DPEP1

dipeptidase 1, the group of M19 metallopeptidases

Basic information

Region (hg38): 16:89613308-89638456

Links

ENSG00000015413

∙ NCBI:1800 ∙ OMIM:179780 ∙ HGNC:3002 ∙ Uniprot:P16444 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

not_specified (50 variants)

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. These statistics are base on transcript: NM_001389466.1. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			49 clinvar	1 clinvar		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPEP1	protein_coding	protein_coding	ENST00000393092	10	25124

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.47e-10	0.175	125414	1	99	125514	0.000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.11	318	267	1.19	0.0000172	2663
Missense in Polyphen		134	123.41	1.0858		1268
Synonymous	-2.90	161	121	1.34	0.00000875	847
Loss of Function	0.543	16	18.5	0.864	7.95e-7	198

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000362	0.000359
Ashkenazi Jewish	0.000703	0.000696
East Asian	0.000272	0.000272
Finnish	0.000555	0.000554
European (Non-Finnish)	0.000470	0.000459
Middle Eastern	0.000272	0.000272
South Asian	0.000394	0.000359
Other	0.000656	0.000653

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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