DPEP1

dipeptidase 1, the group of M19 metallopeptidases

Basic information

Region (hg38): 16:89613308-89638456

Links

ENSG00000015413NCBI:1800OMIM:179780HGNC:3002Uniprot:P16444AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DPEP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPEP1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
0
missense
17
clinvar
1
clinvar
18
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 17 1 0

Variants in DPEP1

This is a list of pathogenic ClinVar variants found in the DPEP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
16-89630421-G-C not specified Uncertain significance (Sep 17, 2021)2368169
16-89635967-G-C not specified Uncertain significance (Jun 30, 2022)2380547
16-89636023-G-A not specified Uncertain significance (Feb 03, 2022)2394931
16-89636282-C-T not specified Uncertain significance (Jun 16, 2024)2364675
16-89636348-A-C not specified Uncertain significance (Feb 06, 2023)2467202
16-89636355-G-A not specified Likely benign (May 26, 2022)2291379
16-89636625-G-A not specified Uncertain significance (Aug 08, 2023)2601529
16-89636626-C-A not specified Uncertain significance (Aug 08, 2023)2601530
16-89637225-C-T not specified Uncertain significance (May 04, 2023)2516309
16-89637316-A-G not specified Uncertain significance (Dec 03, 2021)2263900
16-89637348-C-T not specified Uncertain significance (Jun 02, 2024)3273564
16-89637541-C-T not specified Uncertain significance (Apr 22, 2024)3273565
16-89637665-C-T not specified Uncertain significance (Mar 01, 2023)2454964
16-89637855-G-T not specified Uncertain significance (Dec 19, 2022)2380147
16-89637858-G-A not specified Uncertain significance (May 12, 2024)3273566
16-89637882-G-A not specified Uncertain significance (Jan 04, 2022)2206116
16-89637907-C-T not specified Uncertain significance (Jan 09, 2024)3085422
16-89637936-G-T not specified Uncertain significance (Jul 25, 2023)2613689
16-89638099-C-A not specified Uncertain significance (Sep 08, 2023)2595806
16-89638160-C-T not specified Uncertain significance (May 03, 2023)2543155
16-89638215-T-A not specified Uncertain significance (Oct 05, 2023)3085423

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
DPEP1protein_codingprotein_codingENST00000393092 1025124
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.47e-100.1751254141991255140.000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.113182671.190.00001722663
Missense in Polyphen134123.411.08581268
Synonymous-2.901611211.340.00000875847
Loss of Function0.5431618.50.8647.95e-7198

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003620.000359
Ashkenazi Jewish0.0007030.000696
East Asian0.0002720.000272
Finnish0.0005550.000554
European (Non-Finnish)0.0004700.000459
Middle Eastern0.0002720.000272
South Asian0.0003940.000359
Other0.0006560.000653

dbNSFP

Source: dbNSFP

Function
FUNCTION: Hydrolyzes a wide range of dipeptides. Implicated in the renal metabolism of glutathione and its conjugates. Converts leukotriene D4 to leukotriene E4; it may play an important role in the regulation of leukotriene activity.;
Pathway
Busulfan Pathway, Pharmacodynamics;Eicosanoid Synthesis;Metabolism of lipids;Synthesis of Leukotrienes (LT) and Eoxins (EX);Arachidonic acid metabolism;Leukotriene metabolism;Biological oxidations;Metabolism;Fatty acid metabolism;leukotriene biosynthesis;Aflatoxin activation and detoxification (Consensus)

Recessive Scores

pRec
0.268

Intolerance Scores

loftool
0.857
rvis_EVS
-0.77
rvis_percentile_EVS
13.1

Haploinsufficiency Scores

pHI
0.149
hipred
N
hipred_score
0.146
ghis
0.440

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.844

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Dpep1
Phenotype
normal phenotype;

Gene ontology

Biological process
proteolysis;leukotriene metabolic process;glutathione metabolic process;xenobiotic metabolic process;apoptotic process;antibiotic metabolic process;negative regulation of cell migration;cellular response to drug;negative regulation of apoptotic process;negative regulation of cysteine-type endopeptidase activity involved in apoptotic process;homocysteine metabolic process;cellular response to calcium ion;cellular response to nitric oxide;cellular lactam catabolic process
Cellular component
extracellular space;nucleus;plasma membrane;apical plasma membrane;cell junction;anchored component of membrane;microvillus membrane;apical part of cell;extracellular exosome
Molecular function
protein binding;metalloexopeptidase activity;dipeptidyl-peptidase activity;zinc ion binding;dipeptidase activity;GPI anchor binding;cysteine-type endopeptidase inhibitor activity involved in apoptotic process;metallodipeptidase activity;modified amino acid binding