Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	5184
Gene name	Peptidase D
Gene symbol	PEPD
Synonyms (NCBI Gene)	PROLIDASE
Chromosome	19
Chromosome location	19q13.11
Summary	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 rat

Show/Hide all (18)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121917721	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs121917722	C>T	Pathogenic	Intron variant, coding sequence variant, missense variant
rs121917723	C>T	Pathogenic	Coding sequence variant, missense variant
rs121917724	C>T	Pathogenic	Coding sequence variant, missense variant
rs121917725	G>A,C	Pathogenic	Coding sequence variant, missense variant, stop gained
rs200435937	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs267606943	G>A	Pathogenic	Missense variant, coding sequence variant, intron variant
rs267606944	C>T	Pathogenic	Missense variant, coding sequence variant
rs529315200	C>T	Pathogenic-likely-pathogenic	Stop gained, coding sequence variant
rs542228812	C>A,T	Likely-pathogenic	Splice acceptor variant
rs745834191	TAG>-	Likely-pathogenic, pathogenic	Coding sequence variant, inframe deletion
rs747700126	C>A,G,T	Pathogenic	Coding sequence variant, intron variant, missense variant
rs757386104	CTC>-	Pathogenic	Coding sequence variant, inframe deletion
rs794728008	->TCACGGTGGGCCT	Pathogenic	Inframe insertion, intron variant, coding sequence variant, stop gained
rs797045185	A>C,G	Pathogenic	Missense variant, coding sequence variant
rs1204749077	C>T	Pathogenic	Intron variant, splice acceptor variant
rs1600069637	C>T	Likely-pathogenic	Splice acceptor variant
rs1600147235	G>-	Pathogenic	Frameshift variant, coding sequence variant

Show/Hide all (15)

miRTarBase ID	miRNA	Experiments	Reference
MIRT042567	hsa-miR-423-3p	CLASH	23622248
MIRT2065614	hsa-miR-4300	CLIP-seq
MIRT2065615	hsa-miR-548m	CLIP-seq
MIRT2065616	hsa-miR-920	CLIP-seq
MIRT2293430	hsa-miR-105	CLIP-seq
MIRT2293431	hsa-miR-518a-5p	CLIP-seq
MIRT2293432	hsa-miR-527	CLIP-seq
MIRT2687582	hsa-miR-1343	CLIP-seq
MIRT2687583	hsa-miR-3074-5p	CLIP-seq
MIRT2687584	hsa-miR-3124-3p	CLIP-seq
MIRT2687585	hsa-miR-3153	CLIP-seq
MIRT2687586	hsa-miR-361-5p	CLIP-seq
MIRT2687587	hsa-miR-4646-5p	CLIP-seq
MIRT2687588	hsa-miR-4668-5p	CLIP-seq
MIRT2687589	hsa-miR-548l	CLIP-seq

Show/Hide all (22)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004181	Function	Metallocarboxypeptidase activity	TAS	1972707
GO:0005515	Function	Protein binding	IPI	16713569, 21044950, 32814053
GO:0006508	Process	Proteolysis	IBA
GO:0006508	Process	Proteolysis	IDA	17081196
GO:0006508	Process	Proteolysis	IEA
GO:0006508	Process	Proteolysis	TAS	1972707
GO:0006520	Process	Amino acid metabolic process	TAS	1972707
GO:0008233	Function	Peptidase activity	IBA
GO:0008233	Function	Peptidase activity	IEA
GO:0008235	Function	Metalloexopeptidase activity	IEA
GO:0008237	Function	Metallopeptidase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016805	Function	Dipeptidase activity	IEA
GO:0030145	Function	Manganese ion binding	IEA
GO:0030574	Process	Collagen catabolic process	IEA
GO:0043069	Process	Negative regulation of programmed cell death	IDA	35165443
GO:0046872	Function	Metal ion binding	IEA
GO:0070006	Function	Metalloaminopeptidase activity	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867, 23533145
GO:0102009	Function	Proline dipeptidase activity	IDA	17081196, 35165443
GO:0102009	Function	Proline dipeptidase activity	IEA
GO:0140633	Process	CARD8 inflammasome complex assembly	IDA	33053349

MIM	HGNC	e!Ensembl
613230	8840	ENSG00000124299

P12955

Protein name

Xaa-Pro dipeptidase (X-Pro dipeptidase) (EC 3.4.13.9) (Imidodipeptidase) (Peptidase D) (Proline dipeptidase) (Prolidase)

Protein function

Dipeptidase that catalyzes the hydrolysis of dipeptides with a prolyl (Xaa-Pro) or hydroxyprolyl residue in the C-terminal position (PubMed:17081196, PubMed:35165443). The preferred dipeptide substrate is Gly-Pro, but other Xaa-Pro dipeptides, s

