mammalia PEPD 34
  • 79 (a)
(Gallus gallus)
Aves PEPD 33 34
  • 74.78 (n)
(Anolis carolinensis)
Reptilia PEPD 34
  • 69 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pepd 33
  • 71.6 (n)
Str.5139 33
(Danio rerio)
Actinopterygii pepd 33 34
  • 71.55 (n)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta Dip-C 35 33 34
  • 59.83 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004775 33
  • 57.49 (n)
(Caenorhabditis elegans)
Secernentea K12C11.1 35 33 34
  • 56.62 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes -- 34
  • 27 (a)
-- 36
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G29490 33
  • 56.88 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.1123 33
(Oryza sativa)
Liliopsida Os02g0224400 33
  • 55.74 (n)
Os.27534 33
(Zea mays)
Liliopsida Zm.3239 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.8389 34
  • 50 (a)
-- 34
  • 48 (a)
Species where no ortholog for PEPD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PEPD Gene

Gene Tree for PEPD (if available)
Gene Tree for PEPD (if available)

Paralogs for PEPD Gene Pseudogenes for PEPD Gene

genes like me logo Genes that share paralogs with PEPD: view

No data available for Paralogs for PEPD Gene

Variants for PEPD Gene

Sequence variations from dbSNP and Humsavar for PEPD Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1061338 benign, Prolidase deficiency 33,387,292(-) A/G 3_prime_UTR_variant
rs121917721 pathogenic, Prolidase deficiency, not provided, Prolidase deficiency (PD) [MIM:170100] 33,401,862(-) C/G/T coding_sequence_variant, missense_variant
rs121917722 pathogenic, Prolidase deficiency, Prolidase deficiency (PD) [MIM:170100] 33,464,060(-) C/T coding_sequence_variant, intron_variant, missense_variant
rs121917723 pathogenic, Prolidase deficiency, Prolidase deficiency (PD) [MIM:170100] 33,401,855(-) C/T coding_sequence_variant, missense_variant
rs121917724 pathogenic, Prolidase deficiency, Prolidase deficiency (PD) [MIM:170100] 33,387,892(-) C/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for PEPD Gene

Variant ID Type Subtype PubMed ID
dgv139e55 CNV gain 17911159
dgv2009e59 CNV duplication 20981092
esv2469451 CNV insertion 19546169
esv2677046 CNV deletion 23128226
esv2718472 CNV deletion 23290073
esv2758755 CNV gain 17122850
esv3412309 CNV duplication 20981092
esv3556302 CNV deletion 23714750
esv3556305 CNV deletion 23714750
esv3644189 CNV loss 21293372
esv3644190 CNV loss 21293372
esv3644191 CNV loss 21293372
esv3644192 CNV loss 21293372
nsv1111169 CNV tandem duplication 24896259
nsv1134784 CNV deletion 24896259
nsv470138 CNV gain 18288195
nsv473132 CNV novel sequence insertion 20440878
nsv473839 CNV novel sequence insertion 20440878
nsv513524 CNV insertion 21212237
nsv522571 CNV loss 19592680
nsv525549 CNV gain 19592680
nsv819550 CNV insertion 19587683
nsv828526 CNV loss 20364138
nsv828527 CNV gain 20364138
nsv978804 CNV duplication 23825009

Variation tolerance for PEPD Gene

Residual Variation Intolerance Score: 74.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.60; 89.03% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PEPD Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PEPD Gene

Disorders for PEPD Gene

MalaCards: The human disease database

(10) MalaCards diseases for PEPD Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
prolidase deficiency
  • hyperimidodipeptiduria
bacterial vaginosis
  • vaginosis, bacterial
hypermobility syndrome
  • benign joint hypermobility
legg-calve-perthes disease
  • lcpd
sexual sadism
  • sadism
- elite association - COSMIC cancer census association via MalaCards
Search PEPD in MalaCards View complete list of genes associated with diseases


  • Prolidase deficiency (PD) [MIM:170100]: A multisystem disorder associated with massive iminodipeptiduria and lack of or reduced prolidase activity in erythrocytes, leukocytes, or cultured fibroblasts. Clinical features include skin ulcers, developmental delay, recurrent infections, and a characteristic facies. {ECO:0000269 PubMed:12384772, ECO:0000269 PubMed:2365824, ECO:0000269 PubMed:8198124, ECO:0000269 PubMed:8900231}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for PEPD Gene

prolidase deficiency,with variable expression from no manifestation to severe progressive skin ulceration,decreased resistance to infection,impaired cognitive development

Additional Disease Information for PEPD

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PEPD: view

Publications for PEPD Gene

  1. Mutation analysis of five new patients affected by prolidase deficiency: the lack of enzyme activity causes necrosis-like cell death in cultured fibroblasts. (PMID: 12384772) Forlino A … Cetta G (Human genetics 2002) 3 4 22 58
  2. Expression and molecular analysis of mutations in prolidase deficiency. (PMID: 8900231) Ledoux P … Hechtman P (American journal of human genetics 1996) 3 4 22 58
  3. Four novel PEPD alleles causing prolidase deficiency. (PMID: 8198124) Ledoux P … Hechtman P (American journal of human genetics 1994) 3 4 22 58
  4. Structural organization of the gene for human prolidase (peptidase D) and demonstration of a partial gene deletion in a patient with prolidase deficiency. (PMID: 1972707) Tanoue A … Matsuda I (The Journal of biological chemistry 1990) 2 3 22 58
  5. A single nucleotide change in the prolidase gene in fibroblasts from two patients with polypeptide positive prolidase deficiency. Expression of the mutant enzyme in NIH 3T3 cells. (PMID: 2365824) Tanoue A … Matsuda I (The Journal of clinical investigation 1990) 3 4 22 58

Products for PEPD Gene

  • Addgene plasmids for PEPD

Sources for PEPD Gene

Loading form....