PDB

2IW2 , 2OKN , 5M4G , 5M4J , 5M4L , 5M4Q , 5MBY , 5MBZ , 5MC0 , 5MC1 , 5MC2 , 5MC3 , 5MC4 , 5MC5 , 6H2P , 6H2Q , 6QSB , 6QSC , 6SRE , 6SRF , 6SRG

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF05195	AMP_N	23 → 144	Aminopeptidase P, N-terminal domain	Domain
PF00557	Peptidase_M24	193 → 459	Metallopeptidase family M24	Domain

Sequence

MAAATGPSFWLGNETLKVPLALFALNRQRLCERLRKNPAVQAGSIVVLQGGEETQRYCTD
TGVLFRQESFFHWAFGVTEPGCYGVIDVDTGKSTLFVPRLPASHATWMGKIHSKEHFKEK
YAVDDVQYVDEIASVLTSQKPSVLLTLRGVNTDSGSVCREASFDGISKFEVNNTILHPEI
VECRVFKTDMELEVLRYTNKISSEAHREVMKAVKVGMKEYELESLFEHYCYSRGGMRHSS
YTCICGSGENSAVLHYGHAGAPNDRTIQNGDMCLFDMGGEYYCFASDITCSFPANGKFTA
DQKAVYEAVLRSSRAVMGAMKPGVWWPDMHRLADRIHLEELAHMGILSGSVDAMVQAHLG
AVFMPHGLGHFLGIDVHDVGGYPEGVERIDEPGLRSLRTARHLQPGMVLTVEPGIYFIDH
LLDEALADPARASFLNREVLQRFRGFGGVRIEEDVVVTDSGIELLTCVPRTVEEIEACMA
GCDKAFTPFSGPK

Sequence length

493

Interactions

View interactions

163

Show/Hide Causal Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Megaconial type congenital muscular dystrophy	Likely pathogenic; Pathogenic	rs750548522	RCV004785314
Melanoma	Likely pathogenic	rs121917722	RCV005887120
Nonpapillary renal cell carcinoma	Likely pathogenic; Pathogenic	rs542228812	RCV005912185
PEPD-related disorder	Likely pathogenic; Pathogenic	rs2513410026, rs745834191	RCV003404248 RCV004754394
Prolidase deficiency	Pathogenic; Likely pathogenic	rs764650519, rs1204749077, rs1170952773, rs750548522, rs375391662, rs1305209476, rs121917721, rs121917722, rs121917723, rs121917724, rs121917725, rs267606944, rs794728008, rs267606943, rs797045185 View all (5 more)	RCV001730007 RCV001730008 RCV001782595 RCV001794936 RCV002497819 RCV005023444 RCV003448442 RCV000000232 RCV000000235 RCV000000236 RCV000000237 RCV000000239 RCV000000240 RCV000000241 RCV000000242 RCV000194259 RCV000195145 RCV005208215 RCV000273249 RCV000991408 RCV000995831 RCV000995832
Thyroid cancer, nonmedullary, 1	Pathogenic; Likely pathogenic	rs542228812, rs2513508907	RCV005931427 RCV005931655 RCV005912186

Show/Hide Unknown Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Gastric cancer	Uncertain significance	rs370970279	RCV005930403
Ovarian serous cystadenocarcinoma	Benign; Likely benign	rs200446480	RCV005921426
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs200446480	RCV005921427

Show/Hide Text Mining Associations (28)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Aortic Aneurysm Abdominal	Associate	21247474
Arthritis Rheumatoid	Associate	32013628
Bipolar Disorder	Associate	29930383
Breast Neoplasms	Associate	16875494, 18443378, 23549681, 32918543
Carcinoma Hepatocellular	Associate	26078578
Cardiovascular Diseases	Stimulate	31739742
Connective Tissue Diseases	Associate	38088248
Diabetes Mellitus	Associate	35320353
Diabetes Mellitus Type 2	Associate	19401414, 24086726, 31739742
Ehlers Danlos Syndrome Type VII Autosomal Dominant	Associate	11277941
Erectile Dysfunction	Associate	29930383
Familial Mediterranean Fever	Associate	31846428
Immune System Diseases	Associate	26159719
Inflammation	Associate	31846428
Intellectual Disability	Associate	18806117, 8198124
Lung Neoplasms	Associate	11168680
Neoplasms	Associate	26078578, 29930383, 34880421
Osteoarthritis	Inhibit	34477138
Osteoarthritis Knee	Associate	27777643, 34477138
Osteogenesis Imperfecta	Associate	11277941
Primary Immunodeficiency Diseases	Associate	38644452
Prolidase Deficiency	Inhibit	1688567, 30066404
Prolidase Deficiency	Associate	17142620, 2010534, 37023562, 38088248, 8198124
Prostatic Hyperplasia	Associate	25551736
Pulmonary Disease Chronic Obstructive	Associate	37447386
Schizophrenia	Associate	32065947
Sjogren's Syndrome	Associate	38088248
Skin Ulcer	Associate	18806117, 8198124

PEPD (peptidase D